diff --git a/pkgdown.yml b/pkgdown.yml index de5c464..3bdbd18 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 3.1.11 pkgdown: 2.0.9 pkgdown_sha: ~ articles: {} -last_built: 2024-06-28T07:08Z +last_built: 2024-06-29T04:58Z urls: reference: https://oxford-ihtm.io/codeditr/reference article: https://oxford-ihtm.io/codeditr/articles diff --git a/reference/cod_check_dod.html b/reference/cod_check_dod.html new file mode 100644 index 0000000..4210f04 --- /dev/null +++ b/reference/cod_check_dod.html @@ -0,0 +1,116 @@ + +Check date of death value in cause of death data based on CoDEdit rules — cod_check_dod • codeditr + Skip to contents + + +
+
+
+

Check date of death value in cause of death data based on CoDEdit rules

+ Source: R/cod_check_dod.R +
cod_check_dod.Rd
+
+ +
+

Check date of death value in cause of death data based on CoDEdit rules

+
+ +
+

Usage

+ 
cod_check_dod(dod)
+
+ +
+

Arguments

+
dod
+

Date of death value expressed in terms of the year death +occurred.

+ +
+
+

Value

+ + +

A tibble with number of rows equal to length of dod and +two columns for dod_check and dod_check_note.

+
+ +
+

Examples

+ 
cod_check_dod("2024")
+#> # A tibble: 1 × 2
+#>   dod_check dod_check_note                    
+#>       <int> <chr>                             
+#> 1         0 No issues with date of death value
+
+
+
+
+ + +
+ + + + + + + diff --git a/reference/cod_check_input.html b/reference/cod_check_input.html new file mode 100644 index 0000000..0a504fe --- /dev/null +++ b/reference/cod_check_input.html @@ -0,0 +1,129 @@ + +Check structure and values of input data to CoDEdit tool — cod_check_codedit_input • codeditr + Skip to contents + + +
+
+
+

Check structure and values of input data to CoDEdit tool

+ Source: R/cod_check_input.R +
cod_check_input.Rd
+
+ +
+

Check structure and values of input data to CoDEdit tool

+
+ +
+

Usage

+ 
cod_check_codedit_input(df)
+
+ +
+

Arguments

+
df
+

A data.frame with 6 columns with names "FreeId", "Sex", +"Age Value", "Age Type", "Code", and "Death Date" and compatible +with the input data required by the CoDEdit tool.

+ +
+
+

Value

+ + +

A data.frame containing check codes and check notes for each row +and variable identified with the FreeId of df.

+
+ +
+

Examples

+ 
cod_check_codedit_input(icd10_example)
+#> # A tibble: 3,613 × 7
+#>    sex_check sex_check_note       age_check age_check_note code_check$code_check
+#>        <int> <chr>                    <int> <fct>                          <int>
+#>  1         0 No issues with sex …         0 No issues wit…                     0
+#>  2         0 No issues with sex …         0 No issues wit…                     0
+#>  3         0 No issues with sex …         0 No issues wit…                     0
+#>  4         0 No issues with sex …         0 No issues wit…                     0
+#>  5         0 No issues with sex …         0 No issues wit…                     0
+#>  6         0 No issues with sex …         0 No issues wit…                     0
+#>  7         0 No issues with sex …         0 No issues wit…                     0
+#>  8         0 No issues with sex …         0 No issues wit…                     0
+#>  9         0 No issues with sex …         0 No issues wit…                     0
+#> 10         0 No issues with sex …         0 No issues wit…                     0
+#> # ℹ 3,603 more rows
+#> # ℹ 3 more variables: code_check$code_check_note <chr>, dod_check <int>,
+#> #   dod_check_note <chr>
+
+
+
+
+ + +
+ + + + + + + diff --git a/reference/cod_check_sex.html b/reference/cod_check_sex.html index 098730d..097346b 100644 --- a/reference/cod_check_sex.html +++ b/reference/cod_check_sex.html @@ -66,7 +66,7 @@

Usage

- 
cod_check_sex(sex_value, sex_code)
+ 
cod_check_sex(sex_value, sex_code = c(1, 2))
@@ -79,7 +79,8 @@

Arguments diff --git a/reference/index.html b/reference/index.html index 64aa73b..d6cc48e 100644 --- a/reference/index.html +++ b/reference/index.html @@ -134,6 +134,16 @@

