Grab missing 1.2.10 release and add 1.2.11 info & fix man

DESCRIPTION

@@ -11,7 +11,7 @@ Description: At Novartis, we aimed at standardizing the set of diagnostic plots
     <https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>.
     When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required
     Chart Data instead of exporting it from the 'Monolix' gui.
-Version: 1.2.10
+Version: 1.2.11
 Authors@R: c(
               person("Amine", "Gassem", email="contact@ag-study.com", role=c("aut")),
               person("Bruno", "Bieth", email="biethb@hotmail.com", role="aut"),

NEWS.md

@@ -1,11 +1,16 @@
-# ggPMX 1.2.10
+# ggPMX 1.2.11
 
-- Fix bug so that reading monolix works on R devel (as requested by CRAN)
+* Fix bug so that reading monolix works on R devel (as requested by CRAN)
 
-- Change defaults so that scientific notation is not enabled by default
+* Change defaults so that scientific notation is not enabled by default
   and title is also not added by default
 
-- Monolix 2023 can now be read by ggPMX
+* Monolix 2023 can now be read by ggPMX
+
+# ggPMX 1.2.10
+
+* Skip draft parameter template creation test on CRAN, on some systems
+  it doesn't seem to work correctly.
 
 # ggPMX 1.2.9
 

R/ggPMX-options.R

@@ -56,7 +56,7 @@ getPmxOption <- function(name, default = NULL) {
 #' @section Options used in ggPMX:
 #'
 #' \itemize{
-#' \item {\strong{template_dir:}} {path to template directory}
+#' \item \strong{template_dir:} path to template directory
 #' }
 #'
 #' @examples

R/plot-density.R

@@ -19,30 +19,30 @@
 #'
 #' \strong{labels} is a list that contains:
 #' \itemize{
-#' \item {\strong{title:}} {plot title default  "IWRES density plot"}
-#' \item {\strong{x:}} {x axis label default to "Etas"}
-#' \item {\strong{y:}} {y axis label default to empty}
+#' \item \strong{title:} plot title default  "IWRES density plot"
+#' \item \strong{x:} x axis label default to "Etas"
+#' \item \strong{y:} y axis label default to empty
 #' }
 #'
 #' \strong{var_line} is a list that contains:
 #' \itemize{
-#' \item {\strong{linetype:}} {default to 1}
-#' \item {\strong{color:}} {default to black}
-#' \item {\strong{linewidth:}} {default to 1}
+#' \item \strong{linetype:} default to 1
+#' \item \strong{color:} default to black
+#' \item \strong{linewidth:} default to 1
 #' }
 #'
 #' \strong{snd_line} is a list that contains:
 #' \itemize{
-#' \item {\strong{linetype:}} {default to 2}
-#' \item {\strong{color:}} {default to black}
-#' \item {\strong{linewidth:}} {default to 1}
+#' \item \strong{linetype:} default to 2
+#' \item \strong{color:} default to black
+#' \item \strong{linewidth:} default to 1
 #' }
 #'
 #' \strong{vline} is a list that contains:
 #' \itemize{
-#' \item {\strong{linetype:}} {default to 3}
-#' \item {\strong{color:}} {default to black}
-#' \item {\strong{linewidth:}} {default to 1}
+#' \item \strong{linetype:} default to 3
+#' \item \strong{color:} default to black
+#' \item \strong{linewidth:} default to 1
 #' }
 #'
 pmx_dens <- function(

R/plot-distribution.R

@@ -19,18 +19,18 @@
 #'
 #' \strong{labels} is a list that contains:
 #' \itemize{
-#' \item {\strong{title:}} {plot title default "EBE distribution"}
-#' \item {\strong{subtitle:}} {plot subtitle default empty}
-#' \item {\strong{x:}} {x axis label default to "Etas"}
-#' \item {\strong{y:}} {y axis label default to empty}
-#' \item {\strong{legend:}} {legend title default to "random Effect"}
+#' \item \strong{title:} plot title default "EBE distribution"
+#' \item \strong{subtitle:} plot subtitle default empty
+#' \item \strong{x:} x axis label default to "Etas"
+#' \item \strong{y:} y axis label default to empty
+#' \item \strong{legend:} legend title default to "random Effect"
 #' }
 #' \strong{shrink} is a list that contains:
 #' \itemize{
-#' \item {\strong{fun:}} {shrinkage function can be \code{sd} or \code{var}}
-#' \item {\strong{size:}} {shrinkage text size}
-#' \item {\strong{color:}} {shrinkage text color}
-#' \item {\strong{vjust:}} {shrinkage position vertical adjustment}
+#' \item \strong{fun:} shrinkage function can be \code{sd} or \code{var}
+#' \item \strong{size:} shrinkage text size
+#' \item \strong{color:} shrinkage text color
+#' \item \strong{vjust:} shrinkage position vertical adjustment
 #' }
 distrib <- function(
                     labels,
@@ -109,11 +109,11 @@ wrap_formula <- function(x, origin = "lfacet") {
 }
 
