From d6ee6cf1d920f6722ae85dfb04460996dedde45f Mon Sep 17 00:00:00 2001 From: andrewallenbruce Date: Tue, 9 Apr 2024 05:06:25 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20andrewal?= =?UTF-8?q?lenbruce/pathologie@4a11092fe809fda5a4a6f8aa72e714a356731975=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/pathologie.html | 640 +++++++++++++++++++++++++++++++++--- pkgdown.yml | 2 +- reference/icd10cm.html | 5 +- reference/index.html | 5 - reference/is_valid_icd.html | 8 +- search.json | 2 +- sitemap.xml | 3 - 7 files changed, 594 insertions(+), 71 deletions(-) diff --git a/articles/pathologie.html b/articles/pathologie.html index 46e90ac..8daf856 100644 --- a/articles/pathologie.html +++ b/articles/pathologie.html @@ -116,26 +116,26 @@

ICD-10-CM= px(3)) ), locations = cells_row_groups()) -
+
@@ -708,6 +708,540 @@

The field Parameter#> 10 Z00.6 Encounter for examination for normal comparison and control in clin… #> # ℹ 40 more rows

+
+
+

ICD-10-CM Code Edits +

+
+ex_data() |>
+  dplyr::mutate(patient_age = years_floor(date_of_birth,
+                                          date_of_service)) |>
+  dplyr::left_join(search_edits()) |>
+  dplyr::filter(icd_conflict_group == "Age") |>
+  dplyr::mutate(conflict = apply_age_edits(rule = icd_conflict_rule,
+                                           age = patient_age)) |>
+  dplyr::filter(!is.na(conflict)) |> 
+  dplyr::select(-icd_conflict_group, -conflict) |> 
+  gt(groupname_col = "icd_conflict_rule",
+     row_group_as_column = TRUE) |> 
+  gt_style()
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Adult (Ages 15-124)2015-11-272023-01-08Z00.007Encntr for general adult medical exam w/o abnormal findings
2014-01-252023-06-27Z00.009Encntr for general adult medical exam w/o abnormal findings
2012-05-112022-09-21Z00.0010Encntr for general adult medical exam w/o abnormal findings
Pediatric (Ages 0-17)2005-10-212024-01-18F64.218Gender identity disorder of childhood
2005-10-212023-12-08F64.218Gender identity disorder of childhood
2005-10-212023-12-01F64.218Gender identity disorder of childhood
2005-10-212023-11-16F64.218Gender identity disorder of childhood
2005-10-212024-02-08F64.218Gender identity disorder of childhood
2005-10-212023-11-09F64.218Gender identity disorder of childhood
2005-10-212023-11-02F64.218Gender identity disorder of childhood
+
diff --git a/pkgdown.yml b/pkgdown.yml index 3f82610..946690d 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: pathologie: pathologie.html -last_built: 2024-04-05T19:54Z +last_built: 2024-04-09T05:05Z urls: reference: https://andrewallenbruce.github.io/pathologie/reference article: https://andrewallenbruce.github.io/pathologie/articles diff --git a/reference/icd10cm.html b/reference/icd10cm.html index 1cf6e0d..e778125 100644 --- a/reference/icd10cm.html +++ b/reference/icd10cm.html @@ -84,9 +84,8 @@

Value

Examples

- 
icd10cm(
-   c("F50.8", "G40.311", "Q96.8", "Z62.890", "R45.4", "E06.3", "H00.019", "D50.1", "C4A.70")
-   )
+    
icd10cm( c("F50.8", "G40.311", "Q96.8", "Z62.890", "R45.4", "E06.3",
+"H00.019", "D50.1", "C4A.70") )
 #> # A tibble: 9 × 12
 #>   icd_ch_no icd_ch_abb icd_ch_name icd_ch_range icd_sec_name icd_sec_range order
 #>       <int> <chr>      <chr>       <chr>        <chr>        <chr>         <int>
diff --git a/reference/index.html b/reference/index.html
index 6cfdba6..c328bd2 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -99,11 +99,6 @@ 
All functionsis_valid_icd10cm() 
-        
-        
Check if an ICD-10-CM code is in a valid format

-      

-          
           search_edits() 
         

         
ICD-10-CM Code Edits

diff --git a/reference/is_valid_icd.html b/reference/is_valid_icd.html
index ee00455..6211a02 100644
--- a/reference/is_valid_icd.html
+++ b/reference/is_valid_icd.html
@@ -60,7 +60,7 @@ 
Usage
     

     
Arguments

     
x

-
<chr> string of length(1)

+
<chr> string of length(x) == 1

 
 
 
arg

@@ -68,16 +68,14 @@ 
Arguments
     
Value

     
 
-
<lgl>

-

-
TRUE if valid, FALSE otherwise

+
<lgl> vector; TRUE if valid, FALSE otherwise

     

 
     

