Merge pull request #24 from Big-Life-Lab/cran-hotfix

Cran hotfix

.Rbuildignore

@@ -8,3 +8,4 @@
 ^cran-comments\.md$
 ^README.html
 ^CRAN-RELEASE$
+^CODE_OF_CONDUCT.md

CODE_OF_CONDUCT.md

@@ -0,0 +1,25 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, 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, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or
+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
+insults, or other 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. Project maintainers who do not follow the Code of Conduct may be removed
+from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by
+opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant
+(http://contributor-covenant.org), version 1.0.0, available at
+http://contributor-covenant.org/version/1/0/0/

CONTRIBUTING.md

@@ -6,11 +6,11 @@ This page outlines how to contribute to the `cchsflow` package.
 
 ### Transforming existing CCHS variables
 
-Using the naming conventions described in the [`variables.csv`](https://big-life-lab.github.io/cchsflow/articles/variablesSheet.html) and [`variableDetails.csv`](https://big-life-lab.github.io/cchsflow/articles/variableDetails.html) you can add more CCHS variables that can be transformed and harmonized across cycles.
+Using the naming conventions described in the [`variables.csv`](https://big-life-lab.github.io/cchsflow/articles/variables_sheet.html) and [`variable_details.csv`](https://big-life-lab.github.io/cchsflow/articles/variable_details.html) you can add more CCHS variables that can be transformed and harmonized across cycles.
 
 ### Creating a derived variable
 
-You will first need to create a custom function that will carry out the necessary transformations needed for your derived variable. You will then need to specify your derived variable on `variables.csv` and `variableDetails.csv`. For more information, [click here]('~../Vignettes/howtoaddvariables.html').
+You will first need to create a custom function that will carry out the necessary transformations needed for your derived variable. You will then need to specify your derived variable on `variables.csv` and `variable_details.csv`. For more information, [click here](https://big-life-lab.github.io/cchsflow/articles/how_to_add_variables.html).
 
 ## Documentation
 
@@ -37,11 +37,11 @@ bug, you may also create an associated issue. If possible, try to illustrate you
 ## Pull request
 
 *  Please create a Git branch for each pull request (PR). [Click here](https://help.github.com/en/articles/creating-a-pull-request-from-a-fork) for information on how to create a PR.
-*  Your contributed code should roughly follow the tidyverse [style guide](http://style.tidyverse.org). _Exceptions_ from this guide: function names in PascalCase (e.g. NewFunction()) and variable names as camelCase (e.g newVariable <- "hi").
+*  Your contributed code should roughly follow the tidyverse [style guide](http://style.tidyverse.org).
 *  cchsflow uses [roxygen2](https://cran.r-project.org/package=roxygen2), with
-[Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/markdown.html),
+[Markdown syntax](https://bookdown.org/yihui/rmarkdown/markdown-syntax.html),
 for documentation.
-*  cchsflow uses [testthat](https://cran.r-project.org/package=testthat) (TBA). Adding tests to the PR makes it easier for me to merge your PR into the code base.
+*  cchsflow uses [testthat](https://cran.r-project.org/package=testthat). Adding tests to the PR makes merging the PR into the code base less prone to bugs.
 *  If your PR is a user-visible change, you may add a bullet to the top of `NEWS.md` describing the changes made. You may optionally add your GitHub username, and links to relevant issue(s)/PR(s).
 
 ## Code of Conduct

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: cchsflow
 Type: Package
 Title: Transforming and Harmonizing CCHS Variables
-Version: 1.0.1
+Version: 1.1.0
 Authors@R: c(
     person(given = "Doug",
            family = "Manuel",
-           role = c("aut"),
+           role = c("aut", "cph"),
            email = "[email protected]",
            comment = c(ORCID = "0000-0003-0912-0845")),
     person(given = "Warsame",
@@ -23,19 +23,26 @@ Authors@R: c(
     person(given = "Yulric", 
           family = "Sequeira",
           role = c("ctb"),
-          email = "[email protected]"))
+          email = "[email protected]"),
+    person(given = "The Ottawa Hospital",
+          role = c("cph"),
+          email = "[email protected]"))
 Depends:
   R (>= 3.2),
   haven (>= 1.1.2),
   dplyr (>= 0.8.2),
   sjlabelled (>= 1.0.17),
   stringr (>= 1.2.0),
   magrittr
-Description: Variable transformation and harmonization for the Canadian Community Health Survey from
-            2001 to 2014.
+Description: Variable transformation and harmonization of the Canadian Community Health Survey (CCHS) from
+            2001 to 2014. This is useful for researchers interested in using Canadian population health data
+            across multiple years as it helps combine variables. This package relies on rec_with_table() which was based off sjmisc rec().
+            Lüdecke D (2018). sjmisc: Data and Variable Transformation Functions. Journal of Open Source Software, 3(26), 754. doi: 10.21105/joss.00754.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 URL: https://github.com/Big-Life-Lab/cchsflow
 BugReports: https://github.com/Big-Life-Lab/cchsflow/issues
 RoxygenNote: 7.0.2
+Suggests: 
+    testthat (>= 2.1.0)