 jitter_layer <- function(jitter, strat.color) {
-  
+
   if (is.null(jitter)){
     stop("jitter cannot be null")
   }
-  
+
   if (is.null(strat.color)) {
     jitter$height <- 0 #no jitter in height (y-axis required)
     do.call(geom_jitter, jitter)

R/plot-eta-cov.R

@@ -50,9 +50,9 @@ is_pmxcov <- function(x)
 #'
 #' \strong{labels} is a list that contains:
 #' \itemize{
-#' \item {\strong{title:}} {plot title default  "EBE vs. covariates"}
-#' \item {\strong{x:}} {x axis label default to "Etas"}
-#' \item {\strong{y:}} {y axis label default to empty}
+#' \item \strong{title:} plot title default  "EBE vs. covariates"
+#' \item \strong{x:} x axis label default to "Etas"
+#' \item \strong{y:} y axis label default to empty
 #' }
 eta_cov <- function(
                     labels,

R/plot-qq.R

@@ -42,16 +42,16 @@ pmx_qq_stats <- function(points) {
 #'
 #' \strong{labels} is a list that contains:
 #' \itemize{
-#' \item {\strong{title:}} {plot title default  "EBE vs. covariates"}
-#' \item {\strong{x:}} {x axis label default to "Etas"}
-#' \item {\strong{y:}} {y axis label default to empty}
+#' \item \strong{title:} plot title default  "EBE vs. covariates"
+#' \item \strong{x:} x axis label default to "Etas"
+#' \item \strong{y:} y axis label default to empty
 #' }
 #'
 #' \strong{point} is a list that contains:
 #' \itemize{
-#' \item {\strong{shape:}} {default to 1}
-#' \item {\strong{color:}} {default to black}
-#' \item {\strong{size:}} {default to 1}
+#' \item \strong{shape:} default to 1
+#' \item \strong{color:} default to black
+#' \item \strong{size:} default to 1
 #' }
 #' @param is.hline logical if TRUE add horizontal line y=0 ( TRUE by default)
 #' @param hline geom hline graphical parameters

R/plot-residual.R

@@ -20,17 +20,17 @@
 #'
 #' \strong{point} is a list that contains:
 #' \itemize{
-#' \item {\strong{shape:}} {default to 1}
-#' \item {\strong{color:}} {default to black}
-#' \item {\strong{size:}} {default to 1}
+#' \item \strong{shape:} default to 1
+#' \item \strong{color:} default to black
+#' \item \strong{size:} default to 1
 #' }
 #'
 #' \strong{labels} is a list that contains:
 #' \itemize{
-#' \item {\strong{title:}} {plot title default to AES_X versus AES_Y}
-#' \item {\strong{subtitle:}} {plot subtitle default empty}
-#' \item {\strong{x:}} {x axis label default to AES_X}
-#' \item {\strong{y:}} {y axis label default to AES_Y}
+#' \item \strong{title:} plot title default to AES_X versus AES_Y
+#' \item \strong{subtitle:} plot subtitle default empty
+#' \item \strong{x:} x axis label default to AES_X
+#' \item \strong{y:} y axis label default to AES_Y
 #' }
 residual <- function(x, y, labels = NULL, point = NULL, is.hline = FALSE,
                      hline = NULL, dname = NULL, facets = NULL, bloq = NULL,

R/plot-vpc.R

@@ -65,34 +65,34 @@ pmx_vpc_obs <-
 #'
 #' @param show  \code{charcater} how lines are displayed:
 #' \itemize{
-#' \item {\strong{show=all}} {lines will be displayed for each of
-#' the 3 percentiles. with a shaded area.}
-#' \item {\strong{show=median}} {Show only median line.}
-#' \item {\strong{show=area}} {Show only median line and the shaded area}
+#' \item \strong{show=all} lines will be displayed for each of
+#' the 3 percentiles. with a shaded area.
+#' \item \strong{show=median} Show only median line.
+#' \item \strong{show=area} Show only median line and the shaded area
 
