diff --git a/R/utils.R b/R/utils.R index be1e1c6..d172f67 100644 --- a/R/utils.R +++ b/R/utils.R @@ -176,6 +176,7 @@ recode_sex <- function(input_data, #' @rawNamespace import(tidyr, except = extract) #' @rawNamespace import(dplyr, except = c(last, first, summarize, src, between)) #' @examples +#' \donttest{ #' # Run on a small subset of given data #' df <- as.data.frame(syngrowth) #' df <- df[df$subjid %in% unique(df[, "subjid"])[1:2], ] @@ -193,6 +194,7 @@ recode_sex <- function(input_data, #' #' # Specify all inclusion codes #' wide_df <- longwide(df, inclusion_types = c("Include", "Exclude-Carried-Forward")) +#' } longwide <- function(long_df, id = "id", @@ -329,6 +331,7 @@ longwide <- #' @import data.table #' @rawNamespace import(dplyr, except = c(last, first, summarize, src, between)) #' @examples +#' \donttest{ #' # Simple usage #' # Run on a small subset of given data #' df <- as.data.frame(syngrowth) @@ -347,6 +350,7 @@ longwide <- #' colnames(wide_df)[colnames(wide_df) %in% c("wt", "ht")] <- #' c("weight", "height") #' wide_df_with_bmi <- simple_bmi(wide_df, wtcol = "weight", htcol = "height") +#' } simple_bmi <- function(wide_df, wtcol = "wt", htcol = "ht") { # Verify the specified columns are present if (!all(c(wtcol, htcol) %in% colnames(wide_df))) { diff --git a/cran-comments.md b/cran-comments.md index a0d1e40..63d7611 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,3 +1,44 @@ +# CRAN submission growthcleanr 2.2.0 (2) + +## R CMD check results +There were no ERRORs or WARNINGs. + +There was one NOTE: + +❯ checking installed package size ... NOTE + installed size is 5.9Mb + sub-directories of 1Mb or more: + extdata 5.0Mb + +extdata has been compressed as much as possible -- data in that folder is necessary to run the package. + +## Downstream dependencies +There are currently no downstream dependencies for this package. + +## CRAN test + +We have addressed each of the notes in the test as noted below: + +* Maintainer: 'Carrie Daymont ' + + Size of tarball: 5529566 bytes + +The package has been compressed as much as possible, as noted above -- data included is necessary to run the package. + +* NOTE + Examples with CPU (user + system) or elapsed time > 5s + user system elapsed + simple_bmi 6.542 0.218 0.622 + longwide 6.344 0.230 0.858 + Examples with CPU time > 2.5 times elapsed time + user system elapsed ratio + simple_bmi 6.542 0.218 0.622 10.868 + longwide 6.344 0.230 0.858 7.662 + +Examples have been set to donttest. + +# Previous Submissions + # CRAN submission growthcleanr 2.2.0 (1) ## R CMD check results @@ -47,8 +88,6 @@ Running R code in ‘testthat.R’ had CPU time 3.1 times elapsed time Tests have been set to not run on CRAN. -# Previous Submissions - # CRAN submission growthcleanr 2.2.0 ## R CMD check results diff --git a/docs/articles/adult-algorithm.html b/docs/articles/adult-algorithm.html index 3bd2cb6..005f2e3 100644 --- a/docs/articles/adult-algorithm.html +++ b/docs/articles/adult-algorithm.html @@ -116,7 +116,7 @@

Adult algorithm

-

2023-09-15

+

2024-02-05

Source: vignettes/adult-algorithm.Rmd diff --git a/docs/articles/configuration.html b/docs/articles/configuration.html index c4e025c..4aa5f6e 100644 --- a/docs/articles/configuration.html +++ b/docs/articles/configuration.html @@ -116,7 +116,7 @@

Configuration

-

2023-09-15

+

2024-02-05

Source: vignettes/configuration.Rmd diff --git a/docs/articles/developer-guidelines.html b/docs/articles/developer-guidelines.html index a876afa..40e9284 100644 --- a/docs/articles/developer-guidelines.html +++ b/docs/articles/developer-guidelines.html @@ -116,7 +116,7 @@

Developer guidelines

-

2023-09-15

+

2024-02-05

Source: vignettes/developer-guidelines.Rmd diff --git a/docs/articles/installation.html b/docs/articles/installation.html index 3780c7d..af7aa6f 100644 --- a/docs/articles/installation.html +++ b/docs/articles/installation.html @@ -116,7 +116,7 @@

Installation

-

2023-09-15

+

2024-02-05

Source: vignettes/installation.Rmd diff --git a/docs/articles/large-data-sets.html b/docs/articles/large-data-sets.html index cc7177a..accc8de 100644 --- a/docs/articles/large-data-sets.html +++ b/docs/articles/large-data-sets.html @@ -116,7 +116,7 @@

Working with large data sets

-

2023-09-15

+

2024-02-05

Source: vignettes/large-data-sets.Rmd diff --git a/docs/articles/next-steps.html b/docs/articles/next-steps.html index 30c69ce..c6c9aa7 100644 --- a/docs/articles/next-steps.html +++ b/docs/articles/next-steps.html @@ -116,7 +116,7 @@