Check

Check sex values in cause of death data based on CoDEdit rules
+ cod_check_dod() +
+
Check date of death value in cause of death data based on CoDEdit rules
+
+ + cod_check_codedit_input() +
+
Check structure and values of input data to CoDEdit tool
+
+ cod_check_code() cod_check_code_structure_icd10() cod_check_code_structure_icd11() cod_check_code_ill_defined_icd10() cod_check_code_ill_defined_icd11() cod_check_code_unlikely_icd10() cod_check_code_unlikely_icd11() cod_check_code_sex_icd10_() cod_check_code_sex_icd10() cod_check_code_sex_icd11_() cod_check_code_sex_icd11()
Check cause of death code for code entry mistakes and/or code completeness
diff --git a/search.json b/search.json index 177dbfa..cee7d5c 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":[]},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. 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Violating terms may lead temporary permanent ban.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. 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Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":[]},{"path":"https://oxford-ihtm.io/codeditr/CONTRIBUTING.html","id":"bugs","dir":"","previous_headings":"","what":"Bugs","title":"Contributing","text":"Submit issue issues page","code":""},{"path":"https://oxford-ihtm.io/codeditr/CONTRIBUTING.html","id":"code-contributions","dir":"","previous_headings":"","what":"Code contributions","title":"Contributing","text":"Fork repository Github account Clone version account machine account Make sure track progress upstream .e., version codeditr OxfordIHTM/codeditr, making changes make sure pull changes upstream either git fetch upstream merge later git pull upstream fetch merge one step Make changes new feature branch Please write test tests changes affect code just documentation Push changes account Submit pull request OxfordIHTM/codeditr","code":"git clone https://github.com//codeditr.git git remote add upstream https://github.com/OxfordIHTM/codeditr.git"},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. 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Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://oxford-ihtm.io/codeditr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anita Makori. Author, copyright holder. Ernest Guevarra. Author, maintainer, copyright holder. Sanjeev Pugazhendhi. Thesis advisor, reviewer. Williams Udoh Ituen-Umanah. Reviewer. Proochista Ariana. Reviewer, copyright holder.","code":""},{"path":"https://oxford-ihtm.io/codeditr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Anita Makori, Ernest Guevarra (2024). codeditr: Implementing Cause--Death Data Checks Based World Health Organization's CoDEdit Tool. R package version 0.0.9000, https://oxford-ihtm.io/codeditr/.","code":"@Manual{, title = {codeditr: Implementing Cause-of-Death Data Checks Based on World Health Organization's CoDEdit Tool}, author = {{Anita Makori} and {Ernest Guevarra}}, year = {2024}, note = {R package version 0.0.9000}, url = {https://oxford-ihtm.io/codeditr/}, }"},{"path":"https://oxford-ihtm.io/codeditr/index.html","id":"codeditr-implementing-cause-of-death-data-checks-based-on-the-who-codedit-tool-","dir":"","previous_headings":"","what":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","text":"World Health Organization’s CoDEdit electronic tool intended help producers cause--death statistics strengthening capacity perform routine checks data. package ports original tool built using Microsoft Access R leverage utility function original tool usable application program interface can used building universal tools creating programmatic scientific workflows aimed routine, automated, large-scale monitoring cause--death data.","code":""},{"path":"https://oxford-ihtm.io/codeditr/index.html","id":"what-does-codeditr-do","dir":"","previous_headings":"","what":"What does codeditr do?","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","text":"codeditr package provides functions implementing data quality checks cause--death records. built upon heuristics algorithms CoDEdit v2.0 electronic tool uses evaluate quality cause--death data produced used country level statisticians charge mortality reporting. package, end users ability programmatically create scientific workflows research cause--death data quality build open tools applications routine monitoring cause--death data.","code":""},{"path":"https://oxford-ihtm.io/codeditr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","text":"coeditr yet CRAN can installed Oxford IHTM R-universe : load codeditr","code":"install.packages( \"codeditr\", repos = c(\"https://oxfordihtm.r-universe.dev\", \"https://cloud.r-project.org\") ) # load package library(codeditr)"},{"path":[]},{"path":"https://oxford-ihtm.io/codeditr/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","text":"find codeditr package useful please cite using suggested citation provided call citation() function follows:","code":"citation(\"codeditr\") #> To cite codeditr in publications use: #> #> Anita Makori, Ernest Guevarra (2024). _codeditr: Implementing #> Cause-of-Death Data Checks Based on World Health Organization's #> CoDEdit Tool_. R package version 0.0.9000, #> . #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> title = {codeditr: Implementing Cause-of-Death Data Checks Based on World Health Organization's CoDEdit Tool}, #> author = {{Anita Makori} and {Ernest Guevarra}}, #> year = {2024}, #> note = {R package version 0.0.9000}, #> url = {https://oxford-ihtm.io/codeditr/}, #> }"},{"path":"https://oxford-ihtm.io/codeditr/index.html","id":"community-guidelines","dir":"","previous_headings":"","what":"Community guidelines","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","text":"Feedback, bug reports feature requests welcome; file issues seek support . like contribute package, please see contributing guidelines. project released Contributor Code Conduct. participating project agree abide terms.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_calculate_age.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate age at death based on date of birth and date of death — cod_calculate_age","title":"Calculate age at death based on date of birth and date of death — cod_calculate_age","text":"Calculate age death based date birth date death","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_calculate_age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate age at death based on date of birth and date of death — cod_calculate_age","text":"","code":"cod_calculate_age(dob, dod, date_format = \"%Y-%m-%d\", codedit = TRUE) cod_calculate_ages(dob, dod, date_format = \"%Y-%m-%d\", codedit = TRUE)"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_calculate_age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate age at death based on date of birth and date of death — cod_calculate_age","text":"dob Date birth. ideally standard ISO extended date format \"YYYY-MM-DD\" specified default value date_format. dod Date death. ideally standard ISO extended date format YYYY-MM_DD\" specified default value date_format. date_format Format date values provided. Date formatting handled using strptime() hence needs specified based strptime() requires format argument. default, set standard ISO extended date format expressed \"%Y-%m-%d\" corresponds \"YYYY-MM-DD\". codedit Logical. output based CoDEdit version 2 coding rules. Default TRUE.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_calculate_age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate age at death based on date of birth and date of death — cod_calculate_age","text":"Values age days, months years. codedit TRUE, tibble age value age type required CoDEdit.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_calculate_age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate age at death based on date of birth and date of death — cod_calculate_age","text":"","code":"cod_calculate_age(\"1977-11-05\", Sys.Date()) #> # A tibble: 1 × 2 #> age_value age_type #> #> 1 46 Y cod_calculate_age(\"1965-05-20\", \"2023-10-03\") #> # A tibble: 1 × 2 #> age_value age_type #> #> 1 58 Y"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_age.html","id":null,"dir":"Reference","previous_headings":"","what":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","title":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","text":"Check age values cause death data based CoDEdit rules","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","text":"","code":"cod_check_age(age_value, age_type, age_type_code = c(\"D\", \"M\", \"Y\"))"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","text":"age_value integer value vector values age based CoDEdit rules. age_type vector values age type based CoDEdit rules. either \"D\" age days, \"M\" age months, \"Y\" age years. values different , age_type_code specified correspond day, month, year values age_type. age_type_code character integer vector 3 values indicate values considered pertaining days (first value vector), months (second value vector), years (third value vector).","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","text":"tibble number rows equal length age_value two columns age_check age_check_note.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","text":"","code":"cod_check_age(120, \"Y\") #> # A tibble: 1 × 2 #> age_check age_check_note #> #> 1 0 No issues with age value and age type cod_check_age(28, \"D\") #> # A tibble: 1 × 2 #> age_check age_check_note #> #> 1 1 Should probably be age value of 1 and age type of months (M) cod_check_age(32, \"D\") #> # A tibble: 1 × 2 #> age_check age_check_note #> #> 1 2 Should probably be converted to age value of age type months (M) no…"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","title":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","text":"Check cause death code code entry mistakes /code completeness","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","text":"","code":"cod_check_code(cod, version = c(\"icd10\", \"icd11\"), sex) cod_check_code_structure_icd10(cod) cod_check_code_structure_icd11(cod) cod_check_code_ill_defined_icd10(cod) cod_check_code_ill_defined_icd11(cod) cod_check_code_unlikely_icd10(cod) cod_check_code_unlikely_icd11(cod) cod_check_code_sex_icd10_(cod, sex) cod_check_code_sex_icd10(cod, sex) cod_check_code_sex_icd11_(cod, sex) cod_check_code_sex_icd11(cod, sex)"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","text":"cod character value vector values cause death code/s. version character value ICD version used. either \"icd10\" \"icd11\". Default \"icd10\". sex character value vector values sex individual associated specified cod.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","text":"tibble 2 columns/fields. First integer value indicating whether issue cause death code provided relation potential code entry mistake /issue code completeness.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_code.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","text":"","code":"cod_check_code(\"U100\", sex = 1) #> # A tibble: 1 × 9 #> cod_check_structure cod_check_note_structure cod_check_ill_defined #> #> 1 8 CoD code contains the character val… 0 #> # ℹ 6 more variables: cod_check_note_ill_defined , #> # cod_check_unlikely , cod_check_note_unlikely , #> # cod_check_sex , cod_check_note_sex , cod_check cod_check_code(\"2C6Z\", version = \"icd11\", sex = 1) #> # A tibble: 1 × 9 #> cod_check_structure cod_check_note_structure cod_check_ill_defined #> #> 1 0 No issues found in CoD code 0 #> # ℹ 6 more variables: cod_check_note_ill_defined , #> # cod_check_unlikely , cod_check_note_unlikely , #> # cod_check_sex , cod_check_note_sex , cod_check "},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_sex.html","id":null,"dir":"Reference","previous_headings":"","what":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","title":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","text":"Check sex values cause death data based CoDEdit rules","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_sex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","text":"","code":"cod_check_sex(sex_value, sex_code)"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_sex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","text":"sex_value integer value vector values age based CoDEdit rules. sex_code character integer vector 2 values indicate values considered pertaining males (first value vector) females (second value vector).","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_sex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","text":"tibble number rows equal length sex_value two columns sex_check sex_check_note.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_sex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","text":"","code":"cod_check_sex(\"m\", c(\"m\", \"f\")) #> # A tibble: 1 × 2 #> sex_check sex_check_note #> #> 1 0 No issues with sex value cod_check_sex(\"male\", c(\"male\", \"female\")) #> # A tibble: 1 × 2 #> sex_check sex_check_note #> #> 1 0 No issues with sex value cod_check_sex(1, 1:2) #> # A tibble: 1 × 2 #> sex_check sex_check_note #> #> 1 0 No issues with sex value"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_age_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","title":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","text":"Recode age type cause death data based CoDEdit rules","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_age_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","text":"","code":"cod_recode_age_type(age_type, age_type_code = c(\"D\", \"M\", \"Y\"))"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_age_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","text":"age_type vector values age type based CoDEdit rules. either \"D\" age days, \"M\" age months, \"Y\" age years. values different , age_type_code specified correspond day, month, year values age_type. age_type_code character integer vector 3 values indicate values considered pertaining days (first value vector), months (second value vector), years (third value vector).","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_age_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","text":"character value vector values containing either \"D\", \"M\", \"Y\" days, months, years respectively.