 #' }
 
 #' @param interval \code{numeric} quantiles values default
 #' to \code{c(.05,.95)}
 #' @param median \code{list} containing: \cr
 #' \itemize{
-#' \item {\strong{color}} {\code{charcater}  Color of the median percentile line. Default: "#000000". }
-#' \item {\strong{linewidth}} {\code{numeric}  Thickness of the median percentile line. Default: 1.}
-#' \item {\strong{alpha}} {\code{numeric} Transparency of the median percentile line. Default: 0.7.}
-#' \item {\strong{linetype}} {\code{charcater} Linetype of the median percentile line. Default: "solid".}
+#' \item \strong{color} \code{charcater}  Color of the median percentile line. Default: "#000000".
+#' \item \strong{linewidth} \code{numeric}  Thickness of the median percentile line. Default: 1.
+#' \item \strong{alpha} \code{numeric} Transparency of the median percentile line. Default: 0.7.
+#' \item \strong{linetype} \code{charcater} Linetype of the median percentile line. Default: "solid".
 #' }
 
 #' @param extreme \code{list} containing: \cr
 #' \itemize{
-#' \item {\strong{color}} {\code{charcater} Color of the median percentile line. Default: "#000000". }
-#' \item {\strong{linewidth}} {\code{numeric} Thickness of the median percentile line. Default: 1.}
-#' \item {\strong{alpha}} {\code{numeric} Transparency of the median percentile line. Default: 0.7.}
-#' \item {\strong{linetype}} {\code{charcater} Linetype of the median percentile line. Default: "solid"}
+#' \item \strong{color} \code{charcater} Color of the median percentile line. Default: "#000000".
+#' \item \strong{linewidth} \code{numeric} Thickness of the median percentile line. Default: 1.
+#' \item \strong{alpha} \code{numeric} Transparency of the median percentile line. Default: 0.7.
+#' \item \strong{linetype} \code{charcater} Linetype of the median percentile line. Default: "solid"
 #' }
 #' @param area \code{list} containing: \cr
 #' \itemize{
-#' \item {\strong{fill}} {\code{charcater}  Color of the shaded area. Default: "blue". }
-#' \item {\strong{alpha}} {\code{numeric} Transparency of the sahded area. Default: 0.1.}
+#' \item \strong{fill} \code{charcater}  Color of the shaded area. Default: "blue".
+#' \item \strong{alpha} \code{numeric} Transparency of the sahded area. Default: 0.1.
 #' }
 #'
 #' @family vpc
@@ -142,27 +142,27 @@ pmx_vpc_pi <-
 
 #' @param show  \code{charcater} how areas are displayed:
 #' \itemize{
-#' \item {\strong{show="all"}} {areas will be displayed for each of the 3 percentiles. }
-#' \item {\strong{show="median"}} {Show only median area.}
+#' \item \strong{show="all"} areas will be displayed for each of the 3 percentiles.
+#' \item \strong{show="median"} Show only median area.
 #' }
 
 #' @param interval \code{numeric} quantiles values default to \code{c(.05,.95)}
 #' @param method \code{charcater} which areas are displayed:
 #' \itemize{
-#' \item {\strong{method="ribbon"}} {areas are ribbons.}
-#' \item {\strong{method="rectangle"}} {ares are horizontal rectangles.}
+#' \item \strong{method="ribbon"} areas are ribbons.
+#' \item \strong{method="rectangle"} areas are horizontal rectangles.
 #' }
 
 #' @param median \code{list} containing: \cr
 #' \itemize{
-#' \item {\strong{fill}} { \code{character} Color of the area representing the CI for the median. Default: "#3388cc".}
-#' \item {\strong{alpha}} {\code{numeric} Transparency of the area representing the PI for the median. Default=0.3.}
+#' \item \strong{fill}  \code{character} Color of the area representing the CI for the median. Default: "#3388cc".
+#' \item \strong{alpha} \code{numeric} Transparency of the area representing the PI for the median. Default=0.3.
 #' }
 
 #' @param extreme \code{list} containing: \cr
 #' \itemize{
-#' \item {\strong{fill}} {\code{character} Color of the area representing the CI for the extreme percentiles. Default: "#3388cc".}
-#' \item {\strong{alpha}} {\code{numeric} Transparency of the area representing the PI for the extreme percentiles. Default=0.3.}
+#' \item \strong{fill} \code{character} Color of the area representing the CI for the extreme percentiles. Default: "#3388cc".
+#' \item \strong{alpha} \code{numeric} Transparency of the area representing the PI for the extreme percentiles. Default=0.3.
 #' }
 #'
 #' @export