Skip to content

Commit 96e5433

Browse files
mattfidlermattfidler
committed
Grab missing 1.2.10 release and add 1.2.11 info & fix man
1 parent 4f5bd78 commit 96e5433

21 files changed

+228
-227
lines changed

‎DESCRIPTION

+1-1
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ Description: At Novartis, we aimed at standardizing the set of diagnostic plots
1111
<https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>.
1212
When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required
1313
Chart Data instead of exporting it from the 'Monolix' gui.
14-
Version: 1.2.10
14+
Version: 1.2.11
1515
Authors@R: c(
1616
person("Amine", "Gassem", email="contact@ag-study.com", role=c("aut")),
1717
person("Bruno", "Bieth", email="biethb@hotmail.com", role="aut"),

‎NEWS.md

+9-4
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,16 @@
1-
# ggPMX 1.2.10
1+
# ggPMX 1.2.11
22

3-
- Fix bug so that reading monolix works on R devel (as requested by CRAN)
3+
* Fix bug so that reading monolix works on R devel (as requested by CRAN)
44

5-
- Change defaults so that scientific notation is not enabled by default
5+
* Change defaults so that scientific notation is not enabled by default
66
and title is also not added by default
77

8-
- Monolix 2023 can now be read by ggPMX
8+
* Monolix 2023 can now be read by ggPMX
9+
10+
# ggPMX 1.2.10
11+
12+
* Skip draft parameter template creation test on CRAN, on some systems
13+
it doesn't seem to work correctly.
914

1015
# ggPMX 1.2.9
1116

‎R/ggPMX-options.R

+1-1
Original file line numberDiff line numberDiff line change
@@ -56,7 +56,7 @@ getPmxOption <- function(name, default = NULL) {
5656
#' @section Options used in ggPMX:
5757
#'
5858
#' \itemize{
59-
#' \item {\strong{template_dir:}} {path to template directory}
59+
#' \item \strong{template_dir:} path to template directory
6060
#' }
6161
#'
6262
#' @examples

‎R/plot-density.R

+12-12
Original file line numberDiff line numberDiff line change
@@ -19,30 +19,30 @@
1919
#'
2020
#' \strong{labels} is a list that contains:
2121
#' \itemize{
22-
#' \item {\strong{title:}} {plot title default "IWRES density plot"}
23-
#' \item {\strong{x:}} {x axis label default to "Etas"}
24-
#' \item {\strong{y:}} {y axis label default to empty}
22+
#' \item \strong{title:} plot title default "IWRES density plot"
23+
#' \item \strong{x:} x axis label default to "Etas"
24+
#' \item \strong{y:} y axis label default to empty
2525
#' }
2626
#'
2727
#' \strong{var_line} is a list that contains:
2828
#' \itemize{
29-
#' \item {\strong{linetype:}} {default to 1}
30-
#' \item {\strong{color:}} {default to black}
31-
#' \item {\strong{linewidth:}} {default to 1}
29+
#' \item \strong{linetype:} default to 1
30+
#' \item \strong{color:} default to black
31+
#' \item \strong{linewidth:} default to 1
3232
#' }
3333
#'
3434
#' \strong{snd_line} is a list that contains:
3535
#' \itemize{
36-
#' \item {\strong{linetype:}} {default to 2}
37-
#' \item {\strong{color:}} {default to black}
38-
#' \item {\strong{linewidth:}} {default to 1}
36+
#' \item \strong{linetype:} default to 2
37+
#' \item \strong{color:} default to black
38+
#' \item \strong{linewidth:} default to 1
3939
#' }
4040
#'
4141
#' \strong{vline} is a list that contains:
4242
#' \itemize{
43-
#' \item {\strong{linetype:}} {default to 3}
44-
#' \item {\strong{color:}} {default to black}
45-
#' \item {\strong{linewidth:}} {default to 1}
43+
#' \item \strong{linetype:} default to 3
44+
#' \item \strong{color:} default to black
45+
#' \item \strong{linewidth:} default to 1
4646
#' }
4747
#'
4848
pmx_dens <- function(

‎R/plot-distribution.R

+11-11
Original file line numberDiff line numberDiff line change
@@ -19,18 +19,18 @@
1919
#'
2020
#' \strong{labels} is a list that contains:
2121
#' \itemize{
22-
#' \item {\strong{title:}} {plot title default "EBE distribution"}
23-
#' \item {\strong{subtitle:}} {plot subtitle default empty}
24-
#' \item {\strong{x:}} {x axis label default to "Etas"}
25-
#' \item {\strong{y:}} {y axis label default to empty}
26-
#' \item {\strong{legend:}} {legend title default to "random Effect"}
22+
#' \item \strong{title:} plot title default "EBE distribution"
23+
#' \item \strong{subtitle:} plot subtitle default empty
24+
#' \item \strong{x:} x axis label default to "Etas"
25+
#' \item \strong{y:} y axis label default to empty
26+
#' \item \strong{legend:} legend title default to "random Effect"
2727
#' }
2828
#' \strong{shrink} is a list that contains:
2929
#' \itemize{
30-
#' \item {\strong{fun:}} {shrinkage function can be \code{sd} or \code{var}}
31-
#' \item {\strong{size:}} {shrinkage text size}
32-
#' \item {\strong{color:}} {shrinkage text color}
33-
#' \item {\strong{vjust:}} {shrinkage position vertical adjustment}
30+
#' \item \strong{fun:} shrinkage function can be \code{sd} or \code{var}
31+
#' \item \strong{size:} shrinkage text size
32+
#' \item \strong{color:} shrinkage text color
33+
#' \item \strong{vjust:} shrinkage position vertical adjustment
3434
#' }
3535
distrib <- function(
3636
labels,
@@ -109,11 +109,11 @@ wrap_formula <- function(x, origin = "lfacet") {
109109
}
110110