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_age_type.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","text":"","code":"cod_recode_age_type( age_type = c(rep(\"d\", 3), rep(\"m\", 2), rep(\"y\", 3)), age_type_code = c(\"d\", \"m\", \"y\") ) #> [1] \"D\" \"D\" \"D\" \"M\" \"M\" \"Y\" \"Y\" \"Y\""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_sex.html","id":null,"dir":"Reference","previous_headings":"","what":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","title":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","text":"Recode sex value cause death data based CoDEdit rules","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_sex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","text":"","code":"cod_recode_sex(sex_value, sex_code = c(1L, 2L), codedit = TRUE)"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_sex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","text":"sex_value character integer value vector values signifying sex. sex_code character integer vector 2 values indicate values considered pertaining males (first value vector) females (second value vector). codedit Logical. output based CoDEdit version 2 coding rules. Default TRUE.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_sex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","text":"integer value vector values containing either 1 males 2 females. codedit = TRUE, values equal sex_code values coded 9 (integer). Otherwise, coded NA_integer_.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_sex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","text":"","code":"cod_recode_sex( sex_value = c(rep(\"m\", 2), rep(\"f\", 3)), sex_code = c(\"m\", \"f\") ) #> [1] 1 1 2 2 2"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_structure.html","id":null,"dir":"Reference","previous_headings":"","what":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","title":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","text":"Structure cause--death data CoDEdit tool input data","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_structure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","text":"","code":"cod_structure_input(df, sex, sex_code = c(1, 2), dob, dod, code, id = NULL)"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_structure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","text":"df data.frame raw cause--death data following required variables contains values sex, date birth, date death, cause--death code. sex character value variable name df containing values sex. sex_code character integer vector 2 values indicate values considered pertaining males (first value vector) females (second value vector). dob character value variable name df containing values date birth. dod character value variable name df containing values date death. code character value variable name df containing values cause--death code. id character value variable name df containing unique record identifiers. Default NULL. NULL, unique record identifiers generated.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_structure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","text":"data.frame 6 columns number rows equal df names \"FreeId\", \"Sex\", \"Age Value\", \"Age Type\", \"Code\", \"Death Date\".","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_structure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","text":"","code":"df <- data.frame( id = 1:3, sex = c(1, 1, 2), dob = c(\"1977-11-05\", \"1971-04-04\", \"2012-08-13\"), dod = c(\"2024-06-28\", \"2023-10-11\", \"2023-09-25\"), code = c(\"P219\", \"O230\", \"Q913\") ) cod_structure_input(df, sex = \"sex\", dob = \"dob\", dod = \"dod\", code = \"code\") #> # A tibble: 3 × 6 #> FreeId Sex `Age Value` `Age Type` Code `Death Date` #> #> 1 1 1 110 Y P219 2024 #> 2 2 1 110 Y O230 2023 #> 3 3 2 110 Y Q913 2023"},{"path":"https://oxford-ihtm.io/codeditr/reference/codeditr.html","id":null,"dir":"Reference","previous_headings":"","what":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool — codeditr","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool — codeditr","text":"World Health Organization's CoDEdit electronic tool intended help producers cause--death statistics strengthening capacity perform routine checks data. package ports original tool built using Microsoft Access R leverage utility function original tool usable application program interface can used building universal tools creating programmatic scientific workflows aimed routine, automated, large-scale monitoring cause--death data quality.","code":""},{"path":[]},{"path":"https://oxford-ihtm.io/codeditr/reference/codeditr.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool — codeditr","text":"Maintainer: Ernest Guevarra ernest@guevarra.io (ORCID) [copyright holder] Authors: Anita Makori [copyright holder] contributors: Sanjeev Pugazhendhi [thesis advisor, reviewer] Williams Udoh Ituen-Umanah [reviewer] Proochista Ariana [reviewer, copyright holder]","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/expand_icd10.html","id":null,"dir":"Reference","previous_headings":"","what":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","title":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","text":"Enumerate ICD 10 codes given code range","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/expand_icd10.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","text":"","code":"expand_icd10_code_range(code_range)"},{"path":"https://oxford-ihtm.io/codeditr/reference/expand_icd10.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","text":"code_range character value vector character values indicating range ICD 10 codes. See Details syntax code range/s.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/expand_icd10.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","text":"vector ICD 10 codes within range codes specified code_range.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/expand_icd10.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","text":"","code":"expand_icd10_code_range(\"A71.0-A71.9\") #> [1] \"A71.0\" \"A71.1\" \"A71.2\" \"A71.3\" \"A71.4\" \"A71.5\" \"A71.6\" \"A71.7\" \"A71.8\" #> [10] \"A71.9\" expand_icd10_code_range(\"F50.1,F50.3-F50.9\") #> [1] \"F50.1\" \"F50.3\" \"F50.4\" \"F50.5\" \"F50.6\" \"F50.7\" \"F50.8\" \"F50.9\""},{"path":"https://oxford-ihtm.io/codeditr/reference/get_age.html","id":null,"dir":"Reference","previous_headings":"","what":"Get various age values for all three age types — get_age_values","title":"Get various age values for all three age types — get_age_values","text":"Get various age values three age types","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/get_age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get various age values for all three age types — get_age_values","text":"","code":"get_age_values(age_value, age_type = c(\"D\", \"M\", \"Y\"))"},{"path":"https://oxford-ihtm.io/codeditr/reference/get_age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get various age values for all three age types — get_age_values","text":"age_value integer value age age_type age type specified age value. Can either \"D\" day, \"M\" month, \"Y\" year.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/get_age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get various age values for all three age types — get_age_values","text":"named list age values days, months, years.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/get_age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get various age values for all three age types — get_age_values","text":"","code":"get_age_values(1, \"Y\") #> $days #> [1] 365.25 #> #> $months #> [1] 12 #> #> $years #> [1] 1 #>"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_cod_by_sex.html","id":null,"dir":"Reference","previous_headings":"","what":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","title":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","text":"Sex-specific causes death ICD 10","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_cod_by_sex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","text":"","code":"icd10_cod_by_sex"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_cod_by_sex.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","text":"data frame 3 columns 880 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_cod_by_sex.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","text":"https://icd..int/browse10/Content/statichtml/ICD10Volume2_en_2019.pdf","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_cod_by_sex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","text":"","code":"icd10_cod_by_sex #> # A tibble: 880 × 3 #> code title sex #> #> 1 B26.0 NA 1 #> 2 C60.0 NA 1 #> 3 C60.1 NA 1 #> 4 C60.2 NA 1 #> 5 C60.8 NA 1 #> 6 C60.9 NA 1 #> 7 C61 NA 1 #> 8 C62.0 NA 1 #> 9 C62.1 NA 1 #> 10 C62.9 NA 1 #> # ℹ 870 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","title":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","text":"Example death records dataset ICD10 cause--death coding","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","text":"","code":"icd10_example"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_example.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","text":"data frame 6 columns 3613 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_example.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","text":"https://www..int/standards/classifications/classification--diseases/services/codedit-tool","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","text":"","code":"icd10_example #> # A tibble: 3,613 × 6 #> FreeId Sex `Age Value` `Age Type` Code `Death Date` #> #> 1 XX0001 2 0 D P219 2010 #> 2 XX0002 1 0 D P015 2010 #> 3 XX0003 2 0 D P015 2010 #> 4 XX0004 1 0 D P021 NA #> 5 XX0005 2 5 D O230 2010 #> 6 XX0006 1 0 D P011 2010 #> 7 XX0007 1 0 D Q913 2010 #> 8 XX0008 1 1 D P220 2010 #> 9 XX0009 2 1 D Q790 2010 #> 10 XX0010 1 0 D P027 2010 #> # ℹ 3,603 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_unlikely_cod.html","id":null,"dir":"Reference","previous_headings":"","what":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","title":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","text":"Unlikely causes death ICD 10","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_unlikely_cod.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","text":"","code":"icd10_unlikely_cod"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_unlikely_cod.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","text":"data frame 2 columns 424 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_unlikely_cod.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","text":"https://icd..int/browse10/Content/statichtml/ICD10Volume2_en_2019.pdf","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_unlikely_cod.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","text":"","code":"icd10_unlikely_cod #> # A tibble: 424 × 2 #> code title #> #> 1 A31.1 Cutaneous mycobacterial infection #> 2 A42.8 Other forms of cutaneous actinomycosis #> 3 A53.0 Latent syphilis,unspecified as early or late #> 4 A60.0 Herpesviral infection of genitalia and urogenital tract #> 5 A63.0 Anogenital (venereal) warts #> 6 A71.0-A71.9 Trachoma #> 7 A74.0 Chlamydial conjunctivitis #> 8 B00.2 Herpesviral gingivostomatitis #> 9 B00.5 Herpesviral ocular disease #> 10 B00.8 Herpesviral whitlow #> # ℹ 414 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_cod_by_sex.html","id":null,"dir":"Reference","previous_headings":"","what":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","title":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","text":"Sex-specific causes death ICD 11","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_cod_by_sex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","text":"","code":"icd11_cod_by_sex"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_cod_by_sex.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","text":"data frame 3 columns 547 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_cod_by_sex.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","text":"https://icdcdn..int/icd11referenceguide/en/html/index.html#list--categories-limited----likely--occur--female-persons","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_cod_by_sex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","text":"","code":"icd11_cod_by_sex #> # A tibble: 547 × 3 #> code title sex #> #> 1 2C80 Malignant neoplasms of testis 1 #> 2 2C80.2 Germ cell tumour of testis 1 #> 3 2C80.Y Other specified malignant neoplasms of testis 1 #> 4 2C80.Z Malignant neoplasms of testis, unspecified 1 #> 5 2C81 Malignant neoplasms of penis 1 #> 6 2C81.0 Squamous cell carcinoma of penis 1 #> 7 2C81.1 Melanoma of penis 1 #> 8 2C81.Y Other specified malignant neoplasm of penis 1 #> 9 2C81.Z Malignant neoplasms of penis, unspecified 1 #> 10 2C82 Malignant neoplasms of prostate 1 #> # ℹ 537 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","title":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","text":"Example death records dataset ICD11 cause--death coding","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","text":"","code":"icd11_example"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_example.