Merge pull request #43 from como-ph/dev-v0.1.3

PR for patch release

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,48 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, and in the interest of
+fostering an open and welcoming community, we pledge to respect all people who
+contribute through reporting issues, posting feature requests, updating
+documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free
+experience for everyone, regardless of level of experience, gender, gender
+identity and expression, sexual orientation, disability, personal appearance,
+body size, race, ethnicity, age, religion, or nationality.
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery
+* Personal attacks
+* Trolling or insulting/derogatory comments
+* Public or private harassment
+* Publishing other's private information, such as physical or electronic
+  addresses, without explicit permission
+* Other unethical or unprofessional conduct
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+By adopting this Code of Conduct, project maintainers commit themselves to
+fairly and consistently applying these principles to every aspect of managing
+this project. Project maintainers who do not follow or enforce the Code of
+Conduct may be permanently removed from the project team.
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting a project maintainer at [email protected]. All 
+complaints will be reviewed and investigated and will result in a response that 
+is deemed necessary and appropriate to the circumstances. Maintainers are 
+obligated to maintain confidentiality with regard to the reporter of an incident.
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.3.0, available at
+[http://contributor-covenant.org/version/1/3/0/][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/3/0/

.github/CONTRIBUTING.md

@@ -0,0 +1,35 @@
+# Contributing
+
+## Bugs
+
+* Submit an issue on the [issues page](https://github.com/como-ph/oxcovid19/issues)
+
+## Code contributions
+
+* Fork this repository to your Github account
+
+* Clone your version on your account down to your machine from your account 
+
+```
+git clone https://github.com/<yourgithubusername>/oxcovid19.git
+```
+
+* Make sure to track progress upstream i.e., on our version of `oxcovid19` 
+at `como-ph/oxcovid19`, by doing 
+
+```
+git remote add upstream https://github.com/como-ph/oxcovid19.git
+```
+
+* Before making changes make sure to pull changes in from `upstream` by doing 
+either `git fetch upstream` then merge later or `git pull upstream` to fetch 
+and merge in one step
+
+* Make your changes on a new feature branch
+
+* Please write a test or tests for your changes if they affect code and not just 
+documentation
+
+* Push up changes to your account
+
+* Submit a pull request at `como-ph/oxcovid19`

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: oxcovid19
 Type: Package
 Title: An R API to the Oxford COVID-19 Database
-Version: 0.1.2.9000
+Version: 0.1.3
 Authors@R: c(person(given = "Ernest", family = "Guevarra", 
                     email = "[email protected]", role = c("aut", "cre"),
                     comment = c(ORCID = "0000-0002-4887-4415")),
@@ -15,14 +15,15 @@ Authors@R: c(person(given = "Ernest", family = "Guevarra",
                     comment = c(ORCID = "0000-0001-6647-5453")),
              person(given = "Alexander", family = "Zarebski",
                     role = "aut"))
-Description: The OxCOVID19 Project <https://covid19.eng.ox.ac.uk> aims to increase
-    our understanding of the COVID-19 pandemic and elaborate possible strategies
-    to reduce the impact on the society through the combined power of statistical,
-    mathematical modelling, and machine learning techniques. The OxCOVID19
-    Database is a large, single-centre, multimodal relational database consisting
-    of information (using acknowledged sources) related to COVID-19 pandemic.
-    This package provides an R-specific interface to the OxCOVID19 Database based
-    on widely-used data handling and manipulation approaches in R.
+Description: The OxCOVID19 Project <https://covid19.eng.ox.ac.uk> aims to 
+    increase our understanding of the COVID-19 pandemic and elaborate possible 
+    strategies to reduce the impact on the society through the combined power 
+    of statistical, mathematical modelling, and machine learning techniques. 
+    The OxCOVID19 Database is a large, single-centre, multimodal relational 
+    database consisting of information (using acknowledged sources) related to 
+    COVID-19 pandemic. This package provides an R-specific interface to the 
+    OxCOVID19 Database based on widely-used data handling and manipulation 
+    approaches in R.
 License: GPL-3
 Depends: 
     R (>= 2.10)
@@ -44,13 +45,12 @@ Suggests:
     stringr,
     RColorBrewer,
     ggplot2,
-    DiagrammeR,
     spelling
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
-URL: https://github.com/como-ph/oxcovid19
-BugReports: https://github.com/como-ph/oxcovid19/issues
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
 VignetteBuilder: knitr
+URL: https://como-ph.github.io/oxcovid19/, https://github.com/como-ph/oxcovid19
+BugReports: https://github.com/como-ph/oxcovid19/issues

