Merge pull request #220 from billdenney/release-prep

Prepare for CRAN submission
billdenney · Apr 30, 2023 · 9aab34d · 9aab34d
2 parents 7ab87da + 4856333
commit 9aab34d
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Showing 9 changed files with 37 additions and 12 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -13,6 +13,8 @@ S3method(PKNCAdose,tbl_df)
 S3method(as.data.frame,PKNCAconc)
 S3method(as.data.frame,PKNCAdose)
 S3method(as.data.frame,PKNCAresults)
+S3method(dplyr::group_vars,PKNCAconc)
+S3method(dplyr::group_vars,PKNCAdose)
 S3method(exclude,default)
 S3method(filter,PKNCAconc)
 S3method(filter,PKNCAdose)
@@ -22,6 +24,9 @@ S3method(formula,PKNCAdose)
 S3method(full_join,PKNCAconc)
 S3method(full_join,PKNCAdose)
 S3method(full_join,PKNCAresults)
+S3method(getDataName,PKNCAconc)
+S3method(getDataName,PKNCAdose)
+S3method(getDataName,PKNCAresults)
 S3method(getDepVar,PKNCAconc)
 S3method(getDepVar,PKNCAdose)
 S3method(getGroups,PKNCAconc)
@@ -35,6 +40,9 @@ S3method(group_by,PKNCAresults)
 S3method(inner_join,PKNCAconc)
 S3method(inner_join,PKNCAdose)
 S3method(inner_join,PKNCAresults)
+S3method(is_sparse_pk,PKNCAconc)
+S3method(is_sparse_pk,PKNCAdata)
+S3method(is_sparse_pk,PKNCAresults)
 S3method(left_join,PKNCAconc)
 S3method(left_join,PKNCAdose)
 S3method(left_join,PKNCAresults)
@@ -51,6 +59,7 @@ S3method(print,summary_PKNCAresults)
 S3method(right_join,PKNCAconc)
 S3method(right_join,PKNCAdose)
 S3method(right_join,PKNCAresults)
+S3method(setDuration,PKNCAconc)
 S3method(setDuration,PKNCAdose)
 S3method(setRoute,PKNCAdose)
 S3method(signifString,data.frame)

diff --git a/R/class-PKNCAconc.R b/R/class-PKNCAconc.R
@@ -203,6 +203,7 @@ formula.PKNCAconc <- function(x, ...) {
 #' order.
 #' @export
 #' @importFrom stats model.frame
+#' @method model.frame PKNCAconc
 model.frame.PKNCAconc <- function(formula, ...) {
   formula$data[, all.vars(formula$formula), drop=FALSE]
 }
@@ -265,6 +266,7 @@ group_vars.PKNCAconc <- function(x) {
 }
 
 #' @rdname getDataName
+#' @export
 getDataName.PKNCAconc <- function(object) {
   if (is_sparse_pk(object)) {
     "data_sparse"
@@ -273,6 +275,8 @@ getDataName.PKNCAconc <- function(object) {
   }
 }
 
+#' @rdname setDuration
+#' @export
 setDuration.PKNCAconc <- function(object, duration, ...) {
   if (missing(duration)) {
     object <-
@@ -364,6 +368,7 @@ print.PKNCAconc <- function(x, n=6, summarize=FALSE, ...) {
 }
 
 #' @rdname is_sparse_pk
+#' @export
 is_sparse_pk.PKNCAconc <- function(object) {
   "data_sparse" %in% names(object)
 }

diff --git a/R/class-PKNCAdata.R b/R/class-PKNCAdata.R
@@ -191,6 +191,7 @@ PKNCAdata.default <- function(data.conc, data.dose, ...,
 }
 
 #' @rdname is_sparse_pk
+#' @export
 is_sparse_pk.PKNCAdata <- function(object) {
   is_sparse_pk(object$conc)
 }

diff --git a/R/class-PKNCAdose.R b/R/class-PKNCAdose.R
@@ -50,12 +50,14 @@ PKNCAdose <- function(data, ...)
 
 #' @rdname PKNCAdose
 #' @export
-PKNCAdose.default <- function(data, ...)
+PKNCAdose.default <- function(data, ...) {
   PKNCAdose.data.frame(as.data.frame(data), ...)
+}
 #' @rdname PKNCAdose
 #' @export
-PKNCAdose.tbl_df <- function(data, ...)
+PKNCAdose.tbl_df <- function(data, ...) {
   PKNCAdose.data.frame(as.data.frame(data), ...)
+}
 
 #' @rdname PKNCAdose
 #' @export
@@ -242,6 +244,7 @@ formula.PKNCAdose <-  function(x, ...) {
 #' @rdname model.frame.PKNCAconc
 #' @export
 #' @importFrom stats model.frame
+#' @method model.frame PKNCAdose
 model.frame.PKNCAdose <- function(formula, ...) {
   cbind(getDepVar.PKNCAdose(formula),
         getIndepVar.PKNCAdose(formula),
@@ -281,8 +284,10 @@ group_vars.PKNCAdose <- function(x) {
 }
 
 #' @rdname getDataName
-getDataName.PKNCAdose <- function(object)
+#' @export
+getDataName.PKNCAdose <- function(object) {
   "data"
+}
 
 #' @rdname print.PKNCAconc
 #' @export

diff --git a/R/class-PKNCAresults.R b/R/class-PKNCAresults.R
@@ -59,11 +59,13 @@ as.data.frame.PKNCAresults <- function(x, ..., out.format=c('long', 'wide')) {
 }
 
 #' @rdname getDataName
+#' @export
 getDataName.PKNCAresults <- function(object) {
   "result"
 }
 
 #' @rdname is_sparse_pk
+#' @export
 is_sparse_pk.PKNCAresults <- function(object) {
   is_sparse_pk(object$data)
 }

diff --git a/R/pk.calc.urine.R b/R/pk.calc.urine.R
@@ -32,7 +32,7 @@ pk.calc.ae <- function(conc, volume, check=TRUE) {
   } else if (any(mask_missing_vol)) {
     message_vol <- sprintf("%g of %g volumes are missing", sum(mask_missing_vol), length(conc))
   }
-  message_all <- na.omit(c(message_both, message_conc, message_vol))
+  message_all <- stats::na.omit(c(message_both, message_conc, message_vol))
   ret <- sum(conc*volume)
   if (length(message_all) != 0) {
     message <- paste(message_all, collapse = "; ")

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 <!-- badges: start -->
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/PKNCA)](https://cran.r-project.org/package=PKNCA)
 [![R-CMD-check](https://github.com/billdenney/pknca/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/billdenney/pknca/actions/workflows/R-CMD-check.yaml)
-[![Code_Coverage_Badge](https://codecov.io/github/billdenney/pknca/coverage.svg?branch=main)](https://codecov.io/github/billdenney/pknca?branch=main)
+[![Code_Coverage_Badge](https://codecov.io/github/billdenney/pknca/coverage.svg?branch=main)](https://app.codecov.io/github/billdenney/pknca?branch=main)
 [![CodeFactor](https://www.codefactor.io/repository/github/billdenney/pknca/badge?style=plastic)](https://www.codefactor.io/repository/github/billdenney/pknca)
 [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/2054/badge)](https://bestpractices.coreinfrastructure.org/projects/2054)
 <!-- badges: end -->

diff --git a/man/group_vars.PKNCAconc.Rd b/man/group_vars.PKNCAconc.Rd
diff --git a/man/setDuration.Rd b/man/setDuration.Rd