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","text":"data frame 6 columns 244 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_example.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","text":"https://www..int/standards/classifications/classification--diseases/services/codedit-tool","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","text":"","code":"icd11_example #> # A tibble: 244 × 6 #> freeid sex `Age value` `Age type` Code `Death date` #> #> 1 10001 2 6 Y \"1A40.0\" 2019 #> 2 10002 2 115 Y \"1B10.0\" 2019 #> 3 10003 2 115 Y \"1B10.1\" 2019 #> 4 10004 1 115 Y \"1B10.Z\" 2019 #> 5 10005 2 114 Y \"1B11.0\" 2019 #> 6 10006 2 115 Y \"1B1Z \" 2019 #> 7 10007 2 114 Y \"1B1Z \" 2019 #> 8 10008 1 109 Y \"1B53 \" 2019 #> 9 10009 1 109 Y \"1B7Y \" 2019 #> 10 10010 2 109 Y \"1C60.Z\" 2019 #> # ℹ 234 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_unlikely_cod.html","id":null,"dir":"Reference","previous_headings":"","what":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","title":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","text":"Unlikely causes death ICD 11","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_unlikely_cod.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","text":"","code":"icd11_unlikely_cod"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_unlikely_cod.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","text":"data frame 2 columns 269 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_unlikely_cod.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","text":"https://icd..int/valuesets/viewer/582/en","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_unlikely_cod.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","text":"","code":"icd11_unlikely_cod #> # A tibble: 269 × 2 #> code title #> #> 1 1A94.0 Herpes simplex infection of genitalia or urogenital tract #> 2 1B21.2 Cutaneous non-tuberculous mycobacterial infection #> 3 1B72 Impetigo #> 4 1C10.Y Other specified forms of actinomycosis #> 5 1C20 Chlamydial conjunctivitis #> 6 1C23 Trachoma #> 7 1D84 Viral conjunctivitis #> 8 1E76 Molluscum contagiosum #> 9 1E80 Common warts #> 10 1F00.0 Herpes simplex infection of skin or mucous membrane #> # ℹ 259 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/list_ill_defined_icd11.html","id":null,"dir":"Reference","previous_headings":"","what":"List ill-defined ICD 11 codes — list_ill_defined_icd11","title":"List ill-defined ICD 11 codes — list_ill_defined_icd11","text":"List ill-defined ICD 11 codes","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/list_ill_defined_icd11.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List ill-defined ICD 11 codes — list_ill_defined_icd11","text":"","code":"list_ill_defined_icd11()"},{"path":"https://oxford-ihtm.io/codeditr/reference/list_ill_defined_icd11.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List ill-defined ICD 11 codes — list_ill_defined_icd11","text":"character vector ICD 11 codes classified ill-defined cause death","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/list_ill_defined_icd11.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List ill-defined ICD 11 codes — list_ill_defined_icd11","text":"","code":"list_ill_defined_icd11() #> [1] \"BD10\" \"BD11\" \"BD11.0\" \"BD11.1\" \"BD11.2\" \"BD11.Z\" \"BD12\" #> [8] \"BD13\" \"BD14\" \"BD1Y\" \"BD1Z\" \"BA2Z\" \"BE2Y\" \"BE2Z\" #> [15] \"CB41.0\" \"CB41.2\" \"KB2D\" \"KB2E\" \"MA00\" \"MA01\" \"MA01.0\" #> [22] \"MA01.1\" \"MA01.Z\" \"MA0Y\" \"MA10\" \"MA10.0\" \"MA10.1\" \"MA10.2\" #> [29] \"MA11\" \"MA12\" \"MA12.0\" \"MA12.1\" \"MA12.2\" \"MA12.3\" \"MA12.4\" #> [36] \"MA12.Y\" \"MA13\" \"MA13.0\" \"MA13.00\" \"MA13.0Y\" \"MA13.1\" \"MA13.Y\" #> [43] \"MA14\" \"MA14.0\" \"MA14.1\" \"MA14.10\" \"MA14.11\" \"MA14.12\" \"MA14.13\" #> [50] \"MA14.14\" \"MA14.15\" \"MA14.16\" \"MA14.17\" \"MA14.18\" \"MA14.19\" \"MA14.1A\" #> [57] \"MA14.1B\" \"MA14.1C\" \"MA14.1D\" \"MA14.1E\" \"MA14.Y\" \"MA15.0\" \"MA15.1\" #> [64] \"MA15.Y\" \"MA16\" \"MA16.0\" \"MA16.00\" \"MA16.0Y\" \"MA16.0Z\" \"MA16.1\" #> [71] \"MA16.10\" \"MA16.11\" \"MA16.1Z\" \"MA16.Y\" \"MA16.Z\" \"MA17\" \"MA18\" #> [78] \"MA18.0\" \"MA18.00\" \"MA18.0Y\" \"MA18.0Z\" \"MA18.1\" \"MA18.2\" \"MA18.3\" #> [85] \"MA18.4\" \"MA18.Y\" \"MA18.Z\" \"MA19\" \"MA19.0\" \"MA19.1\" \"MA19.2\" #> [92] \"MA19.Y\" \"MA19.Z\" \"MA1A\" \"MA1A.0\" \"MA1A.1\" \"MA1Y\" \"MA3Y\" #> [99] \"MA50\" \"MA51\" \"MA6Y\" \"MA80\" \"MA80.0\" \"MA80.1\" \"MA80.2\" #> [106] \"MA80.20\" \"MA80.2Y\" \"MA80.2Z\" \"MA80.Y\" \"MA80.Z\" \"MA81\" \"MA82\" #> [113] \"MA82.0\" \"MA82.1\" \"MA82.10\" \"MA82.1Y\" \"MA82.1Z\" \"MA82.2\" \"MA82.Y\" #> [120] \"MA82.Z\" \"MA8Y\" \"MB0Y\" \"MB20\" \"MB20.0\" \"MB20.1\" \"MB20.2\" #> [127] \"MB20.Y\" \"MB21\" \"MB21.0\" \"MB21.1\" \"MB21.10\" \"MB21.11\" \"MB21.12\" #> [134] \"MB21.1Y\" \"MB21.1Z\" \"MB21.2\" \"MB21.3\" \"MB21.4\" \"MB21.5\" \"MB21.6\" #> [141] \"MB21.7\" \"MB21.8\" \"MB21.9\" \"MB21.A\" \"MB21.B\" \"MB21.Y\" \"MB21.Z\" #> [148] \"MB22\" \"MB22.0\" \"MB22.1\" \"MB22.2\" \"MB22.3\" \"MB22.4\" \"MB22.5\" #> [155] \"MB22.6\" \"MB22.7\" \"MB22.Y\" \"MB22.Z\" \"MB23\" \"MB23.0\" \"MB23.1\" #> [162] \"MB23.2\" \"MB23.3\" \"MB23.4\" \"MB23.5\" \"MB23.6\" \"MB23.7\" \"MB23.8\" #> [169] \"MB23.9\" \"MB23.A\" \"MB23.C\" \"MB23.D\" \"MB23.E\" \"MB23.F\" \"MB23.G\" #> [176] \"MB23.H\" \"MB23.J\" \"MB23.K\" \"MB23.L\" \"MB23.M\" \"MB23.N\" \"MB23.Q\" #> [183] \"MB23.R\" \"MB23.S\" \"MB23.Y\" \"MB23.Z\" \"MB24\" \"MB24.0\" \"MB24.1\" #> [190] \"MB24.2\" \"MB24.3\" \"MB24.4\" \"MB24.5\" \"MB24.6\" \"MB24.60\" \"MB24.61\" #> [197] \"MB24.62\" \"MB24.63\" \"MB24.64\" \"MB24.6Y\" \"MB24.6Z\" \"MB24.7\" \"MB24.8\" #> [204] \"MB24.9\" \"MB24.A\" \"MB24.B\" \"MB24.C\" \"MB24.D\" \"MB24.E\" \"MB24.F\" #> [211] \"MB24.G\" \"MB24.H\" \"MB24.Y\" \"MB24.Z\" \"MB25\" \"MB25.0\" \"MB25.00\" #> [218] \"MB25.01\" \"MB25.02\" \"MB25.03\" \"MB25.0Y\" \"MB25.0Z\" \"MB25.1\" \"MB25.2\" #> [225] \"MB25.3\" \"MB25.Y\" \"MB25.Z\" \"MB26\" \"MB26.0\" \"MB26.00\" \"MB26.01\" #> [232] \"MB26.02\" \"MB26.03\" \"MB26.04\" \"MB26.05\" \"MB26.06\" \"MB26.07\" \"MB26.08\" #> [239] \"MB26.09\" \"MB26.0A\" \"MB26.0B\" \"MB26.0C\" \"MB26.0Y\" \"MB26.0Z\" \"MB26.1\" #> [246] \"MB26.10\" \"MB26.11\" \"MB26.12\" \"MB26.1Y\" \"MB26.1Z\" \"MB26.2\" \"MB26.3\" #> [253] \"MB26.4\" \"MB26.5\" \"MB26.6\" \"MB26.7\" \"MB26.8\" \"MB26.9\" \"MB26.A\" #> [260] \"MB26.Y\" \"MB26.Z\" \"MB27\" \"MB27.0\" \"MB27.1\" \"MB27.2\" \"MB27.20\" #> [267] \"MB27.21\" \"MB27.22\" \"MB27.23\" \"MB27.24\" \"MB27.25\" \"MB27.26\" \"MB27.27\" #> [274] \"MB27.2Y\" \"MB27.2Z\" \"MB27.3\" \"MB27.4\" \"MB27.Y\" \"MB27.Z\" \"MB28\" #> [281] \"MB28.0\" \"MB28.1\" \"MB28.2\" \"MB28.3\" \"MB28.4\" \"MB28.5\" \"MB28.6\" #> [288] \"MB28.7\" \"MB28.8\" \"MB28.9\" \"MB28.A\" \"MB28.B\" \"MB28.C\" \"MB28.D\" #> [295] \"MB28.E\" \"MB28.F\" \"MB28.G\" \"MB28.H\" \"MB28.Y\" \"MB28.Z\" \"MB29\" #> [302] \"MB29.0\" \"MB29.1\" 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\"MG52.02\" \"MG52.0Y\" \"MG52.0Z\" \"MG52.Y\" \"MG52.Z\" #> [1219] \"MG53\" \"MG53.0\" \"MG53.Y\" \"MG53.Z\" \"MG54\" \"MG55\" \"MG55.0\" #> [1226] \"MG55.Y\" \"MG55.Z\" \"MG56\" \"MG5Y\" \"MG5Z\" \"MG60\" \"MG61\" #> [1233] \"MG62\" \"MG63\" \"MG64\" \"MG65\" \"MG66\" \"MG67\" \"MG6Y\" #> [1240] \"MG70\" \"MG71\" \"MG71.0\" \"MG71.Y\" \"MG71.Z\" \"MG72\" \"MG7Y\" #> [1247] \"MG7Z\" \"MG9Y\" \"MH10\" \"MH11.0\" \"MH11.1\" \"MH11.Z\" \"MH12\" #> [1254] \"MH12.0\" \"MH12.1\" \"MH12.Y\" \"MH13\" \"MH14\" \"MH2Y\""}] +[{"path":[]},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement ernest@guevarra.io. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://oxford-ihtm.io/codeditr/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":[]},{"path":"https://oxford-ihtm.io/codeditr/CONTRIBUTING.html","id":"bugs","dir":"","previous_headings":"","what":"Bugs","title":"Contributing","text":"Submit issue issues page","code":""},{"path":"https://oxford-ihtm.io/codeditr/CONTRIBUTING.html","id":"code-contributions","dir":"","previous_headings":"","what":"Code contributions","title":"Contributing","text":"Fork repository Github account Clone version account machine account Make sure track progress upstream .e., version codeditr OxfordIHTM/codeditr, making changes make sure pull changes upstream either git fetch upstream merge later git pull upstream fetch merge one step Make changes new feature branch Please write test tests changes affect code just documentation Push changes account Submit pull request OxfordIHTM/codeditr","code":"git clone https://github.com//codeditr.git git remote add upstream https://github.com/OxfordIHTM/codeditr.git"},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. Developers use GNU GPL protect rights two steps: (1) assert copyright software, (2) offer License giving legal permission copy, distribute /modify . developers’ authors’ protection, GPL clearly explains warranty free software. users’ authors’ sake, GPL requires modified versions marked changed, problems attributed erroneously authors previous versions. devices designed deny users access install run modified versions software inside , although manufacturer can . fundamentally incompatible aim protecting users’ freedom change software. systematic pattern abuse occurs area products individuals use, precisely unacceptable. Therefore, designed version GPL prohibit practice products. problems arise substantially domains, stand ready extend provision domains future versions GPL, needed protect freedom users. Finally, every program threatened constantly software patents. States allow patents restrict development use software general-purpose computers, , wish avoid special danger patents applied free program make effectively proprietary. prevent , GPL assures patents used render program non-free. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. Mere interaction user computer network, transfer copy, conveying. interactive user interface displays “Appropriate Legal Notices” extent includes convenient prominently visible feature (1) displays appropriate copyright notice, (2) tells user warranty work (except extent warranties provided), licensees may convey work License, view copy License. interface presents list user commands options, menu, prominent item list meets criterion.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_1-source-code","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"1. Source Code","title":"GNU General Public License","text":"“source code” work means preferred form work making modifications . “Object code” means non-source form work. “Standard Interface” means interface either official standard defined recognized standards body, , case interfaces specified particular programming language, one widely used among developers working language. “System Libraries” executable work include anything, work whole, () included normal form packaging Major Component, part Major Component, (b) serves enable use work Major Component, implement Standard Interface implementation available public source code form. “Major Component”, context, means major essential component (kernel, window system, ) specific operating system () executable work runs, compiler used produce work, object code interpreter used run . “Corresponding Source” work object code form means source code needed generate, install, (executable work) run object code modify work, including scripts control activities. However, include work’s System Libraries, general-purpose tools generally available free programs used unmodified performing activities part work. example, Corresponding Source includes interface definition files associated source files work, source code shared libraries dynamically linked subprograms work specifically designed require, intimate data communication control flow subprograms parts work. Corresponding Source need include anything users can regenerate automatically parts Corresponding Source. Corresponding Source work source code form work.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_2-basic-permissions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"2. Basic Permissions","title":"GNU General Public License","text":"rights granted License granted term copyright Program, irrevocable provided stated conditions met. License explicitly affirms unlimited permission run unmodified Program. output running covered work covered License output, given content, constitutes covered work. License acknowledges rights fair use equivalent, provided copyright law. may make, run propagate covered works convey, without conditions long license otherwise remains force. may convey covered works others sole purpose make modifications exclusively , provide facilities running works, provided comply terms License conveying material control copyright. thus making running covered works must exclusively behalf, direction control, terms prohibit making copies copyrighted material outside relationship . Conveying circumstances permitted solely conditions stated . Sublicensing allowed; section 10 makes unnecessary.