InsightRX · roninsightrx · May 9, 2022 · May 5, 2022 · May 5, 2022 · May 5, 2022
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: clinPK
 Type: Package
 Title: Clinical Pharmacokinetics Toolkit
-Version: 0.10.13
-Date: 2022-03-01
+Version: 0.11.1
+Date: 2022-05-06
 Authors@R: c(person("Ron", "Keizer", email = "ron@insight-rx.com", role
         = "aut"), person("Jasmine", "Hughes", email =
         "jasmine@insight-rx.com", role = "aut"), person("Dominic",
@@ -16,8 +16,8 @@ Description: Calculates equations commonly used in clinical
         chemistry, and conversion of common clinical parameters. Where
         possible and relevant, it provides multiple published and
         peer-reviewed equations within the respective R function.
+URL: https://github.com/InsightRX/clinPK
 License: MIT + file LICENSE
-LazyData: TRUE
 RoxygenNote: 7.1.2
 Suggests: testthat (>= 3.0.0)
 Config/testthat/edition: 3
diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2021
+YEAR: 2022
 COPYRIGHT HOLDER: InsightRX
diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1,17 @@
+# clinPK 0.11.1
+
+## Major changes
+- various corrections in nca() function
+- various updates to AKI staging equations: MDRD equation (use 2006 publication), kDIGO and PRIFLE
+- added equations of MDRD and CKD-EPI without race
+
+## Minor updates
+- refactor of calc_ibw()
+- fixed Boyd equation in calc_bsa()
+- added function to convert flow units
+- updates to 2-sample equation
+- added Cockcroft-Gault equation for spinal cord injury patients
+- consistent handling of missing/unrecognized data in `calc_ibw()`/`calc_ffm()`/`calc_egfr()`
+- various minor fixes and updates
+- various documentation updates
+- added many unit tests, increase overall coverage to >86%
diff --git a/R/calc_aki_stage.R b/R/calc_aki_stage.R
@@ -78,10 +78,10 @@ calc_aki_stage <- function (
 
   if(is.null(scr) && method !='prifle') stop("No serum creatinine values provided.")
   if(is.null(times) && method !='prifle') stop("No sample times (days) provided.")
-  if(class(times) == "Date") {
+  if(inherits(times, "Date")) {
     times <- as.numeric(difftime(times, min(times), units = "days"))
   }
-  if((!class(times[1]) %in% c("numeric","integer")) && method !='prifle') {
+  if(!inherits(times[1], c("numeric","integer")) && method !='prifle') {
     stop("`times` argument should be supplied either as days (numeric) or as Date class.")
   }
   if(length(scr) != length(times) && method !='prifle') stop("Serum creatinine values and vector of sample times should have same length.")
@@ -104,7 +104,7 @@ calc_aki_stage <- function (
     }
   }
   # pRIFLE does not require SCr
-  if(class(baseline_scr) == "character" && method !='prifle') {
+  if(inherits(baseline_scr, "character") && method !='prifle') {
     baseline_scr <- calc_baseline_scr(baseline_scr, 
                                       scr,
                                       times,

diff --git a/R/calc_baseline_scr.R b/R/calc_baseline_scr.R
@@ -16,7 +16,7 @@ calc_baseline_scr <- function(
       baseline_scr <- stats::median(scr, na.rm = TRUE)
       if(verbose) message("To calculate median baseline before treatment start need time of first dose. Using median over whole treatment period.")
     } else {
-      if((!class(first_dose_time) %in% c("numeric","integer"))) {
+      if((!inherits(first_dose_time, c("numeric","integer")))) {
         stop("`first_dose_times` argument should be supplied as numeric (hours).")
       }
       if(any(times <= first_dose_time)) {
@@ -48,7 +48,7 @@ calc_baseline_scr <- function(
   if(baseline_scr == "expected" && method !='prifle') {
     ## TODO: need to implement
   }
-  if(! class(baseline_scr) %in% c("numeric", "integer")) {
+  if(! inherits(baseline_scr, c("numeric", "integer"))) {
     stop("Requested baseline calculation method not recognized.")
   }
 