NEWS.md

@@ -1,14 +1,61 @@
+<!---
+# oxcovid19 0.2.0
+
+This is the fourth [CRAN](https://cran.r-project.org) release of `oxcovid19`. 
+This is a minor release. In this release:
+
+## Enhancements
+
+* Added *merge_* functions to create combined tables for relational analysis
+
+* Added a built-in Shiny package for basic data access and basic data
+  visualisation; this was also a way to demonstrate how the package functions
+  work
+
+* Improved code coverage (from 53% to XX)
+
+## Bug fixes
+
+* addressed issue with `get_data_weather` not working as expected. Issue was
+  with how missing values were reported in the actual datasets (usage of
+  character value NaN rather than NA or special value NaN)
+--->
+
+# oxcovid19 0.1.3
+
+This is a patch release of `oxcovid19` (GitHub and Zenodo release only). This
+is a development release leading up to `oxcovid19` minor 
+[CRAN](https://cran.r-rpoject.org) release v0.2.0 in December 2020.
+
+In this release:
+
+## Enhancements
+
+* Improved documentation with community guidelines that include code of conduct
+  and contributing guidelines
+
+* Improved website (favicon, etc)
+
+* Removed Travis ci/cd
+
+## Bug fixes
+
+* addressed issue with `get_data_weather` not working as expected. Issue was
+  with how missing values were reported in the actual datasets (usage of
+  character value NaN rather than NA or special value NaN)
+
 # oxcovid19 0.1.2
 
-This is the third CRAN release of `oxcovid19`. In this release:
+This is the third [CRAN](https://cran.r-project.org) release of `oxcovid19`. In 
+this release:
 
 ## Enhancements
 
 * added function to get remote table metadata (party to fix CRAN NOTE on non-use
-of imported `dbplyr` package)
+  of imported `dbplyr` package)
 
 * added convenience wrapper functions to retrieve data from specific tables
-based on specified query parameters
+  based on specified query parameters
 
 * added utility function to help in citing appropriate data sources
 
@@ -24,7 +71,8 @@ based on specified query parameters
 
 # oxcovid19 0.1.1
 
-This is the second CRAN release of `oxcovid19`. In this release:
+This is the second [CRAN](https://cran.r-project.org) release of `oxcovid19`. In 
+this release:
 
 ## Enhancements
 
@@ -44,15 +92,19 @@ This is the second CRAN release of `oxcovid19`. In this release:
 
 # oxcovid19 0.1.0
 
-This is the first CRAN release of `oxcovid19`. In this release:
+This is the first [CRAN](https://cran.r-project.org) release of `oxcovid19`. In 
+this release:
 
-* Created a function to open a connection to the PostgreSQL server of the OxCOVID19 Database.
+* Created a function to open a connection to the PostgreSQL server of the 
+  OxCOVID19 Database.
 
-* Created a function to output lists of available tables in the PostgreSQL server and lists of fields in each table in the PostgreSQL server.
+* Created a function to output lists of available tables in the PostgreSQL 
+  server and lists of fields in each table in the PostgreSQL server.
 
 * Created a function to output specified tables for use within R environment.
 
-* Pulled source and structure specifications of tables in PostgreSQL server and saved as package datasets.
+* Pulled source and structure specifications of tables in PostgreSQL server and 
+  saved as package datasets.
 
 * Added README to document package description, installation and use.
 

R/citation.R

@@ -22,7 +22,11 @@
 
 cite_sources <- function(x) {
   ## match sources to tables - epidemiology
-  if(any(unique(x[["source"]]) %in% data_sources[["epidemiology"]][["Source code"]])) {
+  if(
+    any(
+      unique(x[["source"]]) %in% data_sources[["epidemiology"]][["Source code"]]
+    )
+  ) {
     epi_sources <- data_sources$epidemiology %>%
       dplyr::filter(`Source code` %in% unique(x[["source"]])) %>%
       dplyr::mutate(Table = "Epidemiology") %>%
@@ -50,7 +54,11 @@ cite_sources <- function(x) {
   }
 
   ## match sources to tables - mobility
-  if(any(unique(x[["source"]]) %in% data_sources[["mobility"]][["Source code"]])) {
+  if(
+    any(
+      unique(x[["source"]]) %in% data_sources[["mobility"]][["Source code"]]
+    )
+  ) {
     mobility_sources <- data_sources$mobility %>%
       dplyr::filter(`Source code` %in% unique(x[["source"]])) %>%
       dplyr::mutate(Table = "Mobility") %>%
@@ -88,8 +96,8 @@ cite_sources <- function(x) {
     message(
       paste(
         strwrap("Hale, Thomas, Sam Webster, Anna Petherick, Toby Phillips, and
-                Beatriz Kira (2020). Oxford COVID-19 Government Response Tracker,
-                Blavatnik School of Government.",
+                Beatriz Kira (2020). Oxford COVID-19 Government Response
+                Tracker, Blavatnik School of Government.",
                 width = 80),
         "\n"
       )