111111
jitter_layer <- function(jitter, strat.color) {
112-
112+
113113
if (is.null(jitter)){
114114
stop("jitter cannot be null")
115115
}
116-
116+
117117
if (is.null(strat.color)) {
118118
jitter$height <- 0 #no jitter in height (y-axis required)
119119
do.call(geom_jitter, jitter)

‎R/plot-eta-cov.R

+3-3
Original file line numberDiff line numberDiff line change
@@ -50,9 +50,9 @@ is_pmxcov <- function(x)
5050
#'
5151
#' \strong{labels} is a list that contains:
5252
#' \itemize{
53-
#' \item {\strong{title:}} {plot title default "EBE vs. covariates"}
54-
#' \item {\strong{x:}} {x axis label default to "Etas"}
55-
#' \item {\strong{y:}} {y axis label default to empty}
53+
#' \item \strong{title:} plot title default "EBE vs. covariates"
54+
#' \item \strong{x:} x axis label default to "Etas"
55+
#' \item \strong{y:} y axis label default to empty
5656
#' }
5757
eta_cov <- function(
5858
labels,

‎R/plot-qq.R

+6-6
Original file line numberDiff line numberDiff line change
@@ -42,16 +42,16 @@ pmx_qq_stats <- function(points) {
4242
#'
4343
#' \strong{labels} is a list that contains:
4444
#' \itemize{
45-
#' \item {\strong{title:}} {plot title default "EBE vs. covariates"}
46-
#' \item {\strong{x:}} {x axis label default to "Etas"}
47-
#' \item {\strong{y:}} {y axis label default to empty}
45+
#' \item \strong{title:} plot title default "EBE vs. covariates"
46+
#' \item \strong{x:} x axis label default to "Etas"
47+
#' \item \strong{y:} y axis label default to empty
4848
#' }
4949
#'
5050
#' \strong{point} is a list that contains:
5151
#' \itemize{
52-
#' \item {\strong{shape:}} {default to 1}
53-
#' \item {\strong{color:}} {default to black}
54-
#' \item {\strong{size:}} {default to 1}
52+
#' \item \strong{shape:} default to 1
53+
#' \item \strong{color:} default to black
54+
#' \item \strong{size:} default to 1
5555
#' }
5656
#' @param is.hline logical if TRUE add horizontal line y=0 ( TRUE by default)
5757
#' @param hline geom hline graphical parameters

‎R/plot-residual.R

+7-7
Original file line numberDiff line numberDiff line change
@@ -20,17 +20,17 @@
2020
#'
2121
#' \strong{point} is a list that contains:
2222
#' \itemize{
23-
#' \item {\strong{shape:}} {default to 1}
24-
#' \item {\strong{color:}} {default to black}
25-
#' \item {\strong{size:}} {default to 1}
23+
#' \item \strong{shape:} default to 1
24+
#' \item \strong{color:} default to black
25+
#' \item \strong{size:} default to 1
2626
#' }
2727
#'
2828
#' \strong{labels} is a list that contains:
2929
#' \itemize{
30-
#' \item {\strong{title:}} {plot title default to AES_X versus AES_Y}
31-
#' \item {\strong{subtitle:}} {plot subtitle default empty}
32-
#' \item {\strong{x:}} {x axis label default to AES_X}
33-
#' \item {\strong{y:}} {y axis label default to AES_Y}
30+
#' \item \strong{title:} plot title default to AES_X versus AES_Y
31+
#' \item \strong{subtitle:} plot subtitle default empty
32+
#' \item \strong{x:} x axis label default to AES_X
33+
#' \item \strong{y:} y axis label default to AES_Y
3434
#' }
3535
residual <- function(x, y, labels = NULL, point = NULL, is.hline = FALSE,
3636
hline = NULL, dname = NULL, facets = NULL, bloq = NULL,

‎R/plot-vpc.R

+22-22
Original file line numberDiff line numberDiff line change
@@ -65,34 +65,34 @@ pmx_vpc_obs <-
6565
#'
6666
#' @param show \code{charcater} how lines are displayed:
6767
#' \itemize{
68-
#' \item {\strong{show=all}} {lines will be displayed for each of
69-
#' the 3 percentiles. with a shaded area.}
70-
#' \item {\strong{show=median}} {Show only median line.}
71-
#' \item {\strong{show=area}} {Show only median line and the shaded area}
68+
#' \item \strong{show=all} lines will be displayed for each of
69+
#' the 3 percentiles. with a shaded area.
70+
#' \item \strong{show=median} Show only median line.
71+
#' \item \strong{show=area} Show only median line and the shaded area
7272

