Release OsteoBioR 25.02.0

.github/workflows/pkgdown.yaml

@@ -28,7 +28,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
-      
+
       - name: Compile rstan files via rstantools
         run: |
           # R is already installed in the base-image
@@ -49,7 +49,7 @@ jobs:
 
       # Save the generated site to be shared with the next job
       - name: Upload site artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: site
           path: docs
@@ -67,7 +67,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Download site artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: site
           path: docs

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: OsteoBioR
-Version: 24.10.0
+Version: 25.02.0.1
 Title: Temporal Estimation of Isotopic Values
 Description: Estimates the temporal changes of isotopic values of bone and teeth data solely based on the renewal rate of different bones/teeth and given measurements. The package furthermore provides plotting and exporting functionalities.
 Authors@R: c(
@@ -13,19 +13,13 @@ LazyData: true
 ByteCompile: true
 Depends: R (>= 3.5.0), Rcpp (>= 0.12.0)
 Imports:
-  colourpicker,
+  ChangeR (>= 24.11.0.4),
   dplyr,
   ggplot2 (>= 2.2.1),
-  DataTools (>= 23.12.2.3),
+  DataTools (>= 24.10.0.2),
   futile.logger,
-  htmltools,
-  jsonlite,
-  loo,
-  magrittr,
-  mcp,
   methods,
   modules,
-  openxlsx,
   parallel,
   rlang,
   rstan (>= 2.18.1),
@@ -36,7 +30,7 @@ Imports:
   shinyMatrix,
   shinyWidgets,
   shinythemes,
-  shinyTools (>= 24.10.0),
+  shinyTools (>= 25.02.0.2),
   yaml
 LinkingTo: StanHeaders (>= 2.18.0), rstan (>= 2.18.1), BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0)
 Suggests: 

NAMESPACE

@@ -7,17 +7,12 @@ export(config)
 export(defaultInputsForUI)
 export(estimateIntervals)
 export(estimateTimePoint)
-export(exportCSV)
-export(exportFilename)
-export(exportJSON)
-export(exportXLSX)
 export(extractIndividuals)
 export(extractModelOutputs)
 export(extractSavedModels)
 export(getEntry)
 export(getExampleDataMatrix)
 export(getExampleIsotopeVals)
-export(getHelp)
 export(getSeed)
 export(getShiftTime)
 export(getSiteStayTimes)
@@ -45,6 +40,8 @@ import(methods)
 import(rstantools)
 import(shiny)
 import(shinythemes)
+importFrom(ChangeR,changePointsServer)
+importFrom(ChangeR,changePointsUI)
 importFrom(DataTools,checkAnyNonNumericColumns)
 importFrom(DataTools,downloadModelServer)
 importFrom(DataTools,downloadModelUI)
@@ -54,7 +51,7 @@ importFrom(DataTools,importOptions)
 importFrom(DataTools,importServer)
 importFrom(DataTools,importUI)
 importFrom(DataTools,renameExistingNames)
-importFrom(colourpicker,colourInput)
+importFrom(dplyr,"%>%")
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
@@ -87,23 +84,17 @@ importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,sec_axis)
 importFrom(ggplot2,theme)
-importFrom(htmltools,save_html)
-importFrom(jsonlite,toJSON)
-importFrom(loo,loo)
-importFrom(loo,loo_compare)
-importFrom(loo,waic)
-importFrom(magrittr,"%>%")
-importFrom(mcp,mcp)
-importFrom(openxlsx,write.xlsx)
 importFrom(parallel,detectCores)
 importFrom(rlang,.data)
 importFrom(rstan,extract)
 importFrom(rstan,sampling)
+importFrom(shinyTools,addCustomPointsToGGplot)
 importFrom(shinyTools,calculateRescalingFactors)
+importFrom(shinyTools,customPointsServer)
+importFrom(shinyTools,customPointsUI)
 importFrom(shinyTools,dataExportButton)
 importFrom(shinyTools,dataExportServer)
 importFrom(shinyTools,extractTitle)
-importFrom(shinyTools,formatLegendOfGGplot)
 importFrom(shinyTools,formatPointsOfGGplot)
 importFrom(shinyTools,formatScalesOfGGplot)
 importFrom(shinyTools,formatTitlesOfGGplot)
@@ -117,6 +108,7 @@ importFrom(shinyTools,plotRangesServer)
 importFrom(shinyTools,plotRangesUI)
 importFrom(shinyTools,plotTitlesServer)
 importFrom(shinyTools,plotTitlesUI)
+importFrom(shinyTools,setLegendThemeOfGGplot)
 importFrom(shinyTools,shinyTryCatch)
 importFrom(shinyWidgets,pickerInput)
 importFrom(shinyWidgets,updatePickerInput)
@@ -125,16 +117,13 @@ importFrom(shinyjs,alert)
 importFrom(shinyjs,enable)
 importFrom(shinyjs,runjs)
 importFrom(stats,approx)
-importFrom(stats,as.formula)
 importFrom(stats,dnorm)
 importFrom(stats,lm)
 importFrom(stats,median)
 importFrom(stats,na.omit)
 importFrom(stats,quantile)
 importFrom(stats,sd)
 importFrom(utils,combn)
-importFrom(utils,read.csv)
 importFrom(utils,write.csv)
-importFrom(utils,write.table)
 importFrom(yaml,read_yaml)
 useDynLib(OsteoBioR, .registration = TRUE)