Next steps

-

2023-09-15

+

2024-02-05

Source: vignettes/next-steps.Rmd diff --git a/docs/articles/output.html b/docs/articles/output.html index 0e65d5e..88bf09e 100644 --- a/docs/articles/output.html +++ b/docs/articles/output.html @@ -116,7 +116,7 @@

Understanding growthcleanr output

-

2023-09-15

+

2024-02-05

Source: vignettes/output.Rmd diff --git a/docs/articles/prelim-infants-algorithm.html b/docs/articles/prelim-infants-algorithm.html index b263235..89c5ec7 100644 --- a/docs/articles/prelim-infants-algorithm.html +++ b/docs/articles/prelim-infants-algorithm.html @@ -116,7 +116,7 @@

Preliminary infants algorithm

-

2023-09-15

+

2024-02-05

Source: vignettes/prelim-infants-algorithm.Rmd diff --git a/docs/articles/quickstart.html b/docs/articles/quickstart.html index 252f0e7..ade9813 100644 --- a/docs/articles/quickstart.html +++ b/docs/articles/quickstart.html @@ -116,7 +116,7 @@

Quickstart

-

2023-09-15

+

2024-02-05

Source: vignettes/quickstart.Rmd diff --git a/docs/articles/usage.html b/docs/articles/usage.html index 3cf304a..8e78577 100644 --- a/docs/articles/usage.html +++ b/docs/articles/usage.html @@ -116,7 +116,7 @@

Usage

-

2023-09-15

+

2024-02-05

Source: vignettes/usage.Rmd diff --git a/docs/articles/utilities.html b/docs/articles/utilities.html index 97e3f51..6f6ff3c 100644 --- a/docs/articles/utilities.html +++ b/docs/articles/utilities.html @@ -117,7 +117,7 @@

Utilities for computing pediatric BMI percentiles, Z-scores, and related tools

-

2023-09-15

+

2024-02-05

Source: vignettes/utilities.Rmd diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 40472c1..cad980b 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -13,5 +13,5 @@ articles: quickstart: quickstart.html usage: usage.html utilities: utilities.html -last_built: 2023-09-15T16:20Z +last_built: 2024-02-05T13:40Z diff --git a/docs/reference/longwide.html b/docs/reference/longwide.html index d53b5fa..3edd397 100644 --- a/docs/reference/longwide.html +++ b/docs/reference/longwide.html @@ -193,7 +193,8 @@

Value

Examples

- 
# Run on a small subset of given data
+    
# \donttest{
+# Run on a small subset of given data
 df <- as.data.frame(syngrowth)
 df <- df[df$subjid %in% unique(df[, "subjid"])[1:2], ]
 df <- cbind(df,
@@ -210,6 +211,7 @@ 
Examples

 
 # Specify all inclusion codes
 wide_df <- longwide(df, inclusion_types = c("Include", "Exclude-Carried-Forward"))
+# }
diff --git a/docs/reference/simple_bmi.html b/docs/reference/simple_bmi.html index ae32f9d..68a2e4e 100644 --- a/docs/reference/simple_bmi.html +++ b/docs/reference/simple_bmi.html @@ -126,7 +126,8 @@

Value

Examples

- 
# Simple usage
+    
# \donttest{
+# Simple usage
 # Run on a small subset of given data
 df <- as.data.frame(syngrowth)
 df <- df[df$subjid %in% unique(df[, "subjid"])[1:2], ]
@@ -144,6 +145,7 @@ 
Examples

 colnames(wide_df)[colnames(wide_df) %in% c("wt", "ht")] <-
   c("weight", "height")
 wide_df_with_bmi <- simple_bmi(wide_df, wtcol = "weight", htcol = "height")
+# }
diff --git a/man/longwide.Rd b/man/longwide.Rd index afc8964..1b579ab 100644 --- a/man/longwide.Rd +++ b/man/longwide.Rd @@ -70,6 +70,7 @@ transforming output from growthcleanr::cleangrowth() into a format suitable for growthcleanr::ext_bmiz(). } \examples{ +\donttest{ # Run on a small subset of given data df <- as.data.frame(syngrowth) df <- df[df$subjid \%in\% unique(df[, "subjid"])[1:2], ] @@ -88,3 +89,4 @@ wide_df <- longwide(df, include_all = TRUE) # Specify all inclusion codes wide_df <- longwide(df, inclusion_types = c("Include", "Exclude-Carried-Forward")) } +} diff --git a/man/simple_bmi.Rd b/man/simple_bmi.Rd index 553e494..4555c1c 100644 --- a/man/simple_bmi.Rd +++ b/man/simple_bmi.Rd @@ -22,6 +22,7 @@ Returns a data table with the added column "bmi" output from longwide(). } \examples{ +\donttest{ # Simple usage # Run on a small subset of given data df <- as.data.frame(syngrowth) @@ -41,3 +42,4 @@ colnames(wide_df)[colnames(wide_df) \%in\% c("wt", "ht")] <- c("weight", "height") wide_df_with_bmi <- simple_bmi(wide_df, wtcol = "weight", htcol = "height") } +}