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_3-protecting-users-legal-rights-from-anti-circumvention-law","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"3. Protecting Users’ Legal Rights From Anti-Circumvention Law","title":"GNU General Public License","text":"covered work shall deemed part effective technological measure applicable law fulfilling obligations article 11 WIPO copyright treaty adopted 20 December 1996, similar laws prohibiting restricting circumvention measures. convey covered work, waive legal power forbid circumvention technological measures extent circumvention effected exercising rights License respect covered work, disclaim intention limit operation modification work means enforcing, work’s users, third parties’ legal rights forbid circumvention technological measures.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. Conveying Verbatim Copies","title":"GNU General Public License","text":"may convey verbatim copies Program’s source code receive , medium, provided conspicuously appropriately publish copy appropriate copyright notice; keep intact notices stating License non-permissive terms added accord section 7 apply code; keep intact notices absence warranty; give recipients copy License along Program. may charge price price copy convey, may offer support warranty protection fee.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_5-conveying-modified-source-versions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"5. Conveying Modified Source Versions","title":"GNU General Public License","text":"may convey work based Program, modifications produce Program, form source code terms section 4, provided also meet conditions: ) work must carry prominent notices stating modified , giving relevant date. b) work must carry prominent notices stating released License conditions added section 7. requirement modifies requirement section 4 “keep intact notices”. c) must license entire work, whole, License anyone comes possession copy. License therefore apply, along applicable section 7 additional terms, whole work, parts, regardless packaged. License gives permission license work way, invalidate permission separately received . d) work interactive user interfaces, must display Appropriate Legal Notices; however, Program interactive interfaces display Appropriate Legal Notices, work need make . compilation covered work separate independent works, nature extensions covered work, combined form larger program, volume storage distribution medium, called “aggregate” compilation resulting copyright used limit access legal rights compilation’s users beyond individual works permit. Inclusion covered work aggregate cause License apply parts aggregate.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_6-conveying-non-source-forms","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"6. Conveying Non-Source Forms","title":"GNU General Public License","text":"may convey covered work object code form terms sections 4 5, provided also convey machine-readable Corresponding Source terms License, one ways: ) Convey object code , embodied , physical product (including physical distribution medium), accompanied Corresponding Source fixed durable physical medium customarily used software interchange. b) Convey object code , embodied , physical product (including physical distribution medium), accompanied written offer, valid least three years valid long offer spare parts customer support product model, give anyone possesses object code either (1) copy Corresponding Source software product covered License, durable physical medium customarily used software interchange, price reasonable cost physically performing conveying source, (2) access copy Corresponding Source network server charge. c) Convey individual copies object code copy written offer provide Corresponding Source. alternative allowed occasionally noncommercially, received object code offer, accord subsection 6b. d) Convey object code offering access designated place (gratis charge), offer equivalent access Corresponding Source way place charge. need require recipients copy Corresponding Source along object code. place copy object code network server, Corresponding Source may different server (operated third party) supports equivalent copying facilities, provided maintain clear directions next object code saying find Corresponding Source. Regardless server hosts Corresponding Source, remain obligated ensure available long needed satisfy requirements. e) Convey object code using peer--peer transmission, provided inform peers object code Corresponding Source work offered general public charge subsection 6d. separable portion object code, whose source code excluded Corresponding Source System Library, need included conveying object code work. “User Product” either (1) “consumer product”, means tangible personal property normally used personal, family, household purposes, (2) anything designed sold incorporation dwelling. determining whether product consumer product, doubtful cases shall resolved favor coverage. particular product received particular user, “normally used” refers typical common use class product, regardless status particular user way particular user actually uses, expects expected use, product. product consumer product regardless whether product substantial commercial, industrial non-consumer uses, unless uses represent significant mode use product. “Installation Information” User Product means methods, procedures, authorization keys, information required install execute modified versions covered work User Product modified version Corresponding Source. information must suffice ensure continued functioning modified object code case prevented interfered solely modification made. convey object code work section , , specifically use , User Product, conveying occurs part transaction right possession use User Product transferred recipient perpetuity fixed term (regardless transaction characterized), Corresponding Source conveyed section must accompanied Installation Information. requirement apply neither third party retains ability install modified object code User Product (example, work installed ROM). requirement provide Installation Information include requirement continue provide support service, warranty, updates work modified installed recipient, User Product modified installed. Access network may denied modification materially adversely affects operation network violates rules protocols communication across network. Corresponding Source conveyed, Installation Information provided, accord section must format publicly documented (implementation available public source code form), must require special password key unpacking, reading copying.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_7-additional-terms","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"7. Additional Terms","title":"GNU General Public License","text":"“Additional permissions” terms supplement terms License making exceptions one conditions. Additional permissions applicable entire Program shall treated though included License, extent valid applicable law. additional permissions apply part Program, part may used separately permissions, entire Program remains governed License without regard additional permissions. convey copy covered work, may option remove additional permissions copy, part . (Additional permissions may written require removal certain cases modify work.) may place additional permissions material, added covered work, can give appropriate copyright permission. Notwithstanding provision License, material add covered work, may (authorized copyright holders material) supplement terms License terms: ) Disclaiming warranty limiting liability differently terms sections 15 16 License; b) Requiring preservation specified reasonable legal notices author attributions material Appropriate Legal Notices displayed works containing ; c) Prohibiting misrepresentation origin material, requiring modified versions material marked reasonable ways different original version; d) Limiting use publicity purposes names licensors authors material; e) Declining grant rights trademark law use trade names, trademarks, service marks; f) Requiring indemnification licensors authors material anyone conveys material (modified versions ) contractual assumptions liability recipient, liability contractual assumptions directly impose licensors authors. non-permissive additional terms considered “restrictions” within meaning section 10. Program received , part , contains notice stating governed License along term restriction, may remove term. license document contains restriction permits relicensing conveying License, may add covered work material governed terms license document, provided restriction survive relicensing conveying. add terms covered work accord section, must place, relevant source files, statement additional terms apply files, notice indicating find applicable terms. Additional terms, permissive non-permissive, may stated form separately written license, stated exceptions; requirements apply either way.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_8-termination","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"8. Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. Termination rights section terminate licenses parties received copies rights License. rights terminated permanently reinstated, qualify receive new licenses material section 10.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_9-acceptance-not-required-for-having-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"9. Acceptance Not Required for Having Copies","title":"GNU General Public License","text":"required accept License order receive run copy Program. Ancillary propagation covered work occurring solely consequence using peer--peer transmission receive copy likewise require acceptance. However, nothing License grants permission propagate modify covered work. actions infringe copyright accept License. Therefore, modifying propagating covered work, indicate acceptance License .","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_10-automatic-licensing-of-downstream-recipients","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"10. Automatic Licensing of Downstream Recipients","title":"GNU General Public License","text":"time convey covered work, recipient automatically receives license original licensors, run, modify propagate work, subject License. responsible enforcing compliance third parties License. “entity transaction” transaction transferring control organization, substantially assets one, subdividing organization, merging organizations. propagation covered work results entity transaction, party transaction receives copy work also receives whatever licenses work party’s predecessor interest give previous paragraph, plus right possession Corresponding Source work predecessor interest, predecessor can get reasonable efforts. may impose restrictions exercise rights granted affirmed License. example, may impose license fee, royalty, charge exercise rights granted License, may initiate litigation (including cross-claim counterclaim lawsuit) alleging patent claim infringed making, using, selling, offering sale, importing Program portion .","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_11-patents","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"11. Patents","title":"GNU General Public License","text":"“contributor” copyright holder authorizes use License Program work Program based. work thus licensed called contributor’s “contributor version”. contributor’s “essential patent claims” patent claims owned controlled contributor, whether already acquired hereafter acquired, infringed manner, permitted License, making, using, selling contributor version, include claims infringed consequence modification contributor version. purposes definition, “control” includes right grant patent sublicenses manner consistent requirements License. contributor grants non-exclusive, worldwide, royalty-free patent license contributor’s essential patent claims, make, use, sell, offer sale, import otherwise run, modify propagate contents contributor version. following three paragraphs, “patent license” express agreement commitment, however denominated, enforce patent (express permission practice patent covenant sue patent infringement). “grant” patent license party means make agreement commitment enforce patent party. convey covered work, knowingly relying patent license, Corresponding Source work available anyone copy, free charge terms License, publicly available network server readily accessible means, must either (1) cause Corresponding Source available, (2) arrange deprive benefit patent license particular work, (3) arrange, manner consistent requirements License, extend patent license downstream recipients. “Knowingly relying” means actual knowledge , patent license, conveying covered work country, recipient’s use covered work country, infringe one identifiable patents country reason believe valid. , pursuant connection single transaction arrangement, convey, propagate procuring conveyance , covered work, grant patent license parties receiving covered work authorizing use, propagate, modify convey specific copy covered work, patent license grant automatically extended recipients covered work works based . patent license “discriminatory” include within scope coverage, prohibits exercise , conditioned non-exercise one rights specifically granted License. may convey covered work party arrangement third party business distributing software, make payment third party based extent activity conveying work, third party grants, parties receive covered work , discriminatory patent license () connection copies covered work conveyed (copies made copies), (b) primarily connection specific products compilations contain covered work, unless entered arrangement, patent license granted, prior 28 March 2007. Nothing License shall construed excluding limiting implied license defenses infringement may otherwise available applicable patent law.