7373
#' }
7474

7575
#' @param interval \code{numeric} quantiles values default
7676
#' to \code{c(.05,.95)}
7777
#' @param median \code{list} containing: \cr
7878
#' \itemize{
79-
#' \item {\strong{color}} {\code{charcater} Color of the median percentile line. Default: "#000000". }
80-
#' \item {\strong{linewidth}} {\code{numeric} Thickness of the median percentile line. Default: 1.}
81-
#' \item {\strong{alpha}} {\code{numeric} Transparency of the median percentile line. Default: 0.7.}
82-
#' \item {\strong{linetype}} {\code{charcater} Linetype of the median percentile line. Default: "solid".}
79+
#' \item \strong{color} \code{charcater} Color of the median percentile line. Default: "#000000".
80+
#' \item \strong{linewidth} \code{numeric} Thickness of the median percentile line. Default: 1.
81+
#' \item \strong{alpha} \code{numeric} Transparency of the median percentile line. Default: 0.7.
82+
#' \item \strong{linetype} \code{charcater} Linetype of the median percentile line. Default: "solid".
8383
#' }
8484

8585
#' @param extreme \code{list} containing: \cr
8686
#' \itemize{
87-
#' \item {\strong{color}} {\code{charcater} Color of the median percentile line. Default: "#000000". }
88-
#' \item {\strong{linewidth}} {\code{numeric} Thickness of the median percentile line. Default: 1.}
89-
#' \item {\strong{alpha}} {\code{numeric} Transparency of the median percentile line. Default: 0.7.}
90-
#' \item {\strong{linetype}} {\code{charcater} Linetype of the median percentile line. Default: "solid"}
87+
#' \item \strong{color} \code{charcater} Color of the median percentile line. Default: "#000000".
88+
#' \item \strong{linewidth} \code{numeric} Thickness of the median percentile line. Default: 1.
89+
#' \item \strong{alpha} \code{numeric} Transparency of the median percentile line. Default: 0.7.
90+
#' \item \strong{linetype} \code{charcater} Linetype of the median percentile line. Default: "solid"
9191
#' }
9292
#' @param area \code{list} containing: \cr
9393
#' \itemize{
94-
#' \item {\strong{fill}} {\code{charcater} Color of the shaded area. Default: "blue". }
95-
#' \item {\strong{alpha}} {\code{numeric} Transparency of the sahded area. Default: 0.1.}
94+
#' \item \strong{fill} \code{charcater} Color of the shaded area. Default: "blue".
95+
#' \item \strong{alpha} \code{numeric} Transparency of the sahded area. Default: 0.1.
9696
#' }
9797
#'
9898
#' @family vpc
@@ -142,27 +142,27 @@ pmx_vpc_pi <-
142142

143143
#' @param show \code{charcater} how areas are displayed:
144144
#' \itemize{
145-
#' \item {\strong{show="all"}} {areas will be displayed for each of the 3 percentiles. }
146-
#' \item {\strong{show="median"}} {Show only median area.}
145+
#' \item \strong{show="all"} areas will be displayed for each of the 3 percentiles.
146+
#' \item \strong{show="median"} Show only median area.
147147
#' }
148148

149149
#' @param interval \code{numeric} quantiles values default to \code{c(.05,.95)}
150150
#' @param method \code{charcater} which areas are displayed:
151151
#' \itemize{
152-
#' \item {\strong{method="ribbon"}} {areas are ribbons.}
153-
#' \item {\strong{method="rectangle"}} {ares are horizontal rectangles.}
152+
#' \item \strong{method="ribbon"} areas are ribbons.
153+
#' \item \strong{method="rectangle"} areas are horizontal rectangles.
154154
#' }
155155

156156
#' @param median \code{list} containing: \cr
157157
#' \itemize{
158-
#' \item {\strong{fill}} { \code{character} Color of the area representing the CI for the median. Default: "#3388cc".}
159-
#' \item {\strong{alpha}} {\code{numeric} Transparency of the area representing the PI for the median. Default=0.3.}
158+
#' \item \strong{fill} \code{character} Color of the area representing the CI for the median. Default: "#3388cc".
159+
#' \item \strong{alpha} \code{numeric} Transparency of the area representing the PI for the median. Default=0.3.
160160
#' }
161161

162162
#' @param extreme \code{list} containing: \cr
163163
#' \itemize{
164-
#' \item {\strong{fill}} {\code{character} Color of the area representing the CI for the extreme percentiles. Default: "#3388cc".}
165-
#' \item {\strong{alpha}} {\code{numeric} Transparency of the area representing the PI for the extreme percentiles. Default=0.3.}
164+
#' \item \strong{fill} \code{character} Color of the area representing the CI for the extreme percentiles. Default: "#3388cc".
165+
#' \item \strong{alpha} \code{numeric} Transparency of the area representing the PI for the extreme percentiles. Default=0.3.
166166
#' }
167167
#'
168168
#' @export

0 commit comments

Comments
 (0)