Spread curve (#232)

* BUG!!

* Bugfix

* initial MR

* implement in UI

* fix issue kernel density

* get updates from beta (#242)

* MpiIsoApp 24.05.3: Bugfix missing lat/long (#219)

* BUG!!

* Bugfix

* update news.md

---------

Co-authored-by: Antonia Runge <antonia.runge@inwt-statistics.de>

* MpiIsoApp 24.05.4: fix warning (#217)

* fix warning

* extract updatePenalty function

* update news.md

---------

Co-authored-by: Antonia Runge <antonia.runge@inwt-statistics.de>

* MpiIsoApp 24.05.5: optionally download savedMaps (#222)

* optionally download savedMaps

* format new UI

* MpiIsoApp 24.05.6: option to export all plots from savedMaps (#223)

* option to export all plots from savedMaps

* remove not required

* picker input to select savedMaps for download

* shift code

* update news.md

* fix issue with missing thumbnail plot

* return empty list if missing

* cleaner return

* remove option to download savedMaps objects

* add docu

* add param to docu

* MpiIsoApp 24.05.7: Feat/224 warning if creating prob map (#225)

* fix issue with missing thumbnails, fix pch value

* update news.md

* set pch to NA

* doc rcmd and rm rgpt3 and rename r pkg (#227)

* add inwtlab repo to .Rprofile file

* add pkgdown doc

* add pandora base image to pkg down workflow

* remove rgpt3 dependency

* add r-cmd check via actions

* renaming of r-package

* update README

* update NEWS

* MpiIsoApp 24.04.2: replace retired packages (#230)

* add test dataQuery

* replace retired packages

---------

Co-authored-by: Jan Abel <106665518+jan-abel-inwt@users.noreply.github.com>

* add rcmd check badge

---------

Co-authored-by: Jan Abel <jan.abel@office-platform.net>
Co-authored-by: Antonia Runge <antonia.runge@inwt-statistics.de>

* remove warning

* replace deprecated package name

* add deploy job without base-image

* Release versions 24.06.0.2 from beta (#231)

* altitude operations (#191)

* altitude operations

* Fix

* set default differently

* make data points selectable in locateR

* update news

* Fix for older version

* fixes

* fix progress message

* remove comments

---------

Co-authored-by: Antonia Runge <antonia.runge@inwt-statistics.de>

* Fix error with mask (#208)

* add new tests

* extract function centerPlotData

* add tryCatch to plotting of map, add data preview, add logDebugs

* remove deprecated parameter 'mainfolder', add data preview

* update news.md

* catch failing of maskDraw if no data

* update news.md

* fix issue when drawing only centroids, add test

* add tryCatch to left plotting functions

* Version 24.05.0: Feat/202 contour maps (#210)

* option to use simple contour map, some formatting

* update news.md

* Feat/169 centering of coordinates (#215)

* new functions and ui input

* align values

* center predictions

* UI to center data coordinates before modelling

* add logic to center data before modelling to different modelling tabs

* add logic

* remove comments

* update news.md

* update news.md

* rename input to prevent confusion with parameter from batch mode

* extract processing of coordinate data

* extract and apply data augmentation

* fix issue with wrong default zoom when switching the map center

* add more docu

* more docu

* update test because of new logic

* add a vignette to the package about the processing of coordinate data

* update news.md

* fix for data augmentation

* Version 24.05.2: option to select a specific color for "fixed" point colour (#216)

* option to select a specific color for "fixed" point colour

* new button to apply point settings and the logic

* update news.md

* update tests after adding new input

* fix news.md

* MpiIsoApp 24.05.3: Bugfix missing lat/long (#219)

* BUG!!

* Bugfix

* update news.md

---------

Co-authored-by: Antonia Runge <antonia.runge@inwt-statistics.de>

* MpiIsoApp 24.05.4: fix warning (#217)

* fix warning

* extract updatePenalty function

* update news.md

---------

Co-authored-by: Antonia Runge <antonia.runge@inwt-statistics.de>

* MpiIsoApp 24.05.5: optionally download savedMaps (#222)

* optionally download savedMaps

* format new UI

* MpiIsoApp 24.05.6: option to export all plots from savedMaps (#223)

* option to export all plots from savedMaps

* remove not required

* picker input to select savedMaps for download

* shift code

* update news.md

* fix issue with missing thumbnail plot

* return empty list if missing

* cleaner return

* remove option to download savedMaps objects

* add docu

* add param to docu

* MpiIsoApp 24.05.7: Feat/224 warning if creating prob map (#225)