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_12-no-surrender-of-others-freedom","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"12. No Surrender of Others’ Freedom","title":"GNU General Public License","text":"conditions imposed (whether court order, agreement otherwise) contradict conditions License, excuse conditions License. convey covered work satisfy simultaneously obligations License pertinent obligations, consequence may convey . example, agree terms obligate collect royalty conveying convey Program, way satisfy terms License refrain entirely conveying Program.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_13-use-with-the-gnu-affero-general-public-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"13. Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://oxford-ihtm.io/codeditr/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://oxford-ihtm.io/codeditr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anita Makori. Author, copyright holder. Ernest Guevarra. Author, maintainer, copyright holder. Sanjeev Pugazhendhi. Thesis advisor, reviewer. Williams Udoh Ituen-Umanah. Reviewer. Proochista Ariana. Reviewer, copyright holder.","code":""},{"path":"https://oxford-ihtm.io/codeditr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Anita Makori, Ernest Guevarra (2024). codeditr: Implementing Cause--Death Data Checks Based World Health Organization's CoDEdit Tool. R package version 0.0.9000, https://oxford-ihtm.io/codeditr/.","code":"@Manual{, title = {codeditr: Implementing Cause-of-Death Data Checks Based on World Health Organization's CoDEdit Tool}, author = {{Anita Makori} and {Ernest Guevarra}}, year = {2024}, note = {R package version 0.0.9000}, url = {https://oxford-ihtm.io/codeditr/}, }"},{"path":"https://oxford-ihtm.io/codeditr/index.html","id":"codeditr-implementing-cause-of-death-data-checks-based-on-the-who-codedit-tool-","dir":"","previous_headings":"","what":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","text":"World Health Organization’s CoDEdit electronic tool intended help producers cause--death statistics strengthening capacity perform routine checks data. package ports original tool built using Microsoft Access R leverage utility function original tool usable application program interface can used building universal tools creating programmatic scientific workflows aimed routine, automated, large-scale monitoring cause--death data.","code":""},{"path":"https://oxford-ihtm.io/codeditr/index.html","id":"what-does-codeditr-do","dir":"","previous_headings":"","what":"What does codeditr do?","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","text":"codeditr package provides functions implementing data quality checks cause--death records. built upon heuristics algorithms CoDEdit v2.0 electronic tool uses evaluate quality cause--death data produced used country level statisticians charge mortality reporting. package, end users ability programmatically create scientific workflows research cause--death data quality build open tools applications routine monitoring cause--death data.","code":""},{"path":"https://oxford-ihtm.io/codeditr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","text":"coeditr yet CRAN can installed Oxford IHTM R-universe : load codeditr","code":"install.packages( \"codeditr\", repos = c(\"https://oxfordihtm.r-universe.dev\", \"https://cloud.r-project.org\") ) # load package library(codeditr)"},{"path":[]},{"path":"https://oxford-ihtm.io/codeditr/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","text":"find codeditr package useful please cite using suggested citation provided call citation() function follows:","code":"citation(\"codeditr\") #> To cite codeditr in publications use: #> #> Anita Makori, Ernest Guevarra (2024). _codeditr: Implementing #> Cause-of-Death Data Checks Based on World Health Organization's #> CoDEdit Tool_. R package version 0.0.9000, #> . #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> title = {codeditr: Implementing Cause-of-Death Data Checks Based on World Health Organization's CoDEdit Tool}, #> author = {{Anita Makori} and {Ernest Guevarra}}, #> year = {2024}, #> note = {R package version 0.0.9000}, #> url = {https://oxford-ihtm.io/codeditr/}, #> }"},{"path":"https://oxford-ihtm.io/codeditr/index.html","id":"community-guidelines","dir":"","previous_headings":"","what":"Community guidelines","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool","text":"Feedback, bug reports feature requests welcome; file issues seek support . like contribute package, please see contributing guidelines. project released Contributor Code Conduct. participating project agree abide terms.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_calculate_age.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate age at death based on date of birth and date of death — cod_calculate_age","title":"Calculate age at death based on date of birth and date of death — cod_calculate_age","text":"Calculate age death based date birth date death","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_calculate_age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate age at death based on date of birth and date of death — cod_calculate_age","text":"","code":"cod_calculate_age(dob, dod, date_format = \"%Y-%m-%d\", codedit = TRUE) cod_calculate_ages(dob, dod, date_format = \"%Y-%m-%d\", codedit = TRUE)"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_calculate_age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate age at death based on date of birth and date of death — cod_calculate_age","text":"dob Date birth. ideally standard ISO extended date format \"YYYY-MM-DD\" specified default value date_format. dod Date death. ideally standard ISO extended date format YYYY-MM_DD\" specified default value date_format. date_format Format date values provided. Date formatting handled using strptime() hence needs specified based strptime() requires format argument. default, set standard ISO extended date format expressed \"%Y-%m-%d\" corresponds \"YYYY-MM-DD\". codedit Logical. output based CoDEdit version 2 coding rules. Default TRUE.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_calculate_age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate age at death based on date of birth and date of death — cod_calculate_age","text":"Values age days, months years. codedit TRUE, tibble age value age type required CoDEdit.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_calculate_age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate age at death based on date of birth and date of death — cod_calculate_age","text":"","code":"cod_calculate_age(\"1977-11-05\", Sys.Date()) #> # A tibble: 1 × 2 #> age_value age_type #> #> 1 46 Y cod_calculate_age(\"1965-05-20\", \"2023-10-03\") #> # A tibble: 1 × 2 #> age_value age_type #> #> 1 58 Y"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_age.html","id":null,"dir":"Reference","previous_headings":"","what":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","title":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","text":"Check age values cause death data based CoDEdit rules","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","text":"","code":"cod_check_age(age_value, age_type, age_type_code = c(\"D\", \"M\", \"Y\"))"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","text":"age_value integer value vector values age based CoDEdit rules. age_type vector values age type based CoDEdit rules. either \"D\" age days, \"M\" age months, \"Y\" age years. values different , age_type_code specified correspond day, month, year values age_type. age_type_code character integer vector 3 values indicate values considered pertaining days (first value vector), months (second value vector), years (third value vector).","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","text":"tibble number rows equal length age_value two columns age_check age_check_note.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check age values in cause of death data based on CoDEdit rules — cod_check_age","text":"","code":"cod_check_age(120, \"Y\") #> # A tibble: 1 × 2 #> age_check age_check_note #> #> 1 0 No issues with age value and age type cod_check_age(28, \"D\") #> # A tibble: 1 × 2 #> age_check age_check_note #> #> 1 1 Should probably be age value of 1 and age type of months (M) cod_check_age(32, \"D\") #> # A tibble: 1 × 2 #> age_check age_check_note #> #> 1 2 Should probably be converted to age value of age type months (M) no…"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","title":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","text":"Check cause death code code entry mistakes /code completeness","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","text":"","code":"cod_check_code(cod, version = c(\"icd10\", \"icd11\"), sex) cod_check_code_structure_icd10(cod) cod_check_code_structure_icd11(cod) cod_check_code_ill_defined_icd10(cod) cod_check_code_ill_defined_icd11(cod) cod_check_code_unlikely_icd10(cod) cod_check_code_unlikely_icd11(cod) cod_check_code_sex_icd10_(cod, sex) cod_check_code_sex_icd10(cod, sex) cod_check_code_sex_icd11_(cod, sex) cod_check_code_sex_icd11(cod, sex)"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","text":"cod character value vector values cause death code/s. version character value ICD version used. either \"icd10\" \"icd11\". Default \"icd10\". sex character value vector values sex individual associated specified cod.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","text":"tibble 2 columns/fields. First integer value indicating whether issue cause death code provided relation potential code entry mistake /issue code completeness.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_code.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check cause of death code for code entry mistakes and/or code completeness — cod_check_code","text":"","code":"cod_check_code(\"U100\", sex = 1) #> # A tibble: 1 × 9 #> cod_check_structure cod_check_note_structure cod_check_ill_defined #> #> 1 8 CoD code contains the character val… 0 #> # ℹ 6 more variables: cod_check_note_ill_defined , #> # cod_check_unlikely , cod_check_note_unlikely , #> # cod_check_sex , cod_check_note_sex , cod_check cod_check_code(\"2C6Z\", version = \"icd11\", sex = 1) #> # A tibble: 1 × 9 #> cod_check_structure cod_check_note_structure cod_check_ill_defined #> #> 1 0 No issues found in CoD code 0 #> # ℹ 6 more variables: cod_check_note_ill_defined , #> # cod_check_unlikely , cod_check_note_unlikely , #> # cod_check_sex , cod_check_note_sex , cod_check "},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_dod.html","id":null,"dir":"Reference","previous_headings":"","what":"Check date of death value in cause of death data based on CoDEdit rules — cod_check_dod","title":"Check date of death value in cause of death data based on CoDEdit rules — cod_check_dod","text":"Check date death value cause death data based CoDEdit rules","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_dod.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check date of death value in cause of death data based on CoDEdit rules — cod_check_dod","text":"","code":"cod_check_dod(dod)"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_dod.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check date of death value in cause of death data based on CoDEdit rules — cod_check_dod","text":"dod Date death value expressed terms year death occurred.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_dod.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check date of death value in cause of death data based on CoDEdit rules — cod_check_dod","text":"tibble number rows equal length dod two columns dod_check dod_check_note.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_dod.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check date of death value in cause of death data based on CoDEdit rules — cod_check_dod","text":"","code":"cod_check_dod(\"2024\") #> # A tibble: 1 × 2 #> dod_check dod_check_note #> #> 1 0 No issues with date of death value"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Check structure and values of input data to CoDEdit tool — cod_check_codedit_input","title":"Check structure and values of input data to CoDEdit tool — cod_check_codedit_input","text":"Check structure values input data CoDEdit tool","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check structure and values of input data to CoDEdit tool — cod_check_codedit_input","text":"","code":"cod_check_codedit_input(df)"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check structure and values of input data to CoDEdit tool — cod_check_codedit_input","text":"df data.frame 6 columns names \"FreeId\", \"Sex\", \"Age Value\", \"Age Type\", \"Code\", \"Death Date\" compatible input data required CoDEdit tool.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check structure and values of input data to CoDEdit tool — cod_check_codedit_input","text":"data.frame containing check codes check notes row variable identified FreeId df.