diff --git a/search.json b/search.json
index 9847159..fadc920 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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 andrew.bruce@northstarrevenueintegrity.com. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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":"https://andrewallenbruce.github.io/pathologie/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 pathologie authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/articles/pathologie.html","id":"icd-10-cm","dir":"Articles","previous_headings":"","what":"ICD-10-CM","title":"pathologie","text":"T76.02XA Child neglect abandonment, suspected, initial encounter Injury, poisoning certain consequences external causes Range: [S00 - T88] Adult child abuse, neglect maltreatment, suspected Range: [T76 - T76.A2XS] INJ Age Pediatric (Ages 0-17)","code":"icd10cm(icd = \"T76.02XA\") |>    mutate(Chapter = paste0(\"* \", icd_ch_name, \" \\n \", \"* Range: [\", icd_ch_range, \"]\"),          Section = paste0(\"* \", icd_sec_name, \" \\n \", \"* Range: [\", icd_sec_range, \"]\")          ) |>   select(\"ICD-10-Code\"   = icd_code,           Description     = icd_description,           Chapter,          Section,          Abbreviation    = icd_ch_abb,          \"Conflict Group\" = icd_conflict_group,          \"Conflict Rule\"  = icd_conflict_rule) |>    display_long() |>   gt(groupname_col       = \"name\",       row_group_as_column = TRUE) |>   fmt_markdown() |>    gt_style(tablign       = \"right\",             tabsize       = 16,             tabwt         = \"bold\") |>    tab_style(       style              = cell_text(       font               = google_font(name = \"Fira Code\")),       locations          = cells_body(         columns          = contains(\"value\"))) |>   tab_style(     style                = list(       cell_fill(color    = \"powderblue\"),       cell_text(weight   = \"bold\"),       cell_borders(       sides              = c(\"all\"),       color              = \"powderblue\",       weight             = px(3))       ),     locations            = cells_row_groups())"},{"path":"https://andrewallenbruce.github.io/pathologie/articles/pathologie.html","id":"the-nlms-icd-10-cm-api","dir":"Articles","previous_headings":"","what":"The NLM’s ICD-10-CM API","title":"pathologie","text":"National Library Medicine’s ICD-10-CM API RESTful API provides access current ICD-10-CM code set. API allows users search codes code keyword(term), returns code description. Searching case insensitive greedy following examples: Returns seven ICD-10 codes beginning A15: Returns 344 ICD-10 codes associated tuberculosis: Returns two ICD-10 codes associated pleurisy:","code":"icd10api(icd_code = \"A15\") #> # A tibble: 7 × 2 #>   icd_code icd_description                              #>                                               #> 1 A15.0    Tuberculosis of lung                         #> 2 A15.4    Tuberculosis of intrathoracic lymph nodes    #> 3 A15.5    Tuberculosis of larynx, trachea and bronchus #> 4 A15.6    Tuberculous pleurisy                         #> 5 A15.7    Primary respiratory tuberculosis             #> 6 A15.8    Other respiratory tuberculosis               #> 7 A15.9    Respiratory tuberculosis unspecified icd10api(term = \"tuber\", field = \"both\") #> # A tibble: 344 × 2 #>    icd_code icd_description                              #>                                                #>  1 A15.0    Tuberculosis of lung                         #>  2 A15.4    Tuberculosis of intrathoracic lymph nodes    #>  3 A15.5    Tuberculosis of larynx, trachea and bronchus #>  4 A15.6    Tuberculous pleurisy                         #>  5 A15.7    Primary respiratory tuberculosis             #>  6 A15.8    Other respiratory tuberculosis               #>  7 A15.9    Respiratory tuberculosis unspecified         #>  8 A17.0    Tuberculous meningitis                       #>  9 A17.1    Meningeal tuberculoma                        #> 10 A17.81   Tuberculoma of brain and spinal cord         #> # ℹ 334 more rows icd10api(term = \"pleurisy\", field = \"both\") #> # A tibble: 2 × 2 #>   icd_code icd_description      #>                       #> 1 R09.1    Pleurisy             #> 2 A15.6    Tuberculous pleurisy"},{"path":"https://andrewallenbruce.github.io/pathologie/articles/pathologie.html","id":"the-field-parameter","dir":"Articles","previous_headings":"The NLM’s ICD-10-CM API","what":"The field Parameter","title":"pathologie","text":"field parameter allows users specify whether want search ICD-10-CM codes codes terms associated description. defaults \"code\" ’s behavior warrants explanation. ’re searching codes beginning certain letter, must set field parameter \"code\" return codes terms contain letter. instance, following call returns ICD-10 codes descriptions containing letter “Z”: call returns ICD-10 codes containing “Z”:","code":"icd10api(icd_code = \"z\", field = \"both\", limit = 50) #> # A tibble: 50 × 2 #>    icd_code icd_description                                                      #>                                                                        #>  1 A28.8    Other specified zoonotic bacterial diseases, not elsewhere classifi… #>  2 A28.9    Zoonotic bacterial disease, unspecified                              #>  3 A92.5    Zika virus disease                                                   #>  4 B02.0    Zoster encephalitis                                                  #>  5 B02.1    Zoster meningitis                                                    #>  6 B02.30   Zoster ocular disease, unspecified                                   #>  7 B02.31   Zoster conjunctivitis                                                #>  8 B02.32   Zoster iridocyclitis                                                 #>  9 B02.33   Zoster keratitis                                                     #> 10 B02.34   Zoster scleritis                                                     #> # ℹ 40 more rows icd10api(icd_code = \"z\", field = \"code\", limit = 50) #> # A tibble: 50 × 2 #>    icd_code icd_description                                                      #>                                                                        #>  1 Z00.00   Encounter for general adult medical examination without abnormal fi… #>  2 Z00.01   Encounter for general adult medical examination with abnormal findi… #>  3 Z00.110  Health examination for newborn under 8 days old                      #>  4 Z00.111  Health examination for newborn 8 to 28 days old                      #>  5 Z00.121  Encounter for routine child health examination with abnormal findin… #>  6 Z00.129  Encounter for routine child health examination without abnormal fin… #>  7 Z00.2    Encounter for examination for period of rapid growth in childhood    #>  8 Z00.3    Encounter for examination for adolescent development state           #>  9 Z00.5    Encounter for examination of potential donor of organ and tissue     #> 10 Z00.6    Encounter for examination for normal comparison and control in clin… #> # ℹ 40 more rows"},{"path":"https://andrewallenbruce.github.io/pathologie/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andrew Bruce. Author, maintainer, copyright holder.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Bruce (2024). pathologie: Tidy ICD-10-CM Tools. R package version 0.0.1,  https://github.com/andrewallenbruce/pathologie, https://andrewallenbruce.github.io/pathologie/.","code":"@Manual{,   title = {pathologie: Tidy ICD-10-CM Tools},   author = {Andrew Bruce},   year = {2024},   note = {R package version 0.0.1,  https://github.com/andrewallenbruce/pathologie},   url = {https://andrewallenbruce.github.io/pathologie/}, }"},{"path":"https://andrewallenbruce.github.io/pathologie/index.html","id":"pathologie","dir":"","previous_headings":"","what":"Tidy ICD-10-CM Tools","title":"Tidy ICD-10-CM Tools","text":"Tidy ICD-10-CM Interface","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/index.html","id":"package-installation","dir":"","previous_headings":"","what":"📦 Installation","title":"Tidy ICD-10-CM Tools","text":"can install pathologie GitHub :","code":"# install.packages(\"pak\") pak::pak(\"andrewallenbruce/pathologie\")"},{"path":"https://andrewallenbruce.github.io/pathologie/index.html","id":"beginner-usage","dir":"","previous_headings":"","what":"🔰 Usage","title":"Tidy ICD-10-CM Tools","text":"","code":"library(pathologie) library(dplyr) icd10cm(icd = c(\"I10\", \"I15.0\")) |>    glimpse() #> Rows: 2 #> Columns: 10 #> $ icd_ch_no        9, 9 #> $ icd_ch_abb       \"CARDIO\", \"CARDIO\" #> $ icd_ch_name      \"Diseases of the circulatory system\", \"Diseases of the… #> $ icd_ch_range     \"I00 - I99\", \"I00 - I99\" #> $ icd_sec_name     \"Other rheumatic heart diseases\", \"Secondary hypertens… #> $ icd_sec_range    \"I09 - I10\", \"I15 - I15.9\" #> $ order            11397, 11411 #> $ valid            1, 1 #> $ icd_code         \"I10\", \"I15.0\" #> $ icd_description  \"Essential (primary) hypertension\", \"Renovascular hype… icd10api(icd_code = \"I1\") #> # A tibble: 18 × 2 #>    icd_code icd_description                                                      #>                                                                        #>  1 I10      Essential (primary) hypertension                                     #>  2 I11.0    Hypertensive heart disease with heart failure                        #>  3 I11.9    Hypertensive heart disease without heart failure                     #>  4 I12.0    Hypertensive chronic kidney disease with stage 5 chronic kidney dis… #>  5 I12.9    Hypertensive chronic kidney disease with stage 1 through stage 4 ch… #>  6 I13.0    Hypertensive heart and chronic kidney disease with heart failure an… #>  7 I13.10   Hypertensive heart and chronic kidney disease without heart failure… #>  8 I13.11   Hypertensive heart and chronic kidney disease without heart failure… #>  9 I13.2    Hypertensive heart and chronic kidney disease with heart failure an… #> 10 I15.0    Renovascular hypertension                                            #> 11 I15.1    Hypertension secondary to other renal disorders                      #> 12 I15.2    Hypertension secondary to endocrine disorders                        #> 13 I15.8    Other secondary hypertension                                         #> 14 I15.9    Secondary hypertension, unspecified                                  #> 15 I16.0    Hypertensive urgency                                                 #> 16 I16.1    Hypertensive emergency                                               #> 17 I16.9    Hypertensive crisis, unspecified                                     #> 18 I1A.0    Resistant hypertension"},{"path":"https://andrewallenbruce.github.io/pathologie/index.html","id":"balance_scale-code-of-conduct","dir":"","previous_headings":"","what":"⚖️ Code of Conduct","title":"Tidy ICD-10-CM Tools","text":"Please note pathologie project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/index.html","id":"classical_building-governance","dir":"","previous_headings":"","what":"🏛️ Governance","title":"Tidy ICD-10-CM Tools","text":"project primarily maintained Andrew Bruce. authors may occasionally assist duties.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/add_dot.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a dot to an ICD-10 code — add_dot","title":"Add a dot to an ICD-10 code — add_dot","text":"add_dot() adds dot ICD-10 code appropriate position one exist","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/add_dot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a dot to an ICD-10 code — add_dot","text":"","code":"add_dot(x)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/add_dot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a dot to an ICD-10 code — add_dot","text":"x valid ICD-10 code without dot","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/add_dot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a dot to an ICD-10 code — add_dot","text":"valid ICD-10 code dot included","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/add_dot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a dot to an ICD-10 code — add_dot","text":"","code":"add_dot(\"F320\") #> [1] \"F32.0\"  add_dot(\"F32\")  # no dot added if code is only 3-digits #> [1] \"F32\""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_A.html","id":null,"dir":"Reference","previous_headings":"","what":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","title":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","text":"Appendix contains list MS-DRG specification MDC whether MS-DRG medical surgical. MS-DRGs contain patients multiple MDCs (e.g., 014 Allogeneic Bone Marrow Transplant) MDC specified. letter M used designate medical MS-DRG letter P used designate surgical MS-DRG.