diff --git a/R/calc_egfr.R b/R/calc_egfr.R
@@ -53,16 +53,16 @@
 #' @param fail invoke `stop()` if not all covariates available?
 #' @param ... arguments passed on to `calc_abw` or `calc_dosing_weight`
 #' @references \itemize{
-#'   \item Cockcroft-Gault: \href{http://www.ncbi.nlm.nih.gov/pubmed/1244564}{Cockcroft & Gault, Nephron (1976)}
-#'   \item Cockcroft-Gault for spinal cord injury: \href{https://www.ncbi.nlm.nih.gov/pubmed/6835689}{Mirahmadi et al., Paraplegia (1983)}
-#'   \item Revised Lund-Malmo: \href{http://www.ncbi.nlm.nih.gov/pubmed/24334413}{Nyman et al., Clinical Chemistry and Laboratory Medicine (2014)}
+#'   \item Cockcroft-Gault: \href{https://pubmed.ncbi.nlm.nih.gov/1244564/}{Cockcroft & Gault, Nephron (1976)}
+#'   \item Cockcroft-Gault for spinal cord injury: \href{https://pubmed.ncbi.nlm.nih.gov/6835689/}{Mirahmadi et al., Paraplegia (1983)}
+#'   \item Revised Lund-Malmo: \href{https://pubmed.ncbi.nlm.nih.gov/24334413/}{Nyman et al., Clinical Chemistry and Laboratory Medicine (2014)}
 #'   \item MDRD: \href{https://pubmed.ncbi.nlm.nih.gov/11706306/}{Manjunath et al., Curr. Opin. Nephrol. Hypertens. (2001)} 
 #'     and \href{https://academic.oup.com/clinchem/article/53/4/766/5627682}{Levey et al., Clinical Chemistry (2007)}. (See Note.)
 #'   \item CKD-EPI: \href{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763564/}{Levey et al., Annals of Internal Medicine (2009)}. (See Note.)
 #'   \item CKD-EPI (2021): \href{https://www.nejm.org/doi/full/10.1056/NEJMoa2102953}{Inker, et al., NEJM (2021)}.
-#'   \item Schwartz: \href{https://www.ncbi.nlm.nih.gov/pubmed/951142}{Schwartz et al., Pediatrics (1976)}
-#'   \item Schwartz revised / bedside: \href{https://www.ncbi.nlm.nih.gov/pubmed/19158356}{Schwartz et al., Journal of the American Society of Nephrology (2009)}
-#'   \item Jelliffe: \href{https://www.ncbi.nlm.nih.gov/pubmed/4748282}{Jelliffe, Annals of Internal Medicine (1973)}
+#'   \item Schwartz: \href{https://pubmed.ncbi.nlm.nih.gov/951142/}{Schwartz et al., Pediatrics (1976)}
+#'   \item Schwartz revised / bedside: \href{https://pubmed.ncbi.nlm.nih.gov/19158356/}{Schwartz et al., Journal of the American Society of Nephrology (2009)}
+#'   \item Jelliffe: \href{https://pubmed.ncbi.nlm.nih.gov/4748282/}{Jelliffe, Annals of Internal Medicine (1973)}
 #'   \item Jelliffe for unstable renal function: \href{https://pubmed.ncbi.nlm.nih.gov/12169862/}{Jelliffe, American Journal of Nephrology (2002)}
 #'   \item Wright: \href{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2363765/}{Wright et al., British Journal of Cancer (2001)}
 #' }

diff --git a/R/convert_creat_unit.R b/R/convert_creat_unit.R
@@ -9,7 +9,7 @@
 convert_creat_unit <- function(
   value = NULL,
   unit_in = "mg/dL") {
-  if(class(value) == "list" && !is.null(value$value) && !is.null(value$unit)) {
+  if(inherits(value, "list") && !is.null(value$value) && !is.null(value$unit)) {
     unit_in <- value$unit
     value <- value$value
   }

diff --git a/R/nca.R b/R/nca.R
@@ -98,7 +98,7 @@ nca <- function (
       baseline <- data$dv[1]
     }
     data_fit <- data
-    if(class(weights) == "function") { # transform f(y) to vector of weights
+    if(inherits(weights, "function")) { # transform f(y) to vector of weights
       weights <- do.call("weights", args = list(data_fit$dv))
     }
 

diff --git a/R/pk_1cmt_t12.R b/R/pk_1cmt_t12.R
@@ -12,8 +12,8 @@ pk_1cmt_t12 <- function(
   V = 30
 ) {
   ## conversions, if necessary
-  if(class(CL) == "list" && !is.null(CL$value)) { CL <- CL$value }
-  if(class(V) == "list"  && !is.null(V$value)) { V <- V$value }
+  if(inherits(CL, "list") && !is.null(CL$value)) { CL <- CL$value }
+  if(inherits(V, "list")  && !is.null(V$value)) { V <- V$value }
   kel <- CL / V
   t12 <- log(2) / kel
   return(t12)