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check structure and values of input data to CoDEdit tool — cod_check_codedit_input","text":"","code":"cod_check_codedit_input(icd10_example) #> # A tibble: 3,613 × 7 #> sex_check sex_check_note age_check age_check_note code_check$code_check #> #> 1 0 No issues with sex … 0 No issues wit… 0 #> 2 0 No issues with sex … 0 No issues wit… 0 #> 3 0 No issues with sex … 0 No issues wit… 0 #> 4 0 No issues with sex … 0 No issues wit… 0 #> 5 0 No issues with sex … 0 No issues wit… 0 #> 6 0 No issues with sex … 0 No issues wit… 0 #> 7 0 No issues with sex … 0 No issues wit… 0 #> 8 0 No issues with sex … 0 No issues wit… 0 #> 9 0 No issues with sex … 0 No issues wit… 0 #> 10 0 No issues with sex … 0 No issues wit… 0 #> # ℹ 3,603 more rows #> # ℹ 3 more variables: code_check$code_check_note , dod_check , #> # dod_check_note "},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_sex.html","id":null,"dir":"Reference","previous_headings":"","what":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","title":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","text":"Check sex values cause death data based CoDEdit rules","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_sex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","text":"","code":"cod_check_sex(sex_value, sex_code = c(1, 2))"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_sex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","text":"sex_value integer value vector values age based CoDEdit rules. sex_code character integer vector 2 values indicate values considered pertaining males (first value vector) females (second value vector). Default 1 male 2 female.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_sex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","text":"tibble number rows equal length sex_value two columns sex_check sex_check_note.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_check_sex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check sex values in cause of death data based on CoDEdit rules — cod_check_sex","text":"","code":"cod_check_sex(\"m\", c(\"m\", \"f\")) #> # A tibble: 1 × 2 #> sex_check sex_check_note #> #> 1 0 No issues with sex value cod_check_sex(\"male\", c(\"male\", \"female\")) #> # A tibble: 1 × 2 #> sex_check sex_check_note #> #> 1 0 No issues with sex value cod_check_sex(1, 1:2) #> # A tibble: 1 × 2 #> sex_check sex_check_note #> #> 1 0 No issues with sex value"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_age_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","title":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","text":"Recode age type cause death data based CoDEdit rules","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_age_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","text":"","code":"cod_recode_age_type(age_type, age_type_code = c(\"D\", \"M\", \"Y\"))"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_age_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","text":"age_type vector values age type based CoDEdit rules. either \"D\" age days, \"M\" age months, \"Y\" age years. values different , age_type_code specified correspond day, month, year values age_type. age_type_code character integer vector 3 values indicate values considered pertaining days (first value vector), months (second value vector), years (third value vector).","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_age_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","text":"character value vector values containing either \"D\", \"M\", \"Y\" days, months, years respectively.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_age_type.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Recode age type of cause of death data based on CoDEdit rules — cod_recode_age_type","text":"","code":"cod_recode_age_type( age_type = c(rep(\"d\", 3), rep(\"m\", 2), rep(\"y\", 3)), age_type_code = c(\"d\", \"m\", \"y\") ) #> [1] \"D\" \"D\" \"D\" \"M\" \"M\" \"Y\" \"Y\" \"Y\""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_sex.html","id":null,"dir":"Reference","previous_headings":"","what":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","title":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","text":"Recode sex value cause death data based CoDEdit rules","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_sex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","text":"","code":"cod_recode_sex(sex_value, sex_code = c(1L, 2L), codedit = TRUE)"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_sex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","text":"sex_value character integer value vector values signifying sex. sex_code character integer vector 2 values indicate values considered pertaining males (first value vector) females (second value vector). codedit Logical. output based CoDEdit version 2 coding rules. Default TRUE.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_sex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","text":"integer value vector values containing either 1 males 2 females. codedit = TRUE, values equal sex_code values coded 9 (integer). Otherwise, coded NA_integer_.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_recode_sex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Recode sex value of cause of death data based on CoDEdit rules — cod_recode_sex","text":"","code":"cod_recode_sex( sex_value = c(rep(\"m\", 2), rep(\"f\", 3)), sex_code = c(\"m\", \"f\") ) #> [1] 1 1 2 2 2"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_structure.html","id":null,"dir":"Reference","previous_headings":"","what":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","title":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","text":"Structure cause--death data CoDEdit tool input data","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_structure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","text":"","code":"cod_structure_input(df, sex, sex_code = c(1, 2), dob, dod, code, id = NULL)"},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_structure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","text":"df data.frame raw cause--death data following required variables contains values sex, date birth, date death, cause--death code. sex character value variable name df containing values sex. sex_code character integer vector 2 values indicate values considered pertaining males (first value vector) females (second value vector). dob character value variable name df containing values date birth. dod character value variable name df containing values date death. code character value variable name df containing values cause--death code. id character value variable name df containing unique record identifiers. Default NULL. NULL, unique record identifiers generated.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_structure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","text":"data.frame 6 columns number rows equal df names \"FreeId\", \"Sex\", \"Age Value\", \"Age Type\", \"Code\", \"Death Date\".","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/cod_structure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Structure cause-of-death data into CoDEdit tool input data — cod_structure_input","text":"","code":"df <- data.frame( id = 1:3, sex = c(1, 1, 2), dob = c(\"1977-11-05\", \"1971-04-04\", \"2012-08-13\"), dod = c(\"2024-06-28\", \"2023-10-11\", \"2023-09-25\"), code = c(\"P219\", \"O230\", \"Q913\") ) cod_structure_input(df, sex = \"sex\", dob = \"dob\", dod = \"dod\", code = \"code\") #> # A tibble: 3 × 6 #> FreeId Sex `Age Value` `Age Type` Code `Death Date` #> #> 1 1 1 110 Y P219 2024 #> 2 2 1 110 Y O230 2023 #> 3 3 2 110 Y Q913 2023"},{"path":"https://oxford-ihtm.io/codeditr/reference/codeditr.html","id":null,"dir":"Reference","previous_headings":"","what":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool — codeditr","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool — codeditr","text":"World Health Organization's CoDEdit electronic tool intended help producers cause--death statistics strengthening capacity perform routine checks data. package ports original tool built using Microsoft Access R leverage utility function original tool usable application program interface can used building universal tools creating programmatic scientific workflows aimed routine, automated, large-scale monitoring cause--death data quality.","code":""},{"path":[]},{"path":"https://oxford-ihtm.io/codeditr/reference/codeditr.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool — codeditr","text":"Maintainer: Ernest Guevarra ernest@guevarra.io (ORCID) [copyright holder] Authors: Anita Makori [copyright holder] contributors: Sanjeev Pugazhendhi [thesis advisor, reviewer] Williams Udoh Ituen-Umanah [reviewer] Proochista Ariana [reviewer, copyright holder]","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/expand_icd10.html","id":null,"dir":"Reference","previous_headings":"","what":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","title":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","text":"Enumerate ICD 10 codes given code range","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/expand_icd10.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","text":"","code":"expand_icd10_code_range(code_range)"},{"path":"https://oxford-ihtm.io/codeditr/reference/expand_icd10.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","text":"code_range character value vector character values indicating range ICD 10 codes. See Details syntax code range/s.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/expand_icd10.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","text":"vector ICD 10 codes within range codes specified code_range.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/expand_icd10.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Enumerate ICD 10 codes given a code range — expand_icd10_code_range","text":"","code":"expand_icd10_code_range(\"A71.0-A71.9\") #> [1] \"A71.0\" \"A71.1\" \"A71.2\" \"A71.3\" \"A71.4\" \"A71.5\" \"A71.6\" \"A71.7\" \"A71.8\" #> [10] \"A71.9\" expand_icd10_code_range(\"F50.1,F50.3-F50.9\") #> [1] \"F50.1\" \"F50.3\" \"F50.4\" \"F50.5\" \"F50.6\" \"F50.7\" \"F50.8\" \"F50.9\""},{"path":"https://oxford-ihtm.io/codeditr/reference/get_age.html","id":null,"dir":"Reference","previous_headings":"","what":"Get various age values for all three age types — get_age_values","title":"Get various age values for all three age types — get_age_values","text":"Get various age values three age types","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/get_age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get various age values for all three age types — get_age_values","text":"","code":"get_age_values(age_value, age_type = c(\"D\", \"M\", \"Y\"))"},{"path":"https://oxford-ihtm.io/codeditr/reference/get_age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get various age values for all three age types — get_age_values","text":"age_value integer value age age_type age type specified age value. Can either \"D\" day, \"M\" month, \"Y\" year.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/get_age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get various age values for all three age types — get_age_values","text":"named list age values days, months, years.","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/get_age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get various age values for all three age types — get_age_values","text":"","code":"get_age_values(1, \"Y\") #> $days #> [1] 365.25 #> #> $months #> [1] 12 #> #> $years #> [1] 1 #>"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_cod_by_sex.html","id":null,"dir":"Reference","previous_headings":"","what":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","title":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","text":"Sex-specific causes death ICD 10","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_cod_by_sex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","text":"","code":"icd10_cod_by_sex"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_cod_by_sex.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","text":"data frame 3 columns 880 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_cod_by_sex.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","text":"https://icd..int/browse10/Content/statichtml/ICD10Volume2_en_2019.pdf","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_cod_by_sex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sex-specific causes of death for ICD 10 — icd10_cod_by_sex","text":"","code":"icd10_cod_by_sex #> # A tibble: 880 × 3 #> code title sex #> #> 1 B26.0 NA 1 #> 2 C60.0 NA 1 #> 3 C60.1 NA 1 #> 4 C60.2 NA 1 #> 5 C60.8 NA 1 #> 6 C60.9 NA 1 #> 7 C61 NA 1 #> 8 C62.0 NA 1 #> 9 C62.1 NA 1 #> 10 C62.9 NA 1 #> # ℹ 870 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","title":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","text":"Example death records dataset ICD10 cause--death coding","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","text":"","code":"icd10_example"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_example.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","text":"data frame 6 columns 3613 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_example.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","text":"https://www..int/standards/classifications/classification--diseases/services/codedit-tool","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Example death records dataset with ICD10 cause-of-death coding — icd10_example","text":"","code":"icd10_example #> # A tibble: 3,613 × 6 #> FreeId Sex `Age Value` `Age Type` Code `Death Date` #> #> 1 XX0001 2 0 D P219 2010 #> 2 XX0002 1 0 D P015 2010 #> 3 XX0003 2 0 D P015 2010 #> 4 XX0004 1 0 D P021 NA #> 5 XX0005 2 5 D O230 2010 #> 6 XX0006 1 0 D P011 2010 #> 7 XX0007 1 0 D Q913 2010 #> 8 XX0008 1 1 D P220 2010 #> 9 XX0009 2 1 D Q790 2010 #> 10 XX0010 1 0 D P027 2010 #> # ℹ 3,603 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_unlikely_cod.html","id":null,"dir":"Reference","previous_headings":"","what":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","title":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","text":"Unlikely causes death ICD 10","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_unlikely_cod.