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_A.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","text":"","code":"appendix_A(drg = NULL, mdc = NULL, type = NULL, ...)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_A.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","text":"drg  vector 3-digit Diagnosis-Related Group codes mdc  vector 2-digit Major Diagnostic Category codes type  DRG type: M (Medical) P (Surgical) ... Empty dots","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_A.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_A.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","text":"","code":"appendix_A(drg = \"011\") #> # A tibble: 1 × 4 #>   drg   mdc   drg_abb drg_description                                            #>                                                              #> 1 011   NA    P       TRACHEOSTOMY FOR FACE, MOUTH AND NECK DIAGNOSES OR LARYNG…  appendix_A(mdc = \"24\") #> # A tibble: 8 × 4 #>   drg   mdc   drg_abb drg_description                                            #>                                                              #> 1 955   24    P       CRANIOTOMY FOR MULTIPLE SIGNIFICANT TRAUMA                 #> 2 956   24    P       LIMB REATTACHMENT, HIP AND FEMUR PROCEDURES FOR MULTIPLE … #> 3 957   24    P       OTHER O.R. PROCEDURES FOR MULTIPLE SIGNIFICANT TRAUMA WIT… #> 4 958   24    P       OTHER O.R. PROCEDURES FOR MULTIPLE SIGNIFICANT TRAUMA WIT… #> 5 959   24    P       OTHER O.R. PROCEDURES FOR MULTIPLE SIGNIFICANT TRAUMA WIT… #> 6 963   24    M       OTHER MULTIPLE SIGNIFICANT TRAUMA WITH MCC                 #> 7 964   24    M       OTHER MULTIPLE SIGNIFICANT TRAUMA WITH CC                  #> 8 965   24    M       OTHER MULTIPLE SIGNIFICANT TRAUMA WITHOUT CC/MCC"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_B.html","id":null,"dir":"Reference","previous_headings":"","what":"Appendix B: Diagnosis Code/MDC/MS-DRG Index — appendix_B","title":"Appendix B: Diagnosis Code/MDC/MS-DRG Index — appendix_B","text":"Diagnosis Code/MDC/MS-DRG Index lists diagnosis code, well MDC, MS-DRGs diagnosis used define logic DRG either principal secondary diagnosis.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_B.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Appendix B: Diagnosis Code/MDC/MS-DRG Index — appendix_B","text":"","code":"appendix_B()"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_B.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Appendix B: Diagnosis Code/MDC/MS-DRG Index — appendix_B","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_B.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Appendix B: Diagnosis Code/MDC/MS-DRG Index — appendix_B","text":"","code":"head(appendix_B()) #> # A tibble: 6 × 4 #>   icd_code mdc   drg_range drg   #>              #> 1 A00.0    06    371-373   371   #> 2 A00.0    06    371-373   372   #> 3 A00.0    06    371-373   373   #> 4 A00.1    06    371-373   371   #> 5 A00.1    06    371-373   372   #> 6 A00.1    06    371-373   373"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_C.html","id":null,"dir":"Reference","previous_headings":"","what":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","title":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","text":"Appendix C list codes defined either complication comorbidity (CC) major complication comorbidity (MCC) used secondary diagnosis.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_C.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","text":"","code":"appendix_C()"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_C.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_C.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","text":"Part 1 lists codes. code indicated CC MCC. link given collection diagnosis codes , used principal diagnosis, cause CC MCC considered non-CC. Part 2 lists codes assigned Major CC patients discharged alive. Otherwise assigned non-CC. Part 3 lists diagnosis codes designated complication comorbidity (CC) major complication comorbidity (MCC) included definition logic listed DRGs. reported secondary diagnosis grouped one listed DRGs diagnosis excluded acting CC/MCC severity DRG assignment.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_C.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","text":"","code":"head(appendix_C()$cc_mcc) #> # A tibble: 6 × 3 #>   icd_code cc_mcc pdx_group #>              #> 1 A00.0    CC     0002      #> 2 A00.1    CC     0002      #> 3 A00.9    CC     0002      #> 4 A01.00   CC     0003      #> 5 A01.01   CC     0003      #> 6 A01.02   CC     0003       head(appendix_C()$pdx_groups) #> # A tibble: 6 × 2 #>   pdx_icd pdx_group #>           #> 1 A00.0   0002      #> 2 A00.1   0002      #> 3 A00.9   0002      #> 4 A01.00  0003      #> 5 A01.01  0003      #> 6 A01.02  0003"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/apply_age_edits.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply Age Conflict Edits — apply_age_edits","title":"Apply Age Conflict Edits — apply_age_edits","text":"Apply Age Conflict Edits","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/apply_age_edits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply Age Conflict Edits — apply_age_edits","text":"","code":"apply_age_edits(rule, age)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/apply_age_edits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply Age Conflict Edits — apply_age_edits","text":"rule  ICD-10-CM Conflict Rule age  age years","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/apply_age_edits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply Age Conflict Edits — apply_age_edits","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/apply_age_edits.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply Age Conflict Edits — apply_age_edits","text":"","code":"apply_age_edits(    c(\"Pediatric (Ages 0-17)\",      \"Maternity (Ages 9-64)\"),    c(18, 7)) #> [1] \"Age Conflict\" \"Age Conflict\""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/case_chapter_icd10.html","id":null,"dir":"Reference","previous_headings":"","what":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","title":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","text":"Add ICD-10-CM Chapter Labels","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/case_chapter_icd10.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","text":"","code":"case_chapter_icd10(df, col)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/case_chapter_icd10.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","text":"df data frame col  unquoted column name ICD-10-CM codes match","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/case_chapter_icd10.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","text":"tibble chapter column","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/case_chapter_icd10.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","text":"","code":"dplyr::tibble(code = c(\"F50.8\", \"G40.311\", \"Q96.8\", \"Z62.890\", \"R45.4\", \"E06.3\", \"H00.019\", \"D50.1\", \"C4A.70\", \"Z20.818\")) |> case_chapter_icd10(code) #> # A tibble: 10 × 2 #>    code    chapter                                                               #>                                                                        #>  1 F50.8   Mental, behavioral and neurodevelopmental disorders                   #>  2 G40.311 Diseases of the nervous system                                        #>  3 Q96.8   Congenital malformations, deformations and chromosomal abnormalities  #>  4 Z62.890 Factors influencing health status and contact with health services    #>  5 R45.4   Symptoms, signs and abnormal clinical and laboratory findings, not e… #>  6 E06.3   Endocrine, nutritional and metabolic diseases                         #>  7 H00.019 Diseases of the eye and adnexa                                        #>  8 D50.1   Diseases of the blood and blood-forming organs and certain disorders… #>  9 C4A.70  Neoplasms                                                             #> 10 Z20.818 Factors influencing health status and contact with health services"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/display_long.html","id":null,"dir":"Reference","previous_headings":"","what":"Pivot data frame to long format for easy printing — display_long","title":"Pivot data frame to long format for easy printing — display_long","text":"Pivot data frame long format easy printing","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/display_long.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pivot data frame to long format for easy printing — display_long","text":"","code":"display_long(df, cols = dplyr::everything())"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/display_long.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pivot data frame to long format for easy printing — display_long","text":"df  cols  vector bare column name pivot, default dplyr::everything()","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/display_long.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pivot data frame to long format for easy printing — display_long","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/ex_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Example data set — ex_data","title":"Example data set — ex_data","text":"Example data set","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/ex_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example data set — ex_data","text":"","code":"ex_data()"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/ex_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Example data set — ex_data","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_marks.html","id":null,"dir":"Reference","previous_headings":"","what":"gt Marks — gt_marks","title":"gt Marks — gt_marks","text":"gt Marks","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_marks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gt Marks — gt_marks","text":"","code":"gt_marks(tbl, cols)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_marks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gt Marks — gt_marks","text":"tbl  object cols  vector bare column names, e.g. c(mdc, drg)","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_marks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gt Marks — gt_marks","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_style.html","id":null,"dir":"Reference","previous_headings":"","what":"gt Theme — gt_style","title":"gt Theme — gt_style","text":"gt Theme","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_style.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gt Theme — gt_style","text":"","code":"gt_style(tbl, lbl = TRUE, tablign = \"center\", tabsize = 16, tabwt = \"normal\")"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_style.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gt Theme — gt_style","text":"tbl  object lbl  hide column labels; default TRUE tablign  table stub alignment; default \"center\" tabsize  table stub font size pixels; default 16 tabwt  table stub font weight; default \"normal\"","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_style.