Merge pull request #589 from nlmixr2/588-matexp-fortran

588 matexp fortran

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: rxode2
-Version: 2.0.13.9000
+Version: 2.0.14.9000
 Title: Facilities for Simulating from ODE-Based Models
 Authors@R: c(
    person("Matthew L.","Fidler",
       role = c("aut", "cre"), email = "matthew.fidler@gmail.com",
       comment=c(ORCID="0000-0001-8538-6691")),
    person("Melissa", "Hallow",
       role = "aut", email = "hallowkm@uga.edu"),
-   person("Wenping", "Wang", 
+   person("Wenping", "Wang",
       role = c("aut"), email = "wwang8198@gmail.com"),
    person("Zufar", "Mulyukov", role="ctb", email="zufar.mulyukov@novartis.com"),
    person("Alan", "Hindmarsh",role="ctb"),
@@ -77,7 +77,7 @@ Imports:
     backports,
     cli (>= 2.0.0),
     checkmate,
-    ggplot2,
+    ggplot2 (>= 3.4.0),
     inline,
     lotri (>= 0.4.0),
     magrittr,
@@ -104,16 +104,16 @@ Description: Facilities for running simulations from ordinary
     Section 6.3, Appendix A, and Appendix D in the "R Administration and
     Installation" manual. Also the code is mostly released under GPL.  The
     'VODE' and 'LSODA' are in the public domain.  The information is available
-    in the inst/COPYRIGHTS. 
+    in the inst/COPYRIGHTS.
 BugReports: https://github.com/nlmixr2/rxode2/issues/
 NeedsCompilation: yes
 VignetteBuilder: knitr
-License: GPL (>= 3) 
+License: GPL (>= 3)
 URL: https://nlmixr2.github.io/rxode2/,
     https://github.com/nlmixr2/rxode2/
 RoxygenNote: 7.2.3
 Biarch: true
-LinkingTo: 
+LinkingTo:
     rxode2parse (>= 2.0.12),
     rxode2random,
     PreciseSums (>= 0.3),

NEWS.md

@@ -147,7 +147,16 @@ mu-referencing style to run the optimization.
 - Bug fix for some covariate updates that may affect multiple compartment
   models (like issue #581)
 
-# rxode2 2.0.13
+# rxode2 2.1.14
+
+- CRAN requested that FORTRAN `kind` be changed as it was not portable;
+  This was commented code, and simply removed the comment.
+
+- Bug-fix for `geom_amt()`; also now uses `linewidth` and at least `ggplot2 3.4.0`
+
+- Some documentation was cleaned up from `rxode2` 2.1.13
+
+# rxode2 2.1.13
 
 ## Bug fixes
 

R/RcppExports.R

@@ -40,7 +40,7 @@ etTrans <- function(inData, obj, addCmt = FALSE, dropUnits = FALSE, allTimeVar =
 #' @param c1 character vector of items to be expanded
 #' @param c2 second character vector of items to be expanded
 #' @param type 0 for a typical data frame, 1 for symengine sensitivity expansion
-#' @return data frame (when type = 0) or symengine string (when type=1) 
+#' @return data frame (when type = 0) or symengine string (when type=1)
 #' @export
 #' @keywords internal
 rxExpandGrid_ <- function(c1, c2, type) {
@@ -74,7 +74,7 @@ rxExpandSens2_ <- function(state, s1, s2) {
 #'
 #' @param state is the state to expand
 #' @param neta is the number of etas
-#' @param pred type of prediction 
+#' @param pred type of prediction
 #' @keywords internal
 #' @return String of symengine expressions to evaluate to calculate df/deta
 #' @export
@@ -84,7 +84,7 @@ rxExpandFEta_ <- function(state, neta, pred) {
 
 #' Rep R0 for foce
 #'
-#' @param number ETA to substitute
+#' @param neta ETA to substitute
 #'
 #' @return Returns a string of R code to substitute the rx_r expression in the symengine environment .s
 #'
@@ -260,7 +260,7 @@ rxSetupIni <- function(obj, inits = NULL) {
 #'
 #' @param obj rxode2 object
 #'
-#' @param inits A numeric vector of initial conditions.
+#' @param scale A numeric vector scales
 #'
 #' @param extraArgs A list of extra args to parse for initial conditions.
 #'

R/err.R

@@ -46,8 +46,8 @@
   "f"=2:3,
   "dgeom"=1,
   "geom"=1,
-#  "dhyper"=3,
-#  "hyper"=3,
+  #  "dhyper"=3,
+  #  "hyper"=3,
   "dunif"=0:2,
   "unif"=0:2,
   "dweibull"=1:2,
@@ -233,7 +233,7 @@ rxPreferredDistributionName <- function(dist) {
 }
 
