reduce package size, example run itmes to make cran happy

DESCRIPTION

@@ -58,14 +58,13 @@ Imports:
     ggridges,
     rms,
     tibble,
-    patchwork
+    patchwork (>= 1.2.0)
 Suggests:
     knitr,
     rmarkdown
 License: MIT + file LICENSE
 SystemRequirements: pandoc with https support
 LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Encoding: UTF-8
-

NAMESPACE

@@ -29,8 +29,8 @@ export(stat_kmticks)
 import(tidyr)
 importFrom(ggbeeswarm,position_beeswarm)
 importFrom(ggbeeswarm,position_quasirandom)
+importFrom(rlang,)
 importFrom(rlang,.data)
-importFrom(rlang,`:=`)
 importFrom(rlang,sym)
 importFrom(scales,identity_trans)
 importFrom(scales,label_parse)

NEWS.md

@@ -1,14 +1,13 @@
 # ggquickeda 0.3.1
 * rebuilt docs fixed broken link
 * fixing some regressions introduced by bookmarking
-* fixing some errors by the new R rules for logical comparison ||
-* fixing error in aspect.ratio not numeric
-* fixing other regression with ggpairs color and group
-* added support of pasting values of two/three variables
-* added function `ggkmrisktable` to add facettable risk tables, km and split exposures to ntiles
-* added function `gglogisticexpdist`
-* added function `ggcontinuousexpdist`
-* TBD reduce package size ! 
+* fixing some errors by the new R rules for logical comparison length with `|` versus `||`
+* fixing error in aspect.ratio not numeric (was also fixed in ggplot2)
+* fixing other regressions with ggpairs color and group
+* added support of pasting values of two/three variables where it was just a placeholder
+* added function `ggkmrisktable` to add facetable risk tables, km and by ntiles split exposures
+* added function `gglogisticexpdist` and `ggcontinuousexpdist` to add facetable logistic/linear regression with exposures split to  ntiles with exposure distributions by dose/group and optional y axis projections
+* added link to github pages in description thanks to @olivroy
 
 # ggquickeda 0.3.0
 * added options to drop levels for user discrete shape and linetype scales

R/ggcontinuousexpdist.R

@@ -91,11 +91,12 @@ plogis <- function(x) exp(x)/(1+exp(x))
 #'                  yproj_dodge = 20 ,
 #'                  exposure_distribution ="distributions")            
 #' a / b +
-#'plot_layout(guides = "collect") &
+#' plot_layout(guides = "collect") &
 #'  theme(legend.position = "top")
-#'  #Example 2
-#'  effICGI$SEX <- as.factor(effICGI$SEX)
-#'  ggcontinuousexpdist(data = effICGI |>
+#' 
+#' #Example 2
+#' effICGI$SEX <- as.factor(effICGI$SEX)
+#' ggcontinuousexpdist(data = effICGI |>
 #'   dplyr::filter(Endpoint =="ICGI7"),
 #'                  response = "response",
 #'                  endpoint = "Endpoint",

R/gglogisticexpdist.R

@@ -106,11 +106,15 @@ plogis <- function(x) exp(x)/(1+exp(x))
 #'                  dist_position_scaler = 0.15)+
 #'  facet_grid2(Endpoint~expname+DOSE2,scales="free",
 #'  margins = "DOSE2",strip = strip_nested())             
-#' # Example 4                 
-#'gglogisticexpdist(data = effICGI, 
+#'\dontrun{
+#' # Example 4  
+#' effICGI$SEX <- as.factor(effICGI$SEX)               
+#' gglogisticexpdist(data = effICGI  |>
+#'                  dplyr::filter(Endpoint=="ICGI"), 
 #'                  response = "response",
 #'                  endpoint = "Endpoint",
 #'                  DOSE = "DOSE",
+#'                  color_fill = "SEX",
 #'                  exposure_metrics = c("AUC"),
 #'                  exposure_metric_split = c("quartile"),
 #'                  exposure_distribution ="distributions",
@@ -119,15 +123,15 @@ plogis <- function(x) exp(x)/(1+exp(x))
 #'                  lineranges_ypos = -0.2,
 #'                  yproj_xpos = -10,
 #'                  yproj_dodge = 20,
-#'                  prob_text_size = 9,
+#'                  prob_text_size = 6,
 #'                  binlimits_text_size = 6,
-#'                  N_text_size = 5,
+#'                  N_text_size = 4,
 #'                  dist_position_scaler = 0.15)+
 #'                  ggplot2::scale_x_continuous(breaks = seq(0,350,50),
 #'                  expand = ggplot2::expansion(add= c(0,0),mult=c(0,0)))+
 #'                  ggplot2::coord_cartesian(xlim = c(-30,355))+
-#'                  ggplot2::facet_grid(~Endpoint)
-#'\dontrun{
+#'                  ggplot2::facet_grid(Endpoint~expname+color_fill2, margins ="color_fill2" )
+#'
 #' #Example 4b
 #'   effICGI$SEX <- as.factor(effICGI$SEX)
 #'  gglogisticexpdist(data = effICGI |>