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gt Theme — gt_style","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":null,"dir":"Reference","previous_headings":"","what":"National Library of Medicine's ICD-10-CM API — icd10api","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"icd10api() allows search National Library Medicine's ICD-10-CM API code associated term.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"","code":"icd10api(   icd_code = NULL,   term = NULL,   field = c(\"code\", \"both\"),   limit = 500L,   ... )"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"National Library Medicine/National Institute Health","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"icd_code  ICD-10-CM code containing 3 7 characters, excluding dot term  Associated term describing ICD-10-CM code field  code ; default code limit  API limit, defaults 500. Note current limit total number results can retrieved 7,500. ... Empty dots","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"ICD-10-CM (International Classification Diseases, 10th Revision, Clinical Modification) medical coding system classifying diagnoses reasons visits U.S. health care settings.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"links","dir":"Reference","previous_headings":"","what":"Links","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"NIH NLM Clinical Table Service ICD-10-CM API Learn ICD-10-CM.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"Current Version: ICD-10-CM 2024","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"","code":"# Returns the seven codes beginning with `A15` icd10api(icd_code = \"A15\") #> # A tibble: 7 × 2 #>   icd_code icd_description                              #>                                               #> 1 A15.0    Tuberculosis of lung                         #> 2 A15.4    Tuberculosis of intrathoracic lymph nodes    #> 3 A15.5    Tuberculosis of larynx, trachea and bronchus #> 4 A15.6    Tuberculous pleurisy                         #> 5 A15.7    Primary respiratory tuberculosis             #> 6 A15.8    Other respiratory tuberculosis               #> 7 A15.9    Respiratory tuberculosis unspecified          # Returns the first five codes # associated with tuberculosis icd10api(term = \"tuber\", field = \"both\", limit = 5) #> # A tibble: 5 × 2 #>   icd_code icd_description                              #>                                               #> 1 A15.0    Tuberculosis of lung                         #> 2 A15.4    Tuberculosis of intrathoracic lymph nodes    #> 3 A15.5    Tuberculosis of larynx, trachea and bronchus #> 4 A15.6    Tuberculous pleurisy                         #> 5 A15.7    Primary respiratory tuberculosis              # Returns the two codes # associated with pleurisy icd10api(term = \"pleurisy\", field = \"both\") #> # A tibble: 2 × 2 #>   icd_code icd_description      #>                       #> 1 R09.1    Pleurisy             #> 2 A15.6    Tuberculous pleurisy  # If you're searching for codes beginning # with a certain letter, you must set the # `field` param to `\"code\"` or it will # search for terms as well:  # Returns terms containing the letter \"Z\" icd10api(icd_code = \"z\", limit = 5) #> # A tibble: 5 × 2 #>   icd_code icd_description                                                       #>                                                                        #> 1 Z00.00   Encounter for general adult medical examination without abnormal fin… #> 2 Z00.01   Encounter for general adult medical examination with abnormal findin… #> 3 Z00.110  Health examination for newborn under 8 days old                       #> 4 Z00.111  Health examination for newborn 8 to 28 days old                       #> 5 Z00.121  Encounter for routine child health examination with abnormal findings  # Returns codes beginning with \"Z\" icd10api(icd_code = \"z\", field = \"code\", limit = 5) #> # A tibble: 5 × 2 #>   icd_code icd_description                                                       #>                                                                        #> 1 Z00.00   Encounter for general adult medical examination without abnormal fin… #> 2 Z00.01   Encounter for general adult medical examination with abnormal findin… #> 3 Z00.110  Health examination for newborn under 8 days old                       #> 4 Z00.111  Health examination for newborn 8 to 28 days old                       #> 5 Z00.121  Encounter for routine child health examination with abnormal findings  # Will error if results exceed API limit try(icd10api(icd_code = \"I\", field = \"both\")) #> Error in icd10api(icd_code = \"I\", field = \"both\") :  #>   Your search returned 36770 results. #> ✖ The NLM ICD-10-CM API limit is 7,500."},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10cm.html","id":null,"dir":"Reference","previous_headings":"","what":"ICD-10-CM Codes — icd10cm","title":"ICD-10-CM Codes — icd10cm","text":"ICD-10-CM (International Classification Diseases, 10th Revision, Clinical Modification) medical coding system classifying diagnoses reasons visits U.S. health care settings.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10cm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ICD-10-CM Codes — icd10cm","text":"","code":"icd10cm(icd = NULL, ...)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10cm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ICD-10-CM Codes — icd10cm","text":"icd  vector ICD-10-CM codes ... Empty dots","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10cm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ICD-10-CM Codes — icd10cm","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10cm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ICD-10-CM Codes — icd10cm","text":"","code":"icd10cm(    c(\"F50.8\", \"G40.311\", \"Q96.8\", \"Z62.890\", \"R45.4\", \"E06.3\", \"H00.019\", \"D50.1\", \"C4A.70\")    ) #> # A tibble: 9 × 12 #>   icd_ch_no icd_ch_abb icd_ch_name icd_ch_range icd_sec_name icd_sec_range order #>                                               #> 1         2 ONC        Neoplasms   C00 - D49    Merkel cell… C4A - C4A.9    1599 #> 2         3 BLOOD      Diseases o… D50 - D89    Iron defici… D50 - D50.9    3421 #> 3         4 METAB      Endocrine,… E00 - E89    Thyroiditis  E06 - E06.9    3868 #> 4         5 PSYCH      Mental, be… F01 - F99    Eating diso… F50 - F50.9    5946 #> 5         6 NEURO      Diseases o… G00 - G99    Epilepsy an… G40 - G40.919  6329 #> 6         7 EYE        Diseases o… H00 - H59    Hordeolum a… H00 - H00.19   7045 #> 7        17 CONG       Congenital… Q00 - Q99    Turner's sy… Q96 - Q96.9   30028 #> 8        18 SYMP       Symptoms, … R00 - R99    Symptoms an… R45 - R45.89  30559 #> 9        21 STAT       Factors in… Z00 - Z99    Problems re… Z62 - Z62.9   96381 #> # ℹ 5 more variables: valid , icd_code , icd_description , #> #   icd_conflict_group , icd_conflict_rule "},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if string is valid ICD-10-CM code — is_valid_icd","title":"Check if string is valid ICD-10-CM code — is_valid_icd","text":"Check string valid ICD-10-CM code","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if string is valid ICD-10-CM code — is_valid_icd","text":"","code":"is_valid_icd(x, arg = rlang::caller_arg(x), call = rlang::caller_env())"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if string is valid ICD-10-CM code — is_valid_icd","text":"x  string length(1) arg  function argument name current function call  environment function called ","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if string is valid ICD-10-CM code — is_valid_icd","text":"  TRUE valid, FALSE otherwise","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if string is valid ICD-10-CM code — is_valid_icd","text":"","code":"purrr::map_vec( c(\"H00.019\", \"D50.1\", \"C4A.70\", \"Z20.818\", \"11646\", \"E8015\"), is_valid_icd) #> [1] \"H00.019\" \"D50.1\"   \"C4A.70\"  \"Z20.818\" \"11646\"   \"E8015\""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd10cm.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if an ICD-10-CM code is in a valid format — is_valid_icd10cm","title":"Check if an ICD-10-CM code is in a valid format — is_valid_icd10cm","text":"is_valid_icd10cm checks see ICD-10-CM code valid 3 8 characters, starts letter number.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd10cm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if an ICD-10-CM code is in a valid format — is_valid_icd10cm","text":"","code":"is_valid_icd10cm(x)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd10cm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if an ICD-10-CM code is in a valid format — is_valid_icd10cm","text":"x string","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd10cm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if an ICD-10-CM code is in a valid format — is_valid_icd10cm","text":"Boolean","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd10cm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if an ICD-10-CM code is in a valid format — is_valid_icd10cm","text":"","code":"is_valid_icd10cm(\"F320\") # valid #> [1] TRUE is_valid_icd10cm(\"F32\")  # valid #> [1] TRUE is_valid_icd10cm(\"296\")  # invalid #> [1] FALSE"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/mount_board.html","id":null,"dir":"Reference","previous_headings":"","what":"Mount pins board — mount_board","title":"Mount pins board — mount_board","text":"Mount pins board","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/mount_board.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mount pins board — mount_board","text":"","code":"mount_board(source = c(\"local\", \"remote\"))"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/mount_board.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mount pins board — mount_board","text":"`` string; whether source \"local\" \"remote\"","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/mount_board.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mount pins board — mount_board","text":" source = \"local\"  source = \"remote\"","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/pathologie-package.html","id":null,"dir":"Reference","previous_headings":"","what":"pathologie: Tidy ICD-10-CM Tools — pathologie-package","title":"pathologie: Tidy ICD-10-CM Tools — pathologie-package","text":"Tools working ICD-10-CM codes.","code":""},{"path":[]},{"path":"https://andrewallenbruce.github.io/pathologie/reference/pathologie-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"pathologie: Tidy ICD-10-CM Tools — pathologie-package","text":"Maintainer: Andrew Bruce andrew.bruce@northstarrevenueintegrity.com [copyright holder]","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/remove_dot.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove dot from an ICD-10 code — remove_dot","title":"Remove dot from an ICD-10 code — remove_dot","text":"remove_dot() removes dot ICD-10 code exists","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/remove_dot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove dot from an ICD-10 code — remove_dot","text":"","code":"remove_dot(x)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/remove_dot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove dot from an ICD-10 code — remove_dot","text":"x valid ICD-10 code dot","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/remove_dot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove dot from an ICD-10 code — remove_dot","text":"valid ICD-10 code without dot included","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/remove_dot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove dot from an ICD-10 code — remove_dot","text":"","code":"remove_dot(\"F32.0\") #> [1] \"F320\"  remove_dot(\"F32\") #> [1] \"F32\""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":null,"dir":"Reference","previous_headings":"","what":"ICD-10-CM Code Edits — search_edits","title":"ICD-10-CM Code Edits — search_edits","text":"Definitions Medicare Code Edits, version 41.1","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ICD-10-CM Code Edits — search_edits","text":"","code":"search_edits(icd = NULL, ...)