Daniele's transitioning rgdal-terra

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: dynamAedes
-Version: 2.2.0
-Date: 2023-07-31
+Version: 2.2.5
+Date: 2023-10-05
 Title: A Unified Mechanistic Model for the Population Dynamics of Invasive Aedes Mosquitoes
 Authors@R: c(person("Matteo", "Marcantonio", role = c("aut", "cre"), email = "marcantoniomatteo@gmail.com"),person("Daniele", "Da Re", role = c("aut"), email = "dare.daniele@gmail