README.md

@@ -17,7 +17,9 @@ It enables you to quickly explore your data and to detect trends on the fly. You
 
 It also has the `km`, `kmband` and `kmticks` geoms/stats to facilitate the plotting of **Kaplan-Meier** Survival curves. 
 
-For a quick overview using an older version of the app head to this <a href="https://www.youtube.com/watch?v=1rBBmJUIZhs" target="_blank"> Youtube Tutorial </a>.
+For a quick overview using an older version of the app head to this <a href="https://www.youtube.com/watch?v=1rBBmJUIZhs" target="_blank"> Youtube Tutorial </a>. A more recent video tutorial can be found here:
+<a href="https://certara.github.io/R-Certara/articles/lesson_3.html" target="_blank">Certara R School Introduction to ggquickeda </a>.
+
 
 ### Installation and Running information
 ```
@@ -50,9 +52,6 @@ The package has also the following vignettes:
 2. <a href="https://cran.r-project.org/package=ggquickeda/vignettes/AdditionalPlotsStats.html"  target="_blank"> Additional Plots and Stats with ggquickeda </a>.  
 3. <a href="https://cran.r-project.org/package=ggquickeda/vignettes/Visualizing_Summary_Data.html"  target="_blank"> Visualizing Summary Data with ggquickeda </a>.  
 
-### Plot Example
-![Example use case 1 with the included sample_df](vignettes/img/snapshot1.gif)
-
 ### Table Example
 ![Example Descriptive Stats](vignettes/img/snapshot3.1.png)
 

cran-comments.md

@@ -1,21 +1,20 @@
 ## Test environments
-* local Windows 10 install, R 4.2.2
+* local Windows 10 install, R 4.3.2
 * github actions windows-latest (release)
 * github actions macOS-latest (release)
-* github actions ubuntu-20.04 (release)
-* github actions ubuntu-20.04 (devel)
+* github actions ubuntu-latest (devel, release and oldrel-1)
 * win-builder (devel and release)
 
-
 ## R CMD check results
 
-0 errors | 0 warnings | 2 notes
+0 errors | 0 warnings | 3 notes
+
+* This is a significant update fixing several bugs and adding three plotting functions.
+* Notes about unused declared imports from the previous/current builds are false positives since these are used in the shiny app code and are required for it to work properly.
+* Notes about depending on many packages appear and is a choice and a risk I am willing to take, as this package requires all of them to work properly.
+* Notes on examples taking > 5s is necessary since ggplot2 rendering of complex plots is long
+* The package size is now below 5MB  after removing heavy gifs from the readme.
 
-* The package size is now 4917 kb after compressing the vignette pngs even more.l
-* This is a small update adding user experience improvement for the user to be able to save the state of the shiny app.
-* some Notes about unused dependencies from the previous builds on some platforms are false positives since these are used in the shiny app code and are required for it.
-* Note about depending on many packages appear and is a choice and a risk I am willing to take, as this package requires all of them to work properly.
-* An attempt to reduce the size of the package was made by further reducing the readme/vignettes' pngs.
 
 ## Reverse dependencies