* fix issue with missing thumbnails, fix pch value

* update news.md

* set pch to NA

* remove warning

* replace deprecated package name

---------

Co-authored-by: Marcus Groß <marcus.gross@inwt-statistics.de>

* merge changes from beta

---------

Co-authored-by: Marcus Groß <marcus.gross@inwt-statistics.de>
Co-authored-by: Jan Abel <106665518+jan-abel-inwt@users.noreply.github.com>
Co-authored-by: Jan Abel <jan.abel@office-platform.net>

* use older version of gdistance

---------

Co-authored-by: Antonia Runge <antonia.runge@inwt-statistics.de>
Co-authored-by: Jan Abel <106665518+jan-abel-inwt@users.noreply.github.com>
Co-authored-by: Jan Abel <jan.abel@office-platform.net>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: DSSM
 Title: Pandora & IsoMemo spatiotemporal modeling
-Version: 24.08.1
+Version: 24.08.2
 Authors@R: c(
             person("Marcus", "Gross", email = "marcus.gross@inwt-statistics.de", role = c("cre", "aut")),
             person("Antonia", "Runge", email = "antonia.runge@inwt-statistics.de", role = c("aut"))
@@ -21,6 +21,7 @@ Imports:
     elevatr (>= 0.4.2),
     futile.logger,
     jsonlite (>= 1.5),
+    gdistance (>= 1.3-6),
     geometry (>= 0.4.0),
     ggplot2,
     grDevices (>= 3.4.4),

NAMESPACE

@@ -97,6 +97,10 @@ importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,ungroup)
 importFrom(elevatr,get_elev_point)
+importFrom(gdistance,accCost)
+importFrom(gdistance,geoCorrection)
+importFrom(gdistance,shortestPath)
+importFrom(gdistance,transition)
 importFrom(geometry,convhulln)
 importFrom(geometry,inhulln)
 importFrom(ggplot2,aes)
@@ -208,8 +212,11 @@ importFrom(mice,mice)
 importFrom(openxlsx,read.xlsx)
 importFrom(openxlsx,write.xlsx)
 importFrom(pgdraw,pgdraw)
+importFrom(raster,adjacent)
 importFrom(raster,getValues)
+importFrom(raster,ncell)
 importFrom(raster,raster)
+importFrom(raster,rasterFromXYZ)
 importFrom(raster,terrain)
 importFrom(raster,writeRaster)
 importFrom(rcarbon,calibrate)
@@ -231,6 +238,7 @@ importFrom(shinyjs,hide)
 importFrom(shinyjs,runjs)
 importFrom(shinyjs,show)
 importFrom(shinyjs,useShinyjs)
+importFrom(sp,SpatialPixelsDataFrame)
 importFrom(sp,SpatialPoints)
 importFrom(sp,plot)
 importFrom(sp,point.in.polygon)

NEWS.md

@@ -1,3 +1,9 @@
+# DSSM 24.08.2
+
+## New Features
+- _Cost Surface and least-cost path for SpreadR_:
+  - Estimate cost surface and shortest path using the gdistance package
+
 # DSSM 24.08.1
 
 ## Bug Fixes

R/00-Namespace.R

@@ -11,6 +11,7 @@
 #'  ungroup
 #' @importFrom DT datatable renderDataTable dataTableOutput
 #' @importFrom elevatr get_elev_point
+#' @importFrom gdistance transition transition accCost shortestPath geoCorrection
 #' @importFrom geometry convhulln inhulln
 #' @importFrom ggplot2 ggplot theme theme_light coord_cartesian geom_point theme_light theme labs
 #'  geom_errorbar aes_ element_blank element_text position_dodge aes geom_boxplot xlab ylab
@@ -33,7 +34,7 @@
 #' @importFrom mice mice complete
 #' @importFrom openxlsx read.xlsx write.xlsx
 #' @importFrom pgdraw pgdraw
-#' @importFrom raster raster getValues terrain writeRaster
+#' @importFrom raster raster getValues terrain writeRaster rasterFromXYZ adjacent ncell
 #' @importFrom RColorBrewer brewer.pal
 #' @importFrom Rfast spdinv Crossprod rmvnorm
 #' @importFrom rlang .data
@@ -45,7 +46,7 @@
 #' @importFrom stats aggregate as.formula cor cov density dist dnorm dunif kmeans
 #'  mahalanobis median model.matrix na.exclude na.omit pchisq  pf pnorm predict
 #'  qnorm quantile rbeta residuals rgamma rnorm runif sd var
-#' @importFrom sp point.in.polygon plot SpatialPoints
+#' @importFrom sp point.in.polygon plot SpatialPoints SpatialPixelsDataFrame
 #' @importFrom stringi stri_escape_unicode
 #' @importFrom utils available.packages compareVersion install.packages head zip
 #'  packageVersion read.csv read.csv2 write.table installed.packages capture.output