Adapt plots to cohorts

.Rbuildignore

@@ -4,3 +4,4 @@
 ^codecov\.yml$
 ^man-roxygen$
 ^README\.md$
+wip/

.gitignore

@@ -3,3 +3,4 @@
 .RData
 .Ruserdata
 inst/doc
+wip/

DESCRIPTION

@@ -1,58 +1,49 @@
-Package: CBMutils
-Type: Package
-Title: Utilities for modelling carbon based on CBM-CFS3
-Description: Implementation of several components of the Carbon Budget Model of the
-    Canadian Forest Service (v3).
-URL:
-    https://github.com/PredictiveEcology/CBMutils,
-    https://docs.google.com/spreadsheets/d/1SNHvHpr7SVIMfaxOdKENYElwiME75GK-jl3vaVQb6-w
-Date: 2025-03-13
-Version: 1.0
-Authors@R: c(
-    person("Céline",    "Boisvenue", email = "celine.boisvenue@nrcan-rncan.gc.ca", role = c("aut")),
-    person("Alex M",    "Chubaty",   email = "achubaty@for-cast.ca",               role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7146-8135")),
-    person("Eliot",     "McIntire",  email = "eliot.mcintire@nrcan-rncan.gc.ca",   role = c("aut")),
-    person("Ian",       "Eddy",      email = "ian.eddy@nrcan-rncan.gc.ca",         role = c("ctb")),
-    person("Camille",   "Giuliano",  email = "camsgiu@gmail.com",                  role = c("ctb")),
-    person("Susan",     "Murray",    email = "murray.e.susan@gmail.com",           role = c("ctb")),
-    person("Dominique", "Caron",     email = "dominique.caron@nrcan-rncan.gc.ca",  role = c("ctb"))
-    )
-License: GPL-3
-Depends: R (>= 4.2)
-LinkingTo: 
-    Rcpp
-Imports:
-    cowplot,
-    crayon,
-    data.table,
-    fasterize,
-    ggforce,
-    ggplot2,
-    knitr,
-    LandR,
-    magrittr,
-    methods,
-    quickPlot (>= 0.1.8.9001),
-    raster,
-    reproducible,
-    robustbase,
-    Rcpp,
-    RSQLite,
-    scales,
-    sf,
-    sp,
-    terra
-Suggests:
-    covr,
-    devtools,
-    rmarkdown,
-    testthat,
-    withr
-Remotes:
-    PredictiveEcology/LandR@development,
-    PredictiveEcology/quickPlot@development,
-    PredictiveEcology/reproducible@development
-VignetteBuilder: knitr, rmarkdown
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+Package: CBMutils
+Type: Package
+Title: Utilities for modelling carbon based on CBM-CFS3
+Description: Implementation of several components of the Carbon Budget Model of the
+    Canadian Forest Service (v3).
+URL:
+    https://github.com/PredictiveEcology/CBMutils
+Version: 2.0.3.0005
+Authors@R: c(
+    person("Céline",    "Boisvenue", email = "celine.boisvenue@nrcan-rncan.gc.ca", role = c("aut")),
+    person("Alex M",    "Chubaty",   email = "achubaty@for-cast.ca",               role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7146-8135")),
+    person("Eliot",     "McIntire",  email = "eliot.mcintire@nrcan-rncan.gc.ca",   role = c("aut")),
+    person("Ian",       "Eddy",      email = "ian.eddy@nrcan-rncan.gc.ca",         role = c("ctb")),
+    person("Camille",   "Giuliano",  email = "camsgiu@gmail.com",                  role = c("ctb")),
+    person("Susan",     "Murray",    email = "murray.e.susan@gmail.com",           role = c("ctb")),
+    person("Dominique", "Caron",     email = "dominique.caron@nrcan-rncan.gc.ca",  role = c("ctb"))
+    )
+License: GPL-3
+Depends: R (>= 4.2)
+Imports:
+    cowplot,
+    crayon,
+    data.table,
+    exactextractr,
+    ggforce,
+    ggplot2,
+    knitr,
+    LandR,
+    methods,
+    patchwork,
+    reproducible,
+    reticulate,
+    robustbase,
+    RSQLite,
+    scales,
+    terra,
+    withr
+Suggests:
+    covr,
+    devtools,
+    rmarkdown,
+    testthat
+Remotes:
+    PredictiveEcology/LandR@development,
+    PredictiveEcology/reproducible@development
+VignetteBuilder: knitr, rmarkdown
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2