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ICD-10-CM Code Edits — search_edits","text":"icd  vector ICD-10-CM codes ... Empty dots","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ICD-10-CM Code Edits — search_edits","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"ICD-10-CM Code Edits — search_edits","text":"FY 2024 – Version 41.1 (Effective April 1, 2024 September 30, 2024) ICD-10 Definitions Medicare Code Edits file contains following: description coding edit corresponding code lists well edits code lists effective FY 2024.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ICD-10-CM Code Edits — search_edits","text":"","code":"search_edits(c(\"Q96.8\", \"N47.0\", \"R45.4\", \"A33\")) #> # A tibble: 4 × 4 #>   icd_code icd_description                  icd_conflict_group icd_conflict_rule #>                                                              #> 1 A33      Tetanus neonatorum               Age                Perinatal/Newbor… #> 2 N47.0    Adherent prepuce, newborn        Age                Perinatal/Newbor… #> 3 Q96.8    Other variants of Turner's synd… Sex                Female Only       #> 4 N47.0    Adherent prepuce, newborn        Sex                Male Only"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_in.html","id":null,"dir":"Reference","previous_headings":"","what":"Search in data frame — search_in","title":"Search in data frame — search_in","text":"Search data frame","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_in.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search in data frame — search_in","text":"","code":"search_in(df, dfcol, search)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_in.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search in data frame — search_in","text":"df  dfcol  unquoted column search, form df$col search  vector strings search df$col","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_in.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search in data frame — search_in","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":null,"dir":"Reference","previous_headings":"","what":"Medicare Severity Diagnosis-Related Groups — search_msdrg","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"Medicare Severity Diagnosis-Related Group (MS-DRG) classification system used Centers Medicare Medicaid Services (CMS) group patients similar clinical characteristics resource utilization single payment category.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"","code":"search_msdrg(drg = NULL, mdc = NULL, type = NULL, ...)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"drg  vector 3-digit DRG codes mdc  vector 2-digit Major Diagnostic Category codes type  DRG type: Medical Surgical ... Empty dots","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"system primarily used Medicare reimbursement purposes, also adopted many payers basis payment determination. MS-DRGs based principal diagnosis, 24 additional diagnoses, 25 procedures performed stay. small number MS-DRGs, classification also based age, sex, discharge status patient. Hospitals serving severely ill patients receive increased reimbursements, hospitals treating less severely ill patients receive less reimbursement.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"","code":"search_msdrg(drg = \"011\") #> # A tibble: 1 × 6 #>   drg   drg_description                mdc   mdc_description drg_type drg_abbrev #>                                                    #> 1 011   TRACHEOSTOMY FOR FACE,MOUTH &… NA    NA              Surgical P           search_msdrg(mdc = \"24\") #> # A tibble: 8 × 6 #>   drg   drg_description                mdc   mdc_description drg_type drg_abbrev #>                                                    #> 1 955   CRANIOTOMY FOR MULTIPLE SIGNI… 24    Multiple Signi… Surgical P          #> 2 956   LIMB REATTACHMENT, HIP AND FE… 24    Multiple Signi… Surgical P          #> 3 957   OTHER O.R. PROCEDURES FOR MUL… 24    Multiple Signi… Surgical P          #> 4 958   OTHER O.R. PROCEDURES FOR MUL… 24    Multiple Signi… Surgical P          #> 5 959   OTHER O.R. PROCEDURES FOR MUL… 24    Multiple Signi… Surgical P          #> 6 963   OTHER MULTIPLE SIGNIFICANT TR… 24    Multiple Signi… Medical  M          #> 7 964   OTHER MULTIPLE SIGNIFICANT TR… 24    Multiple Signi… Medical  M          #> 8 965   OTHER MULTIPLE SIGNIFICANT TR… 24    Multiple Signi… Medical  M"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/years_floor.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the number of years between two dates — years_floor","title":"Calculate the number of years between two dates — years_floor","text":"Calculate number years two dates","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/years_floor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the number of years between two dates — years_floor","text":"","code":"years_floor(from, to)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/years_floor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the number of years between two dates — years_floor","text":" Start date  End date","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/years_floor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the number of years between two dates — years_floor","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/years_floor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the number of years between two dates — years_floor","text":"","code":"years_floor(    from = as.Date(\"2020-01-01\"),    to   = as.Date(\"2020-01-01\") + 2057) #> [1] 5"},{"path":"https://andrewallenbruce.github.io/pathologie/news/index.html","id":"pathologie-001","dir":"Changelog","previous_headings":"","what":"pathologie 0.0.1","title":"pathologie 0.0.1","text":"Initial commit.","code":""}]
+[{"path":[]},{"path":"https://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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 andrew.bruce@northstarrevenueintegrity.com. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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://andrewallenbruce.github.io/pathologie/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":"https://andrewallenbruce.github.io/pathologie/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 pathologie authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/articles/pathologie.html","id":"icd-10-cm","dir":"Articles","previous_headings":"","what":"ICD-10-CM","title":"pathologie","text":"T76.02XA Child neglect abandonment, suspected, initial encounter Injury, poisoning certain consequences external causes Range: [S00 - T88] Adult child abuse, neglect maltreatment, suspected Range: [T76 - T76.A2XS] INJ Age Pediatric (Ages 0-17)","code":"icd10cm(icd = \"T76.02XA\") |>    mutate(Chapter = paste0(\"* \", icd_ch_name, \" \\n \", \"* Range: [\", icd_ch_range, \"]\"),          Section = paste0(\"* \", icd_sec_name, \" \\n \", \"* Range: [\", icd_sec_range, \"]\")          ) |>   select(\"ICD-10-Code\"   = icd_code,           Description     = icd_description,           Chapter,          Section,          Abbreviation    = icd_ch_abb,          \"Conflict Group\" = icd_conflict_group,          \"Conflict Rule\"  = icd_conflict_rule) |>    display_long() |>   gt(groupname_col       = \"name\",       row_group_as_column = TRUE) |>   fmt_markdown() |>    gt_style(tablign       = \"right\",             tabsize       = 16,             tabwt         = \"bold\") |>    tab_style(       style              = cell_text(       font               = google_font(name = \"Fira Code\")),       locations          = cells_body(         columns          = contains(\"value\"))) |>   tab_style(     style                = list(       cell_fill(color    = \"powderblue\"),       cell_text(weight   = \"bold\"),       cell_borders(       sides              = c(\"all\"),       color              = \"powderblue\",       weight             = px(3))       ),     locations            = cells_row_groups())"},{"path":"https://andrewallenbruce.github.io/pathologie/articles/pathologie.html","id":"the-nlms-icd-10-cm-api","dir":"Articles","previous_headings":"","what":"The NLM’s ICD-10-CM API","title":"pathologie","text":"National Library Medicine’s ICD-10-CM API RESTful API provides access current ICD-10-CM code set. API allows users search codes code keyword(term), returns code description. Searching case insensitive greedy following examples: Returns seven ICD-10 codes beginning A15: Returns 344 ICD-10 codes associated tuberculosis: Returns two ICD-10 codes associated pleurisy:","code":"icd10api(icd_code = \"A15\") #> # A tibble: 7 × 2 #>   icd_code icd_description                              #>                                               #> 1 A15.0    Tuberculosis of lung                         #> 2 A15.4    Tuberculosis of intrathoracic lymph nodes    #> 3 A15.5    Tuberculosis of larynx, trachea and bronchus #> 4 A15.6    Tuberculous pleurisy                         #> 5 A15.7    Primary respiratory tuberculosis             #> 6 A15.8    Other respiratory tuberculosis               #> 7 A15.9    Respiratory tuberculosis unspecified icd10api(term = \"tuber\", field = \"both\") #> # A tibble: 344 × 2 #>    icd_code icd_description                              #>                                                #>  1 A15.0    Tuberculosis of lung                         #>  2 A15.4    Tuberculosis of intrathoracic lymph nodes    #>  3 A15.5    Tuberculosis of larynx, trachea and bronchus #>  4 A15.6    Tuberculous pleurisy                         #>  5 A15.7    Primary respiratory tuberculosis             #>  6 A15.8    Other respiratory tuberculosis               #>  7 A15.9    Respiratory tuberculosis unspecified         #>  8 A17.0    Tuberculous meningitis                       #>  9 A17.1    Meningeal tuberculoma                        #> 10 A17.81   Tuberculoma of brain and spinal cord         #> # ℹ 334 more rows icd10api(term = \"pleurisy\", field = \"both\") #> # A tibble: 2 × 2 #>   icd_code icd_description      #>                       #> 1 R09.1    Pleurisy             #> 2 A15.6    Tuberculous pleurisy"},{"path":"https://andrewallenbruce.github.io/pathologie/articles/pathologie.html","id":"the-field-parameter","dir":"Articles","previous_headings":"The NLM’s ICD-10-CM API","what":"The field Parameter","title":"pathologie","text":"field parameter allows users specify whether want search ICD-10-CM codes codes terms associated description. defaults \"code\" ’s behavior warrants explanation. ’re searching codes beginning certain letter, must set field parameter \"code\" return codes terms contain letter. instance, following call returns ICD-10 codes descriptions containing letter “Z”: call returns ICD-10 codes containing “Z”:","code":"icd10api(icd_code = \"z\", field = \"both\", limit = 50) #> # A tibble: 50 × 2 #>    icd_code icd_description                                                      #>                                                                        #>  1 A28.8    Other specified zoonotic bacterial diseases, not elsewhere classifi… #>  2 A28.9    Zoonotic bacterial disease, unspecified                              #>  3 A92.5    Zika virus disease                                                   #>  4 B02.0    Zoster encephalitis                                                  #>  5 B02.1    Zoster meningitis                                                    #>  6 B02.30   Zoster ocular disease, unspecified                                   #>  7 B02.31   Zoster conjunctivitis                                                #>  8 B02.32   Zoster iridocyclitis                                                 #>  9 B02.33   Zoster keratitis                                                     #> 10 B02.34   Zoster scleritis                                                     #> # ℹ 40 more rows icd10api(icd_code = \"z\", field = \"code\", limit = 50) #> # A tibble: 50 × 2 #>    icd_code icd_description                                                      #>                                                                        #>  1 Z00.00   Encounter for general adult medical examination without abnormal fi… #>  2 Z00.01   Encounter for general adult medical examination with abnormal findi… #>  3 Z00.110  Health examination for newborn under 8 days old                      #>  4 Z00.111  Health examination for newborn 8 to 28 days old                      #>  5 Z00.121  Encounter for routine child health examination with abnormal findin… #>  6 Z00.129  Encounter for routine child health examination without abnormal fin… #>  7 Z00.2    Encounter for examination for period of rapid growth in childhood    #>  8 Z00.3    Encounter for examination for adolescent development state           #>  9 Z00.5    Encounter for examination of potential donor of organ and tissue     #> 10 Z00.6    Encounter for examination for normal comparison and control in clin… #> # ℹ 40 more rows"},{"path":"https://andrewallenbruce.github.io/pathologie/articles/pathologie.html","id":"icd-10-cm-code-edits","dir":"Articles","previous_headings":"","what":"ICD-10-CM Code Edits","title":"pathologie","text":"","code":"ex_data() |>   dplyr::mutate(patient_age = years_floor(date_of_birth,                                           date_of_service)) |>   dplyr::left_join(search_edits()) |>   dplyr::filter(icd_conflict_group == \"Age\") |>   dplyr::mutate(conflict = apply_age_edits(rule = icd_conflict_rule,                                            age = patient_age)) |>   dplyr::filter(!is.na(conflict)) |>    dplyr::select(-icd_conflict_group, -conflict) |>    gt(groupname_col = \"icd_conflict_rule\",      row_group_as_column = TRUE) |>    gt_style()"},{"path":"https://andrewallenbruce.github.io/pathologie/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andrew Bruce. Author, maintainer, copyright holder.