NEWS.md

@@ -1,4 +1,31 @@
-# cchsflow 1.0.1 (Latest build)
+# cchsflow 1.1.0 (Latest build)
+2020-01-08
+
+## Breaking changes
+
+* Changed `data_source` parameter in `rec_with_table()` to `data`.
+
+* Changed order of parameters to have `variables` after `dataset_name`.
+
+## New features
+
+- Added warnings to `set_data_labels()` when a variable is present in details 
+    but missing in variables and vice versa.
+- Added automated testing for functions
+
+## Minor improvements and bug fixes
+
+- Updated `DESCRIPTION` to expand description of package and added The Ottawa
+   Hospital as author.
+- Refactored `age_cat_fun()` to account for age below 0 and include warning
+   messages for respiratory functions.
+- Added trailing white space removal to `set_data_labels()`.
+- Added trailing white space removal to startVariable during `rec_with_table()`.
+- Added missing contributing code of conduct page.
+- Minor formatting changes on vignettes and `README.md` for better clarity.
+- Fixed broken links in articles.
+
+# cchsflow 1.0.1 
 2019-12-19
 
 ## Features

R/age-categorical.R

@@ -30,12 +30,29 @@
 #'  CCHS cycles. As such, a continuous age variable (DHHGAGE_cont) was created
 #'  that harmonized age across all CCHS cycles by taking the midpoint of each
 #'  age category. This new age variable (DHHGAGE_C) categorizes age based on the
-#'  categories used in CCHS cycles from 2007 to 2014.  
+#'  categories used in CCHS cycles from 2007 to 2014.
 #'
 #' @param DHHGAGE_cont continuous age variable
-#' 
+#'
 #' @return a categorical age variable (DHHGAGE_C)
 #'
+#' @examples
+#' # Using age_cat_fun() to create categorical age values from DHHGAGE_cont
+#' # age_cat_fun() is specified in variable_details.csv along with the CCHS
+#' # variables and cycles included.
+#'
+#' # To generate DHHGAGE_C in a cycle, use rec_with_table() and specify
+#' # DHHGAGE_C along with DHHGAGE_cont.
+#'
+#' library(cchsflow)
+#'
+#' cat_age2010 <- rec_with_table(
+#'    data = cchs2010, variable_details =
+#'      variable_details, dataset_name = "cchs2010", variables = c(
+#'      "DHHGAGE_cont", "DHHGAGE_C"
+#'      )
+#'    )
+#'
 #' @export
 age_cat_fun <- function(DHHGAGE_cont) {
   if_else2(

R/alcohol.R

@@ -16,6 +16,10 @@
 #' @param ALWDWKY cchsflow variable name for number of drinks consumed in the
 #'  past week
 #'
+#' @examples
+#' library(cchsflow)
+#'  ?ALWDWKY
+#'
 #' @export
 ALWDWKY <- function(ALWDWKY) {
   # this is for documentation purposes only
@@ -34,6 +38,10 @@ ALWDWKY <- function(ALWDWKY) {
 #'
 #' @param ALWDDLY cchsflow variable name for average daily alcohol consumption
 #'
+#' @examples
+#' library(cchsflow)
+#'  ?ALWDDLY
+#'
 #' @export
 ALWDDLY <- function(ALWDDLY) {
   # this is for documentation purposes only
@@ -65,6 +73,10 @@ ALWDDLY <- function(ALWDDLY) {
 #'
 #' @param ALCDTYP cchsflow variable name for type of drinker
 #'
+#' @examples
+#' library(cchsflow)
+#'  ?ALCDTYP
+#'
 #' @export
 ALCDTYP <- function(ALCDTYP) {
   # this is for documentation purposes only
@@ -91,6 +103,10 @@ ALCDTYP <- function(ALCDTYP) {
 #'
 #' @param ALCDTTM cchsflow variable name for type of drinker (12 months)
 #'
+#' @examples
+#' library(cchsflow)
+#'  ?ALCDTTM
+#'
 #' @export
 ALCDTTM <- function(ALCDTTM) {
   # this is for documentation purposes only

R/bmi.R

@@ -52,7 +52,7 @@
 #'
 #' library(cchsflow)
 #' bmi2010 <- rec_with_table(
-#'   data_source = cchs2010, variable_details =
+#'   data = cchs2010, variable_details =
 #'     variable_details, dataset_name = "cchs2010", variables = c(
 #'     "HWTGHTM",
 #'     "HWTGWTK", "HWTGBMI_der"
@@ -62,7 +62,7 @@
 #' head(bmi2010)
 #'
 #' bmi2012 <- rec_with_table(
-#'   data_source = cchs2012, variable_details =
+#'   data = cchs2012, variable_details =
 #'     variable_details, dataset_name = "cchs2012", variables = c(
 #'     "HWTGHTM",
 #'     "HWTGWTK", "HWTGBMI_der"