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","text":"","code":"icd10_unlikely_cod"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_unlikely_cod.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","text":"data frame 2 columns 424 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_unlikely_cod.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","text":"https://icd..int/browse10/Content/statichtml/ICD10Volume2_en_2019.pdf","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd10_unlikely_cod.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Unlikely causes of death for ICD 10 — icd10_unlikely_cod","text":"","code":"icd10_unlikely_cod #> # A tibble: 424 × 2 #> code title #> #> 1 A31.1 Cutaneous mycobacterial infection #> 2 A42.8 Other forms of cutaneous actinomycosis #> 3 A53.0 Latent syphilis,unspecified as early or late #> 4 A60.0 Herpesviral infection of genitalia and urogenital tract #> 5 A63.0 Anogenital (venereal) warts #> 6 A71.0-A71.9 Trachoma #> 7 A74.0 Chlamydial conjunctivitis #> 8 B00.2 Herpesviral gingivostomatitis #> 9 B00.5 Herpesviral ocular disease #> 10 B00.8 Herpesviral whitlow #> # ℹ 414 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_cod_by_sex.html","id":null,"dir":"Reference","previous_headings":"","what":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","title":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","text":"Sex-specific causes death ICD 11","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_cod_by_sex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","text":"","code":"icd11_cod_by_sex"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_cod_by_sex.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","text":"data frame 3 columns 547 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_cod_by_sex.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","text":"https://icdcdn..int/icd11referenceguide/en/html/index.html#list--categories-limited----likely--occur--female-persons","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_cod_by_sex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sex-specific causes of death for ICD 11 — icd11_cod_by_sex","text":"","code":"icd11_cod_by_sex #> # A tibble: 547 × 3 #> code title sex #> #> 1 2C80 Malignant neoplasms of testis 1 #> 2 2C80.2 Germ cell tumour of testis 1 #> 3 2C80.Y Other specified malignant neoplasms of testis 1 #> 4 2C80.Z Malignant neoplasms of testis, unspecified 1 #> 5 2C81 Malignant neoplasms of penis 1 #> 6 2C81.0 Squamous cell carcinoma of penis 1 #> 7 2C81.1 Melanoma of penis 1 #> 8 2C81.Y Other specified malignant neoplasm of penis 1 #> 9 2C81.Z Malignant neoplasms of penis, unspecified 1 #> 10 2C82 Malignant neoplasms of prostate 1 #> # ℹ 537 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","title":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","text":"Example death records dataset ICD11 cause--death coding","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","text":"","code":"icd11_example"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_example.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","text":"data frame 6 columns 244 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_example.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","text":"https://www..int/standards/classifications/classification--diseases/services/codedit-tool","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Example death records dataset with ICD11 cause-of-death coding — icd11_example","text":"","code":"icd11_example #> # A tibble: 244 × 6 #> freeid sex `Age value` `Age type` Code `Death date` #> #> 1 10001 2 6 Y \"1A40.0\" 2019 #> 2 10002 2 115 Y \"1B10.0\" 2019 #> 3 10003 2 115 Y \"1B10.1\" 2019 #> 4 10004 1 115 Y \"1B10.Z\" 2019 #> 5 10005 2 114 Y \"1B11.0\" 2019 #> 6 10006 2 115 Y \"1B1Z \" 2019 #> 7 10007 2 114 Y \"1B1Z \" 2019 #> 8 10008 1 109 Y \"1B53 \" 2019 #> 9 10009 1 109 Y \"1B7Y \" 2019 #> 10 10010 2 109 Y \"1C60.Z\" 2019 #> # ℹ 234 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_unlikely_cod.html","id":null,"dir":"Reference","previous_headings":"","what":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","title":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","text":"Unlikely causes death ICD 11","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_unlikely_cod.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","text":"","code":"icd11_unlikely_cod"},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_unlikely_cod.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","text":"data frame 2 columns 269 rows:","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_unlikely_cod.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","text":"https://icd..int/valuesets/viewer/582/en","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/icd11_unlikely_cod.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Unlikely causes of death for ICD 11 — icd11_unlikely_cod","text":"","code":"icd11_unlikely_cod #> # A tibble: 269 × 2 #> code title #> #> 1 1A94.0 Herpes simplex infection of genitalia or urogenital tract #> 2 1B21.2 Cutaneous non-tuberculous mycobacterial infection #> 3 1B72 Impetigo #> 4 1C10.Y Other specified forms of actinomycosis #> 5 1C20 Chlamydial conjunctivitis #> 6 1C23 Trachoma #> 7 1D84 Viral conjunctivitis #> 8 1E76 Molluscum contagiosum #> 9 1E80 Common warts #> 10 1F00.0 Herpes simplex infection of skin or mucous membrane #> # ℹ 259 more rows"},{"path":"https://oxford-ihtm.io/codeditr/reference/list_ill_defined_icd11.html","id":null,"dir":"Reference","previous_headings":"","what":"List ill-defined ICD 11 codes — list_ill_defined_icd11","title":"List ill-defined ICD 11 codes — list_ill_defined_icd11","text":"List ill-defined ICD 11 codes","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/list_ill_defined_icd11.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List ill-defined ICD 11 codes — list_ill_defined_icd11","text":"","code":"list_ill_defined_icd11()"},{"path":"https://oxford-ihtm.io/codeditr/reference/list_ill_defined_icd11.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List ill-defined ICD 11 codes — list_ill_defined_icd11","text":"character vector ICD 11 codes classified ill-defined cause death","code":""},{"path":"https://oxford-ihtm.io/codeditr/reference/list_ill_defined_icd11.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List ill-defined ICD 11 codes — list_ill_defined_icd11","text":"","code":"list_ill_defined_icd11() #> [1] \"BD10\" \"BD11\" \"BD11.0\" \"BD11.1\" \"BD11.2\" \"BD11.Z\" \"BD12\" #> [8] \"BD13\" \"BD14\" \"BD1Y\" \"BD1Z\" \"BA2Z\" \"BE2Y\" \"BE2Z\" #> [15] \"CB41.0\" \"CB41.2\" \"KB2D\" \"KB2E\" \"MA00\" \"MA01\" \"MA01.0\" #> [22] \"MA01.1\" \"MA01.Z\" \"MA0Y\" \"MA10\" \"MA10.0\" \"MA10.1\" \"MA10.2\" #> [29] \"MA11\" \"MA12\" \"MA12.0\" \"MA12.1\" \"MA12.2\" \"MA12.3\" \"MA12.4\" #> [36] \"MA12.Y\" \"MA13\" \"MA13.0\" \"MA13.00\" \"MA13.0Y\" \"MA13.1\" \"MA13.Y\" #> [43] \"MA14\" \"MA14.0\" \"MA14.1\" \"MA14.10\" \"MA14.11\" \"MA14.12\" \"MA14.13\" #> [50] \"MA14.14\" \"MA14.15\" \"MA14.16\" \"MA14.17\" \"MA14.18\" \"MA14.19\" \"MA14.1A\" #> [57] \"MA14.1B\" \"MA14.1C\" \"MA14.1D\" \"MA14.1E\" \"MA14.Y\" \"MA15.0\" \"MA15.1\" #> [64] \"MA15.Y\" \"MA16\" \"MA16.0\" \"MA16.00\" \"MA16.0Y\" \"MA16.0Z\" \"MA16.1\" #> [71] \"MA16.10\" \"MA16.11\" \"MA16.1Z\" \"MA16.Y\" \"MA16.Z\" \"MA17\" \"MA18\" #> [78] \"MA18.0\" \"MA18.00\" \"MA18.0Y\" \"MA18.0Z\" \"MA18.1\" \"MA18.2\" \"MA18.3\" #> [85] \"MA18.4\" \"MA18.Y\" \"MA18.Z\" \"MA19\" \"MA19.0\" \"MA19.1\" \"MA19.2\" #> [92] \"MA19.Y\" \"MA19.Z\" \"MA1A\" \"MA1A.0\" \"MA1A.1\" \"MA1Y\" \"MA3Y\" #> [99] \"MA50\" \"MA51\" \"MA6Y\" \"MA80\" \"MA80.0\" \"MA80.1\" \"MA80.2\" #> [106] \"MA80.20\" \"MA80.2Y\" \"MA80.2Z\" \"MA80.Y\" \"MA80.Z\" \"MA81\" \"MA82\" #> [113] \"MA82.0\" \"MA82.1\" \"MA82.10\" \"MA82.1Y\" \"MA82.1Z\" \"MA82.2\" \"MA82.Y\" #> [120] \"MA82.Z\" \"MA8Y\" \"MB0Y\" \"MB20\" \"MB20.0\" \"MB20.1\" \"MB20.2\" #> [127] \"MB20.Y\" \"MB21\" \"MB21.0\" \"MB21.1\" \"MB21.10\" \"MB21.11\" \"MB21.12\" #> [134] \"MB21.1Y\" \"MB21.1Z\" \"MB21.2\" \"MB21.3\" \"MB21.4\" \"MB21.5\" \"MB21.6\" #> [141] \"MB21.7\" \"MB21.8\" \"MB21.9\" \"MB21.A\" \"MB21.B\" \"MB21.Y\" \"MB21.Z\" #> [148] \"MB22\" \"MB22.0\" \"MB22.1\" \"MB22.2\" \"MB22.3\" \"MB22.4\" \"MB22.5\" #> [155] \"MB22.6\" \"MB22.7\" \"MB22.Y\" \"MB22.Z\" \"MB23\" \"MB23.0\" \"MB23.1\" #> [162] \"MB23.2\" \"MB23.3\" \"MB23.4\" \"MB23.5\" \"MB23.6\" \"MB23.7\" \"MB23.8\" #> [169] \"MB23.9\" \"MB23.A\" \"MB23.C\" \"MB23.D\" \"MB23.E\" \"MB23.F\" \"MB23.G\" #> [176] \"MB23.H\" \"MB23.J\" \"MB23.K\" \"MB23.L\" \"MB23.M\" \"MB23.N\" \"MB23.Q\" #> [183] \"MB23.R\" \"MB23.S\" \"MB23.Y\" \"MB23.Z\" \"MB24\" \"MB24.0\" \"MB24.1\" #> [190] \"MB24.2\" \"MB24.3\" \"MB24.4\" \"MB24.5\" \"MB24.6\" \"MB24.60\" \"MB24.61\" #> [197] \"MB24.62\" \"MB24.63\" \"MB24.64\" \"MB24.6Y\" \"MB24.6Z\" \"MB24.7\" \"MB24.8\" #> [204] \"MB24.9\" \"MB24.A\" \"MB24.B\" \"MB24.C\" \"MB24.D\" \"MB24.E\" \"MB24.F\" #> [211] \"MB24.G\" \"MB24.H\" \"MB24.Y\" \"MB24.Z\" \"MB25\" \"MB25.0\" \"MB25.00\" #> [218] \"MB25.01\" \"MB25.02\" \"MB25.03\" \"MB25.0Y\" \"MB25.0Z\" \"MB25.1\" \"MB25.2\" #> [225] \"MB25.3\" \"MB25.Y\" \"MB25.Z\" \"MB26\" \"MB26.0\" \"MB26.00\" \"MB26.01\" #> [232] \"MB26.02\" \"MB26.03\" \"MB26.04\" \"MB26.05\" \"MB26.06\" \"MB26.07\" \"MB26.08\" #> [239] \"MB26.09\" \"MB26.0A\" \"MB26.0B\" \"MB26.0C\" \"MB26.0Y\" \"MB26.0Z\" \"MB26.1\" #> [246] \"MB26.10\" \"MB26.11\" \"MB26.12\" \"MB26.1Y\" \"MB26.1Z\" \"MB26.2\" \"MB26.3\" #> [253] \"MB26.4\" \"MB26.5\" \"MB26.6\" \"MB26.7\" \"MB26.8\" \"MB26.9\" \"MB26.A\" #> [260] \"MB26.Y\" \"MB26.Z\" \"MB27\" \"MB27.0\" \"MB27.1\" \"MB27.2\" \"MB27.20\" #> [267] \"MB27.21\" \"MB27.22\" \"MB27.23\" \"MB27.24\" \"MB27.25\" \"MB27.26\" \"MB27.27\" #> [274] \"MB27.2Y\" \"MB27.2Z\" \"MB27.3\" \"MB27.4\" \"MB27.Y\" \"MB27.Z\" \"MB28\" #> [281] \"MB28.0\" \"MB28.1\" \"MB28.2\" \"MB28.3\" \"MB28.4\" \"MB28.5\" \"MB28.6\" #> [288] \"MB28.7\" \"MB28.8\" \"MB28.9\" \"MB28.A\" \"MB28.B\" \"MB28.C\" \"MB28.D\" #> [295] \"MB28.E\" \"MB28.F\" \"MB28.G\" \"MB28.H\" \"MB28.Y\" \"MB28.Z\" \"MB29\" #> [302] \"MB29.0\" \"MB29.1\" \"MB29.2\" \"MB29.3\" \"MB29.4\" \"MB29.Y\" \"MB29.Z\" #> [309] \"MB2A\" \"MB2A.0\" \"MB2A.1\" \"MB2A.Y\" \"MB2A.Z\" \"MB2Y\" \"MB40\" #> [316] \"MB40.0\" \"MB40.1\" \"MB40.2\" \"MB40.3\" \"MB40.4\" \"MB40.5\" \"MB40.6\" #> [323] \"MB40.7\" \"MB40.8\" \"MB40.9\" \"MB40.Y\" \"MB40.Z\" \"MB41\" \"MB41.0\" #> [330] \"MB41.1\" \"MB41.2\" \"MB41.3\" \"MB41.Y\" \"MB41.Z\" \"MB42\" \"MB43\" #> [337] \"MB44\" \"MB44.0\" \"MB44.1\" \"MB44.2\" \"MB44.3\" \"MB44.Y\" \"MB44.Z\" #> [344] \"MB45\" \"MB45.0\" \"MB45.1\" \"MB45.2\" \"MB45.3\" \"MB45.4\" \"MB45.Y\" #> [351] \"MB45.Z\" \"MB46\" \"MB46.0\" \"MB46.1\" \"MB46.2\" \"MB46.3\" \"MB46.4\" #> [358] \"MB46.5\" \"MB46.Y\" \"MB46.Z\" \"MB47\" \"MB47.0\" \"MB47.1\" \"MB47.2\" #> [365] \"MB47.3\" \"MB47.4\" \"MB47.5\" \"MB47.6\" \"MB47.7\" \"MB47.8\" \"MB47.9\" #> [372] \"MB47.A\" \"MB47.B\" \"MB47.C\" \"MB47.D\" \"MB47.Y\" \"MB47.Z\" \"MB48\" #> [379] \"MB48.0\" \"MB48.00\" \"MB48.0Y\" \"MB48.0Z\" \"MB48.1\" \"MB48.2\" \"MB48.3\" #> [386] \"MB48.4\" \"MB48.Y\" \"MB48.Z\" \"MB49\" \"MB4A\" \"MB4B\" \"MB4B.0\" #> [393] \"MB4B.1\" \"MB4B.2\" \"MB4B.3\" \"MB4B.4\" \"MB4B.5\" \"MB4B.Y\" \"MB4B.Z\" #> [400] \"MB4C\" \"MB4D\" \"MB50\" \"MB50.0\" \"MB50.1\" \"MB50.Z\" \"MB51\" #> [407] \"MB51.0\" \"MB51.1\" \"MB51.Z\" \"MB52\" \"MB53\" \"MB53.0\" \"MB53.1\" #> [414] \"MB53.2\" \"MB53.Z\" \"MB54\" \"MB54.0\" \"MB54.1\" \"MB54.Z\" \"MB55\" #> [421] \"MB55.0\" \"MB55.1\" \"MB55.Z\" \"MB56\" \"MB57\" \"MB57.0\" \"MB57.1\" #> [428] \"MB57.2\" \"MB57.3\" \"MB57.Y\" \"MB57.Z\" \"MB5Y\" \"MB5Z\" \"MB60\" #> [435] \"MB6Y\" \"MB70\" \"MB70.0\" \"MB70.1\" \"MB70.2\" \"MB70.3\" \"MB70.4\" #> [442] \"MB70.5\" \"MB70.6\" \"MB70.7\" \"MB70.8\" \"MB70.Y\" \"MB70.Z\" \"MB71\" #> [449] \"MB71.0\" \"MB71.Y\" \"MB71.Z\" \"MB72\" \"MB7Y\" \"MB9Y\" \"MC10\" #> [456] \"MC11\" \"MC12\" \"MC13\" \"MC14\" \"MC15\" \"MC16\" \"MC17\" #> [463] \"MC18\" \"MC19\" \"MC1A\" \"MC1B\" \"MC1C\" \"MC1D\" \"MC1Y\" #> [470] \"MC20\" \"MC20.0\" \"MC20.1\" \"MC20.2\" \"MC20.Y\" \"MC21\" \"MC21.0\" #> [477] \"MC21.1\" \"MC21.Y\" \"MC21.Z\" \"MC2Y\" \"MC40\" \"MC41\" \"MC4Y\" #> [484] \"MC6Y\" \"MC80\" \"MC80.0\" \"MC80.00\" \"MC80.01\" \"MC80.02\" \"MC80.03\" #> [491] \"MC80.0Y\" \"MC80.0Z\" \"MC80.1\" \"MC80.Y\" \"MC80.Z\" \"MC81\" \"MC81.0\" #> [498] \"MC81.1\" \"MC81.2\" \"MC81.3\" \"MC81.4\" \"MC81.Y\" \"MC81.Z\" \"MC82\" #> [505] \"MC82.0\" \"MC82.1\" \"MC82.2\" \"MC82.3\" \"MC82.4\" \"MC82.Z\" \"MC83\" #> [512] \"MC83.0\" \"MC83.1\" \"MC83.Z\" \"MC84\" \"MC85\" \"MC86\" \"MC87\" #> [519] \"MC88\" \"MC8Y\" \"MC90\" \"MC91\" \"MC9Y\" \"MD10\" \"MD11\" #> [526] \"MD11.0\" \"MD11.1\" \"MD11.2\" \"MD11.3\" \"MD11.4\" \"MD11.5\" \"MD11.6\" #> [533] \"MD11.7\" \"MD11.8\" \"MD11.80\" \"MD11.8Y\" \"MD11.8Z\" \"MD11.9\" \"MD11.A\" #> [540] \"MD11.B\" \"MD11.C\" \"MD11.D\" \"MD11.Y\" \"MD11.Z\" \"MD12\" \"MD20\" #> [547] \"MD21\" \"MD22\" \"MD23\" \"MD24\" \"MD2Z\" \"MD30\" \"MD30.0\" #> [554] \"MD30.1\" \"MD30.Z\" \"MD31\" \"MD32\" \"MD33\" \"MD34\" 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