diff --git a/R/pk_2cmt_t12.R b/R/pk_2cmt_t12.R
@@ -17,10 +17,10 @@ pk_2cmt_t12 <- function(
 ) {
   phase <- match.arg(phase)
   ## conversions, if necessary
-  if(class(CL) == "list" && !is.null(CL$value)) { CL <- CL$value }
-  if(class(V) == "list"  && !is.null(V$value)) { V <- V$value }
-  if(class(Q) == "list"  && !is.null(Q$value)) { Q <- Q$value }
-  if(class(V2) == "list" && !is.null(V2$value)) { V2 <- V2$value }
+  if(inherits(CL, "list") && !is.null(CL$value)) { CL <- CL$value }
+  if(inherits(V, "list")  && !is.null(V$value)) { V <- V$value }
+  if(inherits(Q, "list")  && !is.null(Q$value)) { Q <- Q$value }
+  if(inherits(V2, "list") && !is.null(V2$value)) { V2 <- V2$value }
   kel <- CL / V
   k12 <- Q / V
   k21 <- Q / V2

diff --git a/R/pk_2cmt_t12_interval.R b/R/pk_2cmt_t12_interval.R
@@ -20,10 +20,10 @@ pk_2cmt_t12_interval <- function(
   t_inf = NULL
 ) {
   ## conversions, if necessary
-  if(class(CL) == "list" && !is.null(CL$value)) { CL <- CL$value }
-  if(class(V) == "list"  && !is.null(V$value)) { V <- V$value }
-  if(class(Q) == "list"  && !is.null(Q$value)) { Q <- Q$value }
-  if(class(V2) == "list" && !is.null(V2$value)) { V2 <- V2$value }
+  if(inherits(CL, "list") && !is.null(CL$value)) { CL <- CL$value }
+  if(inherits(V, "list")  && !is.null(V$value)) { V <- V$value }
+  if(inherits(Q, "list")  && !is.null(Q$value)) { Q <- Q$value }
+  if(inherits(V2, "list") && !is.null(V2$value)) { V2 <- V2$value }
   if(!is.null(t_inf)) {
     conc <- pk_2cmt_inf_ss(t=c(t_inf, tau), dose = 1000, tau = tau, t_inf = t_inf, CL=CL, V=V, Q=Q, V2=V2)
   } else {

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,23 +1,43 @@
 ## Test environments
-
-* Ubuntu 16.04 (local), R 3.4.0
-* Ubuntu 12.04.5 LTS (travis-ci), R 3.4.0
-* Windows (CRAN win-builder), R 3.4.0
-
+- R-hub windows-x86_64-devel (r-devel)
+- R-hub ubuntu-gcc-release (r-release)
+- R-hub fedora-clang-devel (r-devel)
+- Winbuilder (r-release)
 
 ## R CMD check results
-
-R CMD check results
-0 errors | 0 warnings | 0 notes
-
-R CMD check succeeded
-
-
-## Downstream dependencies
-
-None
-
-
-## Misc
-
-First submission to CRAN
+❯ On windows-x86_64-devel (r-devel), ubuntu-gcc-release (r-release), fedora-clang-devel (r-devel)
+  checking CRAN incoming feasibility ... NOTE
+  Maintainer: 'Kara Woo <kara@insight-rx.com>'
+
+  New maintainer:
+    Kara Woo <kara@insight-rx.com>
+  Old maintainer(s):
+    Ron Keizer <ronkeizer@gmail.com>
+
+  Found the following (possibly) invalid URLs:
+    URL: https://academic.oup.com/clinchem/article/53/4/766/5627682
+      From: man/calc_egfr.Rd
+      Status: 403
+      Message: Forbidden
+    URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763564/
+      From: man/calc_egfr.Rd
+      Status: 403
+      Message: Forbidden
+    URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238883/
+      From: man/calc_aki_stage.Rd
+      Status: 403
+      Message: Forbidden
+
+❯ On windows-x86_64-devel (r-devel)
+  checking for detritus in the temp directory ... NOTE
+  Found the following files/directories:
+    'lastMiKTeXException'
+
+0 errors ✔ | 0 warnings ✔ | 2 notes ✖
+
+## Maintainer notes
+
+This release involves a change in maintainer from Ron Keizer to Kara Woo.
+
+The three URLs that show 403 responses are valid and correct, but forbid
+requests with `curl` in the User-Agent header.
diff --git a/man/calc_egfr.Rd b/man/calc_egfr.Rd