NAMESPACE

@@ -1,112 +1,71 @@
 # Generated by roxygen2: do not edit by hand
 
-export(.pooldef)
-export(.pooldefids)
-export(.poolids)
-export(.poolnames)
-export(ComputeGrowthAndDeclineMatrices)
-export(ComputeGrowthAndDeclineMatrices2)
-export(ComputeGrowthIncrements)
-export(ComputeOvermatureDecline)
-export(NPP)
 export(NPPplot)
-export(Spinup)
-export(StepPools)
-export(StepPoolsRef)
+export(ReticulateFindPython)
+export(adjustStandAges)
 export(b_m)
 export(barPlot)
 export(biomProp)
-export(biomassTurnoverMatrix)
+export(boudewynSubsetTables)
 export(calcC)
-export(calcTurnoverRates)
 export(carbonOutPlot)
-export(checkProp)
-export(checkTransactions)
-export(computeBioTurnoverMatrices)
-export(computeDomDecayMatrices)
-export(computeDomTurnoverMatrices)
-export(computeSlowDecayMatrices)
-export(computeSlowMixingMatrix)
 export(convertAGB2pools)
 export(convertM3biom)
 export(cumPoolsCreate)
 export(cumPoolsCreateAGB)
 export(cumPoolsSmooth)
-export(decayRate)
-export(domDecayMatrix)
-export(domDecayMatrixItem)
-export(domTurnOverMatrix)
+export(dataPrep_disturbanceRasters)
+export(dataPrep_disturbanceRastersURL)
+export(distMatch)
 export(gcidsCreate)
-export(getDecayRates)
-export(getIdentityCoordinateMatrix)
-export(getTable)
-export(hash)
-export(histDist)
-export(loadDisturbanceMatrixIds)
-export(m3ToBiomIncOnlyPlots)
 export(m3ToBiomPlots)
-export(m3ToVolCheckPlots)
-export(matrixDT)
-export(matrixHash)
 export(nmfac)
-export(plotCarbonRasters)
-export(prepInputsEcozones)
-export(prepInputsVRI)
-export(prepInputsVRIage)
-export(query)
-export(readSqlFile)
-export(retrieveSpuRaster)
 export(sapfac)
 export(seeDist)
 export(simDist)
-export(slowDecayMatrix)
 export(spatialPlot)
-export(spatialRaster)
-export(spatialUnitDecayRates)
-export(spuDist)
+export(sppMatch)
+export(spuDistList)
 export(spuDistMatch)
-export(ws3Build)
-exportClasses(dataset)
+export(spuHistDist)
 import(methods)
 importFrom(RSQLite,dbConnect)
 importFrom(RSQLite,dbDisconnect)
 importFrom(RSQLite,dbDriver)
-importFrom(RSQLite,dbGetQuery)
 importFrom(RSQLite,dbListTables)
 importFrom(RSQLite,dbReadTable)
-importFrom(Rcpp,sourceCpp)
 importFrom(cowplot,plot_grid)
 importFrom(crayon,red)
+importFrom(crayon,yellow)
 importFrom(data.table,as.data.table)
 importFrom(data.table,copy)
 importFrom(data.table,data.table)
+importFrom(data.table,key)
 importFrom(data.table,melt)
 importFrom(data.table,melt.data.table)
-importFrom(data.table,merge.data.table)
 importFrom(data.table,rbindlist)
-importFrom(data.table,set)
 importFrom(data.table,setkey)
+importFrom(data.table,setkeyv)
 importFrom(data.table,setnames)
-importFrom(data.table,setorderv)
-importFrom(fasterize,fasterize)
+importFrom(exactextractr,exact_resample)
 importFrom(ggforce,facet_wrap_paginate)
 importFrom(ggforce,theme_no_axes)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,expansion)
-importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_col)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_raster)
 importFrom(ggplot2,ggplot)
-importFrom(ggplot2,ggsave)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,guide_legend)
 importFrom(ggplot2,guides)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_fill_brewer)
 importFrom(ggplot2,scale_fill_continuous)
 importFrom(ggplot2,scale_fill_discrete)
+importFrom(ggplot2,scale_fill_manual)
 importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,sec_axis)
@@ -115,40 +74,28 @@ importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_classic)
 importFrom(ggplot2,xlab)
 importFrom(knitr,kable)
-importFrom(magrittr,"%>%")
-importFrom(quickPlot,Plot)
-importFrom(quickPlot,clearPlot)
-importFrom(raster,"crs<-")
-importFrom(raster,couldBeLonLat)
-importFrom(raster,crop)
-importFrom(raster,crs)
-importFrom(raster,extent)
-importFrom(raster,mosaic)
-importFrom(raster,ncell)
-importFrom(raster,raster)
-importFrom(raster,shapefile)
-importFrom(raster,stack)
-importFrom(reproducible,checkPath)
-importFrom(reproducible,postProcess)
-importFrom(reproducible,prepInputs)
+importFrom(patchwork,plot_annotation)
+importFrom(patchwork,plot_layout)
+importFrom(patchwork,wrap_plots)
+importFrom(reproducible,preProcess)
 importFrom(robustbase,nlrob)
 importFrom(scales,pretty_breaks)
-importFrom(sf,st_as_sf)
-importFrom(sf,st_crop)
-importFrom(sf,st_crs)
-importFrom(sf,st_read)
-importFrom(sf,st_transform)
-importFrom(sp,identicalCRS)
-importFrom(sp,spTransform)
 importFrom(stats,approx)
 importFrom(stats,as.formula)
 importFrom(stats,na.omit)
 importFrom(stats,predict)
 importFrom(stats,runif)
-importFrom(stats,time)
+importFrom(terra,cellSize)
+importFrom(terra,compareGeom)
+importFrom(terra,crs)
+importFrom(terra,disagg)
+importFrom(terra,mosaic)
+importFrom(terra,nlyr)
+importFrom(terra,project)
 importFrom(terra,rast)
 importFrom(terra,res)
 importFrom(terra,unwrap)
 importFrom(terra,values)
+importFrom(utils,download.file)
 importFrom(utils,tail)
-useDynLib(CBMutils, .registration = TRUE)
+importFrom(utils,unzip)