 .rxTransformHasBounds <- function(distribution) {
-    (as.integer(distribution) %in% 5:14)
+  (as.integer(distribution) %in% 5:14)
 }
 
 .rxAddPropLevels <- c(
@@ -336,7 +336,7 @@ rxDemoteAddErr <- function(errType) {
 
 .incompatibleErr <- function(err1, err2) {
   .errs <- sort(c(err1, err2))
-   paste0("`", .errs[1], "` and `", .errs[2], "` are incompatible")
+  paste0("`", .errs[1], "` and `", .errs[2], "` are incompatible")
 }
 #' Combine error types to get the model F type
 #'
@@ -545,12 +545,11 @@ rxDemoteAddErr <- function(errType) {
 #'   `oldErrType` to zero assuming that there is no prior
 #'   distribution.
 #'
-#' @param newTransform This is the new distribution that is being
+#' @param newErrType This is the new distribution that is being
 #'   "added" to the current transformation.  These assumes the inputs
 #'   are in the preferred distribution name, as determined by
 #'   `rxPreferredDistributionName()`
 #'
-#'
 #' @return The new transformation as a factor
 #'
 #' @author Matthew Fidler
@@ -598,7 +597,7 @@ rxErrTypeCombine <- function(oldErrType, newErrType) {
       env$.numeric <- -(expression[[2]])
       return(TRUE)
     } else if (identical(expression[[1]], quote(`+`)) &&
-          is.numeric(expression[[2]])) {
+                 is.numeric(expression[[2]])) {
       env$.numeric <- expression[[2]]
       return(TRUE)
     }
@@ -627,7 +626,7 @@ rxErrTypeCombine <- function(oldErrType, newErrType) {
   dexp=c("a"), #7
   f=c("a", "b", "c"), #8
   geom=c("a"), #9
-#  hyper=c("a", "b", "c"), #10
+  #  hyper=c("a", "b", "c"), #10
   unif=c("a", "b"), #11
   weibull=c("a", "b"), #12
   cauchy=c("a", "b"),
@@ -1183,7 +1182,7 @@ rxErrTypeCombine <- function(oldErrType, newErrType) {
           setNames(
             c("linCmtA" = 1L, "linCmtB" = 2L,
               "linCmtC" = 3L
-            )[match.arg(linCmtSens)],
+              )[match.arg(linCmtSens)],
             NULL
           ), verbose
         ))
@@ -1257,8 +1256,8 @@ rxErrTypeCombine <- function(oldErrType, newErrType) {
   }
   .mod <- eval(parse(text=paste0("quote({", .var, "=1+2\n", deparse1(expr), "})")))
   .ini <- as.data.frame(eval(parse(text=paste0("lotri({\n",
-                             paste(paste(allNames(expr[[3]]), "<- 1"), collapse="\n"),
-                             "\n})"))))
+                                               paste(paste(allNames(expr[[3]]), "<- 1"), collapse="\n"),
+                                               "\n})"))))
   .env <- try(.errProcessExpression(.mod, .ini, checkMissing=FALSE), silent=TRUE)
   if (inherits(.env, "try-error")) return(FALSE)
   if (uiEnv) return(.env)
@@ -1267,7 +1266,7 @@ rxErrTypeCombine <- function(oldErrType, newErrType) {
 #'  Is Normal, Cauchy or t distribution model specification?
 #'
 #' @param expr Expression
-#' 
+#'
 #' @return TRUE if this is a normal/t/cauchy model, FALSE otherwise
 #' @author Matthew L. Fidler
 #' @noRd

R/genShinyApp.template.R

@@ -43,7 +43,7 @@
 #'     dosing regimen simulation web application. Users may want to
 #'     modify the code to experiment creating shiny applications for
 #'     their specific `rxode2` models.
-#' @seealso [rxode2()],[eventTable()], and the package \pkg{shiny} (<https://shiny.rstudio.com>).
+#' @seealso [rxode2()],[eventTable()], and the package \pkg{shiny} (<https://shiny.posit.co>).
 #'
 #' @examples
 #' \donttest{

R/geom-amt.R

@@ -3,8 +3,7 @@
     stop("need 'amt' aesthetic")
   } else if (!any(names(data) == "x") && any(names(data) == "time")) {
     data$x <- data$time
-  } else if (any(names(data) == "x")) {
-  } else {
+  } else if (!any(names(data) == "x")) {
     stop("need 'x' aesthetic")
   }
   ret <- data[!is.na(data$amt), c("x", "amt")]
@@ -88,7 +87,7 @@ StatAmt <- ggplot2::ggproto("StatAmt", ggplot2::Stat,
 #' # of course you can make it a bit more visible
 #'
 #' plot(bidQd, C2) + geom_amt(aes(amt=amt), col="red", lty=1, linewidth=1.2)
-#' 
+#'
 #' }
 #' @export
 #' @inheritParams ggplot2::stat_identity