fix CRAN URL to be canonical format to please R CMD check

jackwasey · Sep 3, 2015 · 02463d1 · 02463d1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,7 +9,7 @@ Description: Calculate comorbidities, Charlson scores, perform fast and accurate
     from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. Any
     other mapping of codes, such as ICD-10, to comorbidities can be used.
 Version: 1.2.1
-Date: 2015-04-20
+Date: 2015-09-03
 Authors@R: c(
     person(given = "Jack O.", family = "Wasey", role = c("aut", "cre", "cph"),
     email = c("jack@jackwasey.com")),

diff --git a/NEWS.md b/NEWS.md
@@ -35,7 +35,7 @@
 * Bug fixes (see [github](https://github.com/jackwasey/icd9/issues?q=is%3Aissue+is%3Aclosed))
 * API changes
     - no more validation except in the icd9IsValidXxx functions. Removed stopIfInvalidIcd9, icd9InvalidActions
-    - internalized utility functions. They are also packaged and tested in [jwutil](http://cran.r-project.org/web/packages/jwutil/index.html)
+    - internalized utility functions. They are also packaged and tested in [jwutil](https://github.com/jackwasey/jwutil)
     - deprecated icd9ValidXxx in favour of icd9IsValidXxx
     - deprecated icd9ComorbditiesXxx replacing with briefer icd9ComorbidXxx
     - stopped exporting benchmarking and SAS code processing.

diff --git a/R/util.R b/R/util.R
@@ -73,9 +73,6 @@ saveInDataDir <- function(var, suffix = "") {
 #' @description when saving data as text files for distribution, printing large
 #'   amounts of text containing TRUE and FALSE is inefficient. Convert to binary
 #'   takes more R memory, but allows more compact output
-#' @details Taken from my
-#'   \href{https://github.com/jackwasey/jwutil}{\code{jwutil} package}, which is
-#'   also intermittently on CRAN
 #' @param x dataframe which may contain logical fields
 #' @return data frame without logical fields
 #' @keywords internal manip
@@ -103,9 +100,6 @@ logicalToBinary <- function(x) {
 #' @description Be careful: this may throw funny results for exotic regex, but
 #'   so far, it seems okay. it also drops the first result which always seems to
 #'   be a duplicate or whole-string match.
-#' @details Taken from my
-#'   \href{http://cran.r-project.org/web/packages/jwutil/index.html}{\code{jwutil}
-#'   package}.
 #' @param pattern regular expression: if it has bracketed sections, these
 #'   submatches are returned
 #' @param text is the string to match against. This vector should be the same

diff --git a/README.Rmd b/README.Rmd
@@ -29,8 +29,8 @@ patientData <- data.frame(
 # icd9
 
 [![Build Status](https://travis-ci.org/jackwasey/icd9.svg?branch=master)](https://travis-ci.org/jackwasey/icd9) [![Coverage Status](https://coveralls.io/repos/jackwasey/icd9/badge.svg?branch=master)](https://coveralls.io/r/jackwasey/icd9?branch=master)
-[![CRAN version](http://www.r-pkg.org/badges/version/icd9)](http://cran.r-project.org/web/packages/icd9/index.html)
-[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/icd9)](http://cran.r-project.org/web/packages/icd9/index.html) (RStudio mirror only)
+[![CRAN version](http://www.r-pkg.org/badges/version/icd9)](https://cran.r-project.org/package=icd9)
+[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/icd9)](https://cran.r-project.org/package=icd9) (RStudio mirror only)
 
 # ICD-9 comorbidities, manipulation and validation
 

diff --git a/README.md b/README.md
@@ -1,8 +1,9 @@
 <!-- README.md is generated from README.Rmd. Please edit that file and render with rmarkdown::render("README.Rmd")-->
+
 icd9
 ====
 
-[![Build Status](https://travis-ci.org/jackwasey/icd9.svg?branch=master)](https://travis-ci.org/jackwasey/icd9) [![Coverage Status](https://coveralls.io/repos/jackwasey/icd9/badge.svg?branch=master)](https://coveralls.io/r/jackwasey/icd9?branch=master) [![CRAN version](http://www.r-pkg.org/badges/version/icd9)](http://cran.r-project.org/web/packages/icd9/index.html) [![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/icd9)](http://cran.r-project.org/web/packages/icd9/index.html) (RStudio mirror only)
+[![Build Status](https://travis-ci.org/jackwasey/icd9.svg?branch=master)](https://travis-ci.org/jackwasey/icd9) [![Coverage Status](https://coveralls.io/repos/jackwasey/icd9/badge.svg?branch=master)](https://coveralls.io/r/jackwasey/icd9?branch=master) [![CRAN version](http://www.r-pkg.org/badges/version/icd9)](https://cran.r-project.org/package=icd9) [![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/icd9)](https://cran.r-project.org/package=icd9) (RStudio mirror only)
 
 ICD-9 comorbidities, manipulation and validation
 ================================================
@@ -47,7 +48,7 @@ Examples
 
 See the vignette and code help for many more. Here's a taste:
 
-``` r
+``` {.r}
 patientData
 #>   visitId  icd9  poa
 #> 1    1000 40201    Y

diff --git a/man/logicalToBinary.Rd b/man/logicalToBinary.Rd
@@ -17,11 +17,6 @@ when saving data as text files for distribution, printing large
   amounts of text containing TRUE and FALSE is inefficient. Convert to binary
   takes more R memory, but allows more compact output
 }
-\details{
-Taken from my
-  \href{https://github.com/jackwasey/jwutil}{\code{jwutil} package}, which is
-  also intermittently on CRAN
-}
 \keyword{internal}
 \keyword{manip}
 
diff --git a/man/strMultiMatch.Rd b/man/strMultiMatch.Rd
@@ -39,10 +39,5 @@ Be careful: this may throw funny results for exotic regex, but
   pairs of parenthesis, then the first (by default) becomes the name, and the
   second the value.
 }
-\details{
-Taken from my
-  \href{http://cran.r-project.org/web/packages/jwutil/index.html}{\code{jwutil}
-  package}.
-}
 \keyword{internal}
 
diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd
@@ -65,7 +65,7 @@ or
 ```{r getcomorbidities1a}
 icd9ComorbidQuanDeyo(patientData)[, 1:8]
 ```
-and things work beautifully using [magrittr](http://cran.r-project.org/web/packages/magrittr/index.html) `%>%` to chain functions together. This is not a dependency for this package, but is recommended because of the frequent need to chain together icd9 commands, and greater clarity.
+and things work beautifully using [magrittr](https://cran.r-project.org/package=magrittr) `%>%` to chain functions together. This is not a dependency for this package, but is recommended because of the frequent need to chain together icd9 commands, and greater clarity.
 ```{r getcomorbidities2}
 patientData %>% icd9FilterPoaYes %>% icd9ComorbidAhrq %>% extract(1:8)
 ```
@@ -326,4 +326,4 @@ data.frame(icd9 = lost_since_27, desc = lost_since_27 %>% icd9Explain)
 
 ## Conclusion
 
-This package allows fluid, fast and accurate manipulation of ICD-9 codes, especially when combined with [magrittr](http://cran.r-project.org/web/packages/magrittr/index.html). Suggestions, contributions and comments are welcome via [github](https://github.com/jackwasey/icd9/issues).
+This package allows fluid, fast and accurate manipulation of ICD-9 codes, especially when combined with [magrittr](https://cran.r-project.org/package=magrittr). Suggestions, contributions and comments are welcome via [github](https://github.com/jackwasey/icd9/issues).