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Bruce (2024). pathologie: Tidy ICD-10-CM Tools. R package version 0.0.1,  https://github.com/andrewallenbruce/pathologie, https://andrewallenbruce.github.io/pathologie/.","code":"@Manual{,   title = {pathologie: Tidy ICD-10-CM Tools},   author = {Andrew Bruce},   year = {2024},   note = {R package version 0.0.1,  https://github.com/andrewallenbruce/pathologie},   url = {https://andrewallenbruce.github.io/pathologie/}, }"},{"path":"https://andrewallenbruce.github.io/pathologie/index.html","id":"pathologie","dir":"","previous_headings":"","what":"Tidy ICD-10-CM Tools","title":"Tidy ICD-10-CM Tools","text":"Tidy ICD-10-CM Interface","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/index.html","id":"package-installation","dir":"","previous_headings":"","what":"📦 Installation","title":"Tidy ICD-10-CM Tools","text":"can install pathologie GitHub :","code":"# install.packages(\"pak\") pak::pak(\"andrewallenbruce/pathologie\")"},{"path":"https://andrewallenbruce.github.io/pathologie/index.html","id":"beginner-usage","dir":"","previous_headings":"","what":"🔰 Usage","title":"Tidy ICD-10-CM Tools","text":"","code":"library(pathologie) library(dplyr) icd10cm(icd = c(\"I10\", \"I15.0\")) |>    glimpse() #> Rows: 2 #> Columns: 10 #> $ icd_ch_no        9, 9 #> $ icd_ch_abb       \"CARDIO\", \"CARDIO\" #> $ icd_ch_name      \"Diseases of the circulatory system\", \"Diseases of the… #> $ icd_ch_range     \"I00 - I99\", \"I00 - I99\" #> $ icd_sec_name     \"Other rheumatic heart diseases\", \"Secondary hypertens… #> $ icd_sec_range    \"I09 - I10\", \"I15 - I15.9\" #> $ order            11397, 11411 #> $ valid            1, 1 #> $ icd_code         \"I10\", \"I15.0\" #> $ icd_description  \"Essential (primary) hypertension\", \"Renovascular hype… icd10api(icd_code = \"I1\") #> # A tibble: 18 × 2 #>    icd_code icd_description                                                      #>                                                                        #>  1 I10      Essential (primary) hypertension                                     #>  2 I11.0    Hypertensive heart disease with heart failure                        #>  3 I11.9    Hypertensive heart disease without heart failure                     #>  4 I12.0    Hypertensive chronic kidney disease with stage 5 chronic kidney dis… #>  5 I12.9    Hypertensive chronic kidney disease with stage 1 through stage 4 ch… #>  6 I13.0    Hypertensive heart and chronic kidney disease with heart failure an… #>  7 I13.10   Hypertensive heart and chronic kidney disease without heart failure… #>  8 I13.11   Hypertensive heart and chronic kidney disease without heart failure… #>  9 I13.2    Hypertensive heart and chronic kidney disease with heart failure an… #> 10 I15.0    Renovascular hypertension                                            #> 11 I15.1    Hypertension secondary to other renal disorders                      #> 12 I15.2    Hypertension secondary to endocrine disorders                        #> 13 I15.8    Other secondary hypertension                                         #> 14 I15.9    Secondary hypertension, unspecified                                  #> 15 I16.0    Hypertensive urgency                                                 #> 16 I16.1    Hypertensive emergency                                               #> 17 I16.9    Hypertensive crisis, unspecified                                     #> 18 I1A.0    Resistant hypertension"},{"path":"https://andrewallenbruce.github.io/pathologie/index.html","id":"balance_scale-code-of-conduct","dir":"","previous_headings":"","what":"⚖️ Code of Conduct","title":"Tidy ICD-10-CM Tools","text":"Please note pathologie project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/index.html","id":"classical_building-governance","dir":"","previous_headings":"","what":"🏛️ Governance","title":"Tidy ICD-10-CM Tools","text":"project primarily maintained Andrew Bruce. authors may occasionally assist duties.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/add_dot.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a dot to an ICD-10 code — add_dot","title":"Add a dot to an ICD-10 code — add_dot","text":"add_dot() adds dot ICD-10 code appropriate position one exist","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/add_dot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a dot to an ICD-10 code — add_dot","text":"","code":"add_dot(x)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/add_dot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a dot to an ICD-10 code — add_dot","text":"x valid ICD-10 code without dot","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/add_dot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a dot to an ICD-10 code — add_dot","text":"valid ICD-10 code dot included","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/add_dot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a dot to an ICD-10 code — add_dot","text":"","code":"add_dot(\"F320\") #> [1] \"F32.0\"  add_dot(\"F32\")  # no dot added if code is only 3-digits #> [1] \"F32\""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_A.html","id":null,"dir":"Reference","previous_headings":"","what":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","title":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","text":"Appendix contains list MS-DRG specification MDC whether MS-DRG medical surgical. MS-DRGs contain patients multiple MDCs (e.g., 014 Allogeneic Bone Marrow Transplant) MDC specified. letter M used designate medical MS-DRG letter P used designate surgical MS-DRG.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_A.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","text":"","code":"appendix_A(drg = NULL, mdc = NULL, type = NULL, ...)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_A.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","text":"drg  vector 3-digit Diagnosis-Related Group codes mdc  vector 2-digit Major Diagnostic Category codes type  DRG type: M (Medical) P (Surgical) ... Empty dots","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_A.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_A.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Appendix A: List of MS-DRGs Version 41.1 — appendix_A","text":"","code":"appendix_A(drg = \"011\") #> # A tibble: 1 × 4 #>   drg   mdc   drg_abb drg_description                                            #>                                                              #> 1 011   NA    P       TRACHEOSTOMY FOR FACE, MOUTH AND NECK DIAGNOSES OR LARYNG…  appendix_A(mdc = \"24\") #> # A tibble: 8 × 4 #>   drg   mdc   drg_abb drg_description                                            #>                                                              #> 1 955   24    P       CRANIOTOMY FOR MULTIPLE SIGNIFICANT TRAUMA                 #> 2 956   24    P       LIMB REATTACHMENT, HIP AND FEMUR PROCEDURES FOR MULTIPLE … #> 3 957   24    P       OTHER O.R. PROCEDURES FOR MULTIPLE SIGNIFICANT TRAUMA WIT… #> 4 958   24    P       OTHER O.R. PROCEDURES FOR MULTIPLE SIGNIFICANT TRAUMA WIT… #> 5 959   24    P       OTHER O.R. PROCEDURES FOR MULTIPLE SIGNIFICANT TRAUMA WIT… #> 6 963   24    M       OTHER MULTIPLE SIGNIFICANT TRAUMA WITH MCC                 #> 7 964   24    M       OTHER MULTIPLE SIGNIFICANT TRAUMA WITH CC                  #> 8 965   24    M       OTHER MULTIPLE SIGNIFICANT TRAUMA WITHOUT CC/MCC"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_B.html","id":null,"dir":"Reference","previous_headings":"","what":"Appendix B: Diagnosis Code/MDC/MS-DRG Index — appendix_B","title":"Appendix B: Diagnosis Code/MDC/MS-DRG Index — appendix_B","text":"Diagnosis Code/MDC/MS-DRG Index lists diagnosis code, well MDC, MS-DRGs diagnosis used define logic DRG either principal secondary diagnosis.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_B.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Appendix B: Diagnosis Code/MDC/MS-DRG Index — appendix_B","text":"","code":"appendix_B()"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_B.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Appendix B: Diagnosis Code/MDC/MS-DRG Index — appendix_B","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_B.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Appendix B: Diagnosis Code/MDC/MS-DRG Index — appendix_B","text":"","code":"head(appendix_B()) #> # A tibble: 6 × 4 #>   icd_code mdc   drg_range drg   #>              #> 1 A00.0    06    371-373   371   #> 2 A00.0    06    371-373   372   #> 3 A00.0    06    371-373   373   #> 4 A00.1    06    371-373   371   #> 5 A00.1    06    371-373   372   #> 6 A00.1    06    371-373   373"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_C.html","id":null,"dir":"Reference","previous_headings":"","what":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","title":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","text":"Appendix C list codes defined either complication comorbidity (CC) major complication comorbidity (MCC) used secondary diagnosis.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_C.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","text":"","code":"appendix_C()"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_C.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_C.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","text":"Part 1 lists codes. code indicated CC MCC. link given collection diagnosis codes , used principal diagnosis, cause CC MCC considered non-CC. Part 2 lists codes assigned Major CC patients discharged alive. Otherwise assigned non-CC. Part 3 lists diagnosis codes designated complication comorbidity (CC) major complication comorbidity (MCC) included definition logic listed DRGs. reported secondary diagnosis grouped one listed DRGs diagnosis excluded acting CC/MCC severity DRG assignment.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/appendix_C.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Appendix C: Complications or Comorbidities Exclusion list — appendix_C","text":"","code":"head(appendix_C()$cc_mcc) #> # A tibble: 6 × 3 #>   icd_code cc_mcc pdx_group #>              #> 1 A00.0    CC     0002      #> 2 A00.1    CC     0002      #> 3 A00.9    CC     0002      #> 4 A01.00   CC     0003      #> 5 A01.01   CC     0003      #> 6 A01.02   CC     0003       head(appendix_C()$pdx_groups) #> # A tibble: 6 × 2 #>   pdx_icd pdx_group #>           #> 1 A00.0   0002      #> 2 A00.1   0002      #> 3 A00.9   0002      #> 4 A01.00  0003      #> 5 A01.01  0003      #> 6 A01.02  0003"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/apply_age_edits.