From 02463d117423c235a12b4e6edb4fe5ab44815c5b Mon Sep 17 00:00:00 2001 From: Jack Wasey Date: Thu, 3 Sep 2015 14:04:55 -0400 Subject: [PATCH] fix CRAN URL to be canonical format to please R CMD check --- DESCRIPTION | 2 +- NEWS.md | 2 +- R/util.R | 6 ------ README.Rmd | 4 ++-- README.md | 5 +++-- man/logicalToBinary.Rd | 5 ----- man/strMultiMatch.Rd | 5 ----- vignettes/introduction.Rmd | 4 ++-- 8 files changed, 9 insertions(+), 24 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d403dce8..1912ad3a 100644 --- 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 index 7afa915d..292b97d8 100644 --- 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 index 2ab886e0..6901e8df 100644 --- 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 index c6810bb4..03ab9257 100644 --- 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 index 10cab205..61ced5af 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,9 @@ + 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 index ec78ed20..c768b6c6 100644 --- 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 index 5d9bbc2a..0149314b 100644 --- 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 index c5f1ca59..8678097b 100644 --- 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).