NEWS.md

@@ -1,3 +1,16 @@
+# OsteoBioR 25.02.0
+
+## New Features
+- option to add custom points to a plot
+- option to use custom legend labels for the plot (#69)
+- new logos and links in header
+
+# OsteoBioR 24.11.0
+
+## Updates
+- integration of modules from _ChangeR_ package for break-point detection (#72)
+- option to set the "x" and "y" columns for mcp modelling
+
 # OsteoBioR 24.10.0
 
 ## Updates

R/01-plotFormatting.R

@@ -1,32 +1,36 @@
 getStyleForIndividuals <- function(pointStyleList, input) {
   # pointStyleList are reactive values -> lapply over the names and not(!) the list itself
-  style <- lapply(names(pointStyleList), function(x) {pointStyleList[[x]][input]}) %>% 
+  style <- lapply(names(pointStyleList), function(individual) {pointStyleList[[individual]][input]}) %>% 
     unlist()
   names(style) <- names(pointStyleList)
 
   style
 }
 
-getDefaultPointFormatForModels <- function(pointStyleList, modelNames) {
+# Get the default point format for models
+# 
+# @param pointStyleList list of point styles for each model
+# @param modelNames names of the models
+# @param isFullReset if TRUE, all point styles are reset to the default values
+getDefaultPointFormatForModels <- function(pointStyleList, modelNames, isFullReset = FALSE) {
   # default colours
   defaultColours <- ggplot2::scale_color_discrete()$palette(n = length(modelNames))
   names(defaultColours) <- modelNames
 
   # setup lists with default values for style specs
   for (i in modelNames) {
-    if (is.null(pointStyleList[[i]])) 
+    if (is.null(pointStyleList[[i]]) || isFullReset) {
       pointStyleList[[i]] <- config()[["defaultPointStyle"]][["dataPoints"]]
-    # use default colour per model
-    pointStyleList[[i]]["color"] <- defaultColours[i]
+      # use default colour per model
+      pointStyleList[[i]]["color"] <- defaultColours[i]
+    }
   }
 
   return(pointStyleList)
 }
 
 getDefaultTextFormat <- function() {
-  list(legendTitle  = config()[["defaultIntervalTimePlotTitle"]],
-       legendText  = config()[["defaultIntervalTimePlotText"]],
-       plotTitle  = config()[["defaultIntervalTimePlotTitle"]],
+  list(plotTitle  = config()[["defaultIntervalTimePlotTitle"]],
        xAxisTitle = config()[["defaultIntervalTimePlotTitle"]],
        yAxisTitle = config()[["defaultIntervalTimePlotTitle"]],
        yAxisTitle2 = config()[["defaultIntervalTimePlotTitle"]],