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply Age Conflict Edits — apply_age_edits","title":"Apply Age Conflict Edits — apply_age_edits","text":"Apply Age Conflict Edits","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/apply_age_edits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply Age Conflict Edits — apply_age_edits","text":"","code":"apply_age_edits(rule, age)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/apply_age_edits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply Age Conflict Edits — apply_age_edits","text":"rule  ICD-10-CM Conflict Rule age  age years","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/apply_age_edits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply Age Conflict Edits — apply_age_edits","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/apply_age_edits.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply Age Conflict Edits — apply_age_edits","text":"","code":"apply_age_edits(    c(\"Pediatric (Ages 0-17)\",      \"Maternity (Ages 9-64)\"),    c(18, 7)) #> [1] \"Age Conflict\" \"Age Conflict\""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/case_chapter_icd10.html","id":null,"dir":"Reference","previous_headings":"","what":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","title":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","text":"Add ICD-10-CM Chapter Labels","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/case_chapter_icd10.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","text":"","code":"case_chapter_icd10(df, col)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/case_chapter_icd10.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","text":"df data frame col  unquoted column name ICD-10-CM codes match","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/case_chapter_icd10.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","text":"tibble chapter column","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/case_chapter_icd10.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add ICD-10-CM Chapter Labels — case_chapter_icd10","text":"","code":"dplyr::tibble(code = c(\"F50.8\", \"G40.311\", \"Q96.8\", \"Z62.890\", \"R45.4\", \"E06.3\", \"H00.019\", \"D50.1\", \"C4A.70\", \"Z20.818\")) |> case_chapter_icd10(code) #> # A tibble: 10 × 2 #>    code    chapter                                                               #>                                                                        #>  1 F50.8   Mental, behavioral and neurodevelopmental disorders                   #>  2 G40.311 Diseases of the nervous system                                        #>  3 Q96.8   Congenital malformations, deformations and chromosomal abnormalities  #>  4 Z62.890 Factors influencing health status and contact with health services    #>  5 R45.4   Symptoms, signs and abnormal clinical and laboratory findings, not e… #>  6 E06.3   Endocrine, nutritional and metabolic diseases                         #>  7 H00.019 Diseases of the eye and adnexa                                        #>  8 D50.1   Diseases of the blood and blood-forming organs and certain disorders… #>  9 C4A.70  Neoplasms                                                             #> 10 Z20.818 Factors influencing health status and contact with health services"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/display_long.html","id":null,"dir":"Reference","previous_headings":"","what":"Pivot data frame to long format for easy printing — display_long","title":"Pivot data frame to long format for easy printing — display_long","text":"Pivot data frame long format easy printing","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/display_long.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pivot data frame to long format for easy printing — display_long","text":"","code":"display_long(df, cols = dplyr::everything())"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/display_long.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pivot data frame to long format for easy printing — display_long","text":"df  cols  vector bare column name pivot, default dplyr::everything()","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/display_long.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pivot data frame to long format for easy printing — display_long","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/ex_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Example data set — ex_data","title":"Example data set — ex_data","text":"Example data set","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/ex_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example data set — ex_data","text":"","code":"ex_data()"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/ex_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Example data set — ex_data","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_marks.html","id":null,"dir":"Reference","previous_headings":"","what":"gt Marks — gt_marks","title":"gt Marks — gt_marks","text":"gt Marks","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_marks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gt Marks — gt_marks","text":"","code":"gt_marks(tbl, cols)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_marks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gt Marks — gt_marks","text":"tbl  object cols  vector bare column names, e.g. c(mdc, drg)","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_marks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gt Marks — gt_marks","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_style.html","id":null,"dir":"Reference","previous_headings":"","what":"gt Theme — gt_style","title":"gt Theme — gt_style","text":"gt Theme","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_style.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gt Theme — gt_style","text":"","code":"gt_style(tbl, lbl = TRUE, tablign = \"center\", tabsize = 16, tabwt = \"normal\")"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_style.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gt Theme — gt_style","text":"tbl  object lbl  hide column labels; default TRUE tablign  table stub alignment; default \"center\" tabsize  table stub font size pixels; default 16 tabwt  table stub font weight; default \"normal\"","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/gt_style.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gt Theme — gt_style","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":null,"dir":"Reference","previous_headings":"","what":"National Library of Medicine's ICD-10-CM API — icd10api","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"icd10api() allows search National Library Medicine's ICD-10-CM API code associated term.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"","code":"icd10api(   icd_code = NULL,   term = NULL,   field = c(\"code\", \"both\"),   limit = 500L,   ... )"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"National Library Medicine/National Institute Health","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"icd_code  ICD-10-CM code containing 3 7 characters, excluding dot term  Associated term describing ICD-10-CM code field  code ; default code limit  API limit, defaults 500. Note current limit total number results can retrieved 7,500. ... Empty dots","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"ICD-10-CM (International Classification Diseases, 10th Revision, Clinical Modification) medical coding system classifying diagnoses reasons visits U.S. health care settings.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"links","dir":"Reference","previous_headings":"","what":"Links","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"NIH NLM Clinical Table Service ICD-10-CM API Learn ICD-10-CM.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"Current Version: ICD-10-CM 2024","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10api.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"National Library of Medicine's ICD-10-CM API — icd10api","text":"","code":"# Returns the seven codes beginning with `A15` icd10api(icd_code = \"A15\") #> # A tibble: 7 × 2 #>   icd_code icd_description                              #>                                               #> 1 A15.0    Tuberculosis of lung                         #> 2 A15.4    Tuberculosis of intrathoracic lymph nodes    #> 3 A15.5    Tuberculosis of larynx, trachea and bronchus #> 4 A15.6    Tuberculous pleurisy                         #> 5 A15.7    Primary respiratory tuberculosis             #> 6 A15.8    Other respiratory tuberculosis               #> 7 A15.9    Respiratory tuberculosis unspecified          # Returns the first five codes # associated with tuberculosis icd10api(term = \"tuber\", field = \"both\", limit = 5) #> # A tibble: 5 × 2 #>   icd_code icd_description                              #>                                               #> 1 A15.0    Tuberculosis of lung                         #> 2 A15.4    Tuberculosis of intrathoracic lymph nodes    #> 3 A15.5    Tuberculosis of larynx, trachea and bronchus #> 4 A15.6    Tuberculous pleurisy                         #> 5 A15.7    Primary respiratory tuberculosis              # Returns the two codes # associated with pleurisy icd10api(term = \"pleurisy\", field = \"both\") #> # A tibble: 2 × 2 #>   icd_code icd_description      #>                       #> 1 R09.1    Pleurisy             #> 2 A15.6    Tuberculous pleurisy  # If you're searching for codes beginning # with a certain letter, you must set the # `field` param to `\"code\"` or it will # search for terms as well:  # Returns terms containing the letter \"Z\" icd10api(icd_code = \"z\", limit = 5) #> # A tibble: 5 × 2 #>   icd_code icd_description                                                       #>                                                                        #> 1 Z00.00   Encounter for general adult medical examination without abnormal fin… #> 2 Z00.01   Encounter for general adult medical examination with abnormal findin… #> 3 Z00.110  Health examination for newborn under 8 days old                       #> 4 Z00.111  Health examination for newborn 8 to 28 days old                       #> 5 Z00.121  Encounter for routine child health examination with abnormal findings  # Returns codes beginning with \"Z\" icd10api(icd_code = \"z\", field = \"code\", limit = 5) #> # A tibble: 5 × 2 #>   icd_code icd_description                                                       #>                                                                        #> 1 Z00.00   Encounter for general adult medical examination without abnormal fin… #> 2 Z00.01   Encounter for general adult medical examination with abnormal findin… #> 3 Z00.110  Health examination for newborn under 8 days old                       #> 4 Z00.111  Health examination for newborn 8 to 28 days old                       #> 5 Z00.121  Encounter for routine child health examination with abnormal findings  # Will error if results exceed API limit try(icd10api(icd_code = \"I\", field = \"both\")) #> Error in icd10api(icd_code = \"I\", field = \"both\") :  #>   Your search returned 36770 results. #> ✖ The NLM ICD-10-CM API limit is 7,500."},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10cm.html","id":null,"dir":"Reference","previous_headings":"","what":"ICD-10-CM Codes — icd10cm","title":"ICD-10-CM Codes — icd10cm","text":"ICD-10-CM (International Classification Diseases, 10th Revision, Clinical Modification) medical coding system classifying diagnoses reasons visits U.S. health care settings.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10cm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ICD-10-CM Codes — icd10cm","text":"","code":"icd10cm(icd = NULL, ...)