R/label-utils.R

@@ -6,6 +6,37 @@
 #' @param data_to_label newly transformed dataset
 #' @param variable_details variable_details.csv
 #' @param variables_sheet variables.csv
+#'
+#' @return labeled data_to_label
+#'
+#' @examples
+#' library(cchsflow)
+#' library(sjlabelled)
+#' bmi2010 <- rec_with_table(
+#'   data = cchs2010, variable_details =
+#'     variable_details, dataset_name = "cchs2010", variables = c(
+#'     "HWTGHTM",
+#'     "HWTGWTK", "HWTGBMI_der"
+#'   )
+#' )
+#'
+#' bmi2012 <- rec_with_table(
+#'   data = cchs2012, variable_details =
+#'     variable_details, dataset_name = "cchs2012", variables = c(
+#'     "HWTGHTM",
+#'     "HWTGWTK", "HWTGBMI_der"
+#'   )
+#' )
+#'
+#' combined_bmi <- bind_rows(bmi2010, bmi2012)
+#'
+#' get_label(combined_bmi)
+#'
+#' labeled_combined_data <- set_data_labels(combined_bmi,
+#'  variable_details,
+#'  variables)
+#'
+#' get_label(labeled_combined_data)
 #' @export
 set_data_labels <-
   function(data_to_label,
@@ -15,6 +46,8 @@ set_data_labels <-
     variable_names <- unique(colnames(data_to_label))
     # extract only relevant variable info
     if (!is.null(variable_details)) {
+      variable_details[[pkg.globals$argument.Variables]] <- sapply(
+        variable_details[[pkg.globals$argument.Variables]], trimws)
       variable_details <-
         variable_details[variable_details[[pkg.globals$argument.Variables]]
                          %in% variable_names, ]
@@ -25,6 +58,8 @@ set_data_labels <-
       }
     }
     if (!is.null(variables_sheet)) {
+      variables_sheet[[pkg.globals$argument.Variables]] <- sapply(
+        variables_sheet[[pkg.globals$argument.Variables]], trimws)
       variables_sheet <-
         variables_sheet[variables_sheet[[pkg.globals$argument.Variables]] %in%
                           variable_names, ]
@@ -137,6 +172,12 @@ create_label_list_element <- function(variable_rows) {
 #' @return Returns labeled data
 label_data <- function(label_list, data_to_label) {
   for (variable_name in names(label_list)) {
+    if (is.na(label_list[[variable_name]]$type)) {
+      warning(paste(variable_name,
+                    "is missing from variable_details or variables
+                    (if it was also passed) please verify correct spelling"))
+      next()
+    }
     if (label_list[[variable_name]]$type == pkg.globals$argument.CatType) {
       if (class(data_to_label[[variable_name]]) != "factor") {
         data_to_label[[variable_name]] <-

R/percent-time-canada.R

@@ -34,7 +34,7 @@
 #'
 #' library(cchsflow)
 #' pct_time2010 <- rec_with_table(
-#'   data_source = cchs2010, variable_details = variable_details,
+#'   data = cchs2010, variable_details = variable_details,
 #'   dataset_name = "cchs2010", variables = c(
 #'     "DHHGAGE_cont", "SDCGCBG",
 #'     "SDCGRES", "pct_time_der"
@@ -43,7 +43,7 @@
 #' head(pct_time2010)
 #'
 #' pct_time2012 <- rec_with_table(
-#'   data_source = cchs2012, variable_details = variable_details,
+#'   data = cchs2012, variable_details = variable_details,
 #'   dataset_name = "cchs2012", variables = c(
 #'     "DHHGAGE_cont", "SDCGCBG",
 #'     "SDCGRES", "pct_time_der"
@@ -66,15 +66,11 @@
 #' @export
 pct_time_fun <-
   function(DHHGAGE_cont, SDCGCBG, SDCGRES) {
-    SDCGRES_fun <- function(SDCGRES) {
-      if_else2(
-        SDCGRES == 1, 4.5,
-        if_else2(SDCGRES == 2, 15, NA)
-      )
+    if (is_equal(SDCGCBG, 1)) {
+      return(1)
     }
-    SDCGRES <- SDCGRES_fun(SDCGRES)
-    if_else2(
-      SDCGCBG == 1, 1,
-      if_else2(SDCGCBG == 2, (SDCGRES / DHHGAGE_cont), NA)
-    )
+    DHHGAGE_cont <- if_else2(DHHGAGE_cont > 0, DHHGAGE_cont, return(NA))
+    SDCGRES <- if_else2(SDCGRES == 1, 4.5,
+                        if_else2(SDCGRES == 2, 15, return(NA)))
+    if_else2(SDCGCBG == 2, (SDCGRES / DHHGAGE_cont), NA)
   }