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10cm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ICD-10-CM Codes — icd10cm","text":"icd  vector ICD-10-CM codes ... Empty dots","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10cm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ICD-10-CM Codes — icd10cm","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/icd10cm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ICD-10-CM Codes — icd10cm","text":"","code":"icd10cm( c(\"F50.8\", \"G40.311\", \"Q96.8\", \"Z62.890\", \"R45.4\", \"E06.3\", \"H00.019\", \"D50.1\", \"C4A.70\") ) #> # A tibble: 9 × 12 #>   icd_ch_no icd_ch_abb icd_ch_name icd_ch_range icd_sec_name icd_sec_range order #>                                               #> 1         2 ONC        Neoplasms   C00 - D49    Merkel cell… C4A - C4A.9    1599 #> 2         3 BLOOD      Diseases o… D50 - D89    Iron defici… D50 - D50.9    3421 #> 3         4 METAB      Endocrine,… E00 - E89    Thyroiditis  E06 - E06.9    3868 #> 4         5 PSYCH      Mental, be… F01 - F99    Eating diso… F50 - F50.9    5946 #> 5         6 NEURO      Diseases o… G00 - G99    Epilepsy an… G40 - G40.919  6329 #> 6         7 EYE        Diseases o… H00 - H59    Hordeolum a… H00 - H00.19   7045 #> 7        17 CONG       Congenital… Q00 - Q99    Turner's sy… Q96 - Q96.9   30028 #> 8        18 SYMP       Symptoms, … R00 - R99    Symptoms an… R45 - R45.89  30559 #> 9        21 STAT       Factors in… Z00 - Z99    Problems re… Z62 - Z62.9   96381 #> # ℹ 5 more variables: valid , icd_code , icd_description , #> #   icd_conflict_group , icd_conflict_rule "},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if string is valid ICD-10-CM code — is_valid_icd","title":"Check if string is valid ICD-10-CM code — is_valid_icd","text":"Check string valid ICD-10-CM code","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if string is valid ICD-10-CM code — is_valid_icd","text":"","code":"is_valid_icd(x, arg = rlang::caller_arg(x), call = rlang::caller_env())"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if string is valid ICD-10-CM code — is_valid_icd","text":"x  string length(x) == 1 arg  function argument name current function call  environment function called ","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if string is valid ICD-10-CM code — is_valid_icd","text":" vector; TRUE valid, FALSE otherwise","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if string is valid ICD-10-CM code — is_valid_icd","text":"","code":"purrr::map_vec( c(\"H00.019\", \"D50.1\", \"C4A.70\", \"Z20.818\", \"11646\", \"E8015\"), is_valid_icd) #> [1] \"H00.019\" \"D50.1\"   \"C4A.70\"  \"Z20.818\" \"11646\"   \"E8015\""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/mount_board.html","id":null,"dir":"Reference","previous_headings":"","what":"Mount pins board — mount_board","title":"Mount pins board — mount_board","text":"Mount pins board","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/mount_board.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mount pins board — mount_board","text":"","code":"mount_board(source = c(\"local\", \"remote\"))"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/mount_board.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mount pins board — mount_board","text":"`` string; whether source \"local\" \"remote\"","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/mount_board.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mount pins board — mount_board","text":" source = \"local\"  source = \"remote\"","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/pathologie-package.html","id":null,"dir":"Reference","previous_headings":"","what":"pathologie: Tidy ICD-10-CM Tools — pathologie-package","title":"pathologie: Tidy ICD-10-CM Tools — pathologie-package","text":"Tools working ICD-10-CM codes.","code":""},{"path":[]},{"path":"https://andrewallenbruce.github.io/pathologie/reference/pathologie-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"pathologie: Tidy ICD-10-CM Tools — pathologie-package","text":"Maintainer: Andrew Bruce andrew.bruce@northstarrevenueintegrity.com [copyright holder]","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/remove_dot.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove dot from an ICD-10 code — remove_dot","title":"Remove dot from an ICD-10 code — remove_dot","text":"remove_dot() removes dot ICD-10 code exists","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/remove_dot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove dot from an ICD-10 code — remove_dot","text":"","code":"remove_dot(x)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/remove_dot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove dot from an ICD-10 code — remove_dot","text":"x valid ICD-10 code dot","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/remove_dot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove dot from an ICD-10 code — remove_dot","text":"valid ICD-10 code without dot included","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/remove_dot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove dot from an ICD-10 code — remove_dot","text":"","code":"remove_dot(\"F32.0\") #> [1] \"F320\"  remove_dot(\"F32\") #> [1] \"F32\""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":null,"dir":"Reference","previous_headings":"","what":"ICD-10-CM Code Edits — search_edits","title":"ICD-10-CM Code Edits — search_edits","text":"Definitions Medicare Code Edits, version 41.1","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ICD-10-CM Code Edits — search_edits","text":"","code":"search_edits(icd = NULL, ...)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ICD-10-CM Code Edits — search_edits","text":"icd  vector ICD-10-CM codes ... Empty dots","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ICD-10-CM Code Edits — search_edits","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"ICD-10-CM Code Edits — search_edits","text":"FY 2024 – Version 41.1 (Effective April 1, 2024 September 30, 2024) ICD-10 Definitions Medicare Code Edits file contains following: description coding edit corresponding code lists well edits code lists effective FY 2024.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_edits.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ICD-10-CM Code Edits — search_edits","text":"","code":"search_edits(c(\"Q96.8\", \"N47.0\", \"R45.4\", \"A33\")) #> # A tibble: 4 × 4 #>   icd_code icd_description                  icd_conflict_group icd_conflict_rule #>                                                              #> 1 A33      Tetanus neonatorum               Age                Perinatal/Newbor… #> 2 N47.0    Adherent prepuce, newborn        Age                Perinatal/Newbor… #> 3 Q96.8    Other variants of Turner's synd… Sex                Female Only       #> 4 N47.0    Adherent prepuce, newborn        Sex                Male Only"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_in.html","id":null,"dir":"Reference","previous_headings":"","what":"Search in data frame — search_in","title":"Search in data frame — search_in","text":"Search data frame","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_in.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search in data frame — search_in","text":"","code":"search_in(df, dfcol, search)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_in.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search in data frame — search_in","text":"df  dfcol  unquoted column search, form df$col search  vector strings search df$col","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_in.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search in data frame — search_in","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":null,"dir":"Reference","previous_headings":"","what":"Medicare Severity Diagnosis-Related Groups — search_msdrg","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"Medicare Severity Diagnosis-Related Group (MS-DRG) classification system used Centers Medicare Medicaid Services (CMS) group patients similar clinical characteristics resource utilization single payment category.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"","code":"search_msdrg(drg = NULL, mdc = NULL, type = NULL, ...)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"drg  vector 3-digit DRG codes mdc  vector 2-digit Major Diagnostic Category codes type  DRG type: Medical Surgical ... Empty dots","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"system primarily used Medicare reimbursement purposes, also adopted many payers basis payment determination. MS-DRGs based principal diagnosis, 24 additional diagnoses, 25 procedures performed stay. small number MS-DRGs, classification also based age, sex, discharge status patient. Hospitals serving severely ill patients receive increased reimbursements, hospitals treating less severely ill patients receive less reimbursement.","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/search_msdrg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Medicare Severity Diagnosis-Related Groups — search_msdrg","text":"","code":"search_msdrg(drg = \"011\") #> # A tibble: 1 × 6 #>   drg   drg_description                mdc   mdc_description drg_type drg_abbrev #>                                                    #> 1 011   TRACHEOSTOMY FOR FACE,MOUTH &… NA    NA              Surgical P           search_msdrg(mdc = \"24\") #> # A tibble: 8 × 6 #>   drg   drg_description                mdc   mdc_description drg_type drg_abbrev #>                                                    #> 1 955   CRANIOTOMY FOR MULTIPLE SIGNI… 24    Multiple Signi… Surgical P          #> 2 956   LIMB REATTACHMENT, HIP AND FE… 24    Multiple Signi… Surgical P          #> 3 957   OTHER O.R. PROCEDURES FOR MUL… 24    Multiple Signi… Surgical P          #> 4 958   OTHER O.R. PROCEDURES FOR MUL… 24    Multiple Signi… Surgical P          #> 5 959   OTHER O.R. PROCEDURES FOR MUL… 24    Multiple Signi… Surgical P          #> 6 963   OTHER MULTIPLE SIGNIFICANT TR… 24    Multiple Signi… Medical  M          #> 7 964   OTHER MULTIPLE SIGNIFICANT TR… 24    Multiple Signi… Medical  M          #> 8 965   OTHER MULTIPLE SIGNIFICANT TR… 24    Multiple Signi… Medical  M"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/years_floor.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the number of years between two dates — years_floor","title":"Calculate the number of years between two dates — years_floor","text":"Calculate number years two dates","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/years_floor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the number of years between two dates — years_floor","text":"","code":"years_floor(from, to)"},{"path":"https://andrewallenbruce.github.io/pathologie/reference/years_floor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the number of years between two dates — years_floor","text":" Start date  End date","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/years_floor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the number of years between two dates — years_floor","text":"tibble","code":""},{"path":"https://andrewallenbruce.github.io/pathologie/reference/years_floor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the number of years between two dates — years_floor","text":"","code":"years_floor(    from = as.Date(\"2020-01-01\"),    to   = as.Date(\"2020-01-01\") + 2057) #> [1] 5"},{"path":"https://andrewallenbruce.github.io/pathologie/news/index.html","id":"pathologie-001","dir":"Changelog","previous_headings":"","what":"pathologie 0.0.1","title":"pathologie 0.0.1","text":"Initial commit.","code":""}]
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+++ b/sitemap.xml
@@ -69,9 +69,6 @@
   
     https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd.html
   
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-    https://andrewallenbruce.github.io/pathologie/reference/is_valid_icd10cm.html
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     https://andrewallenbruce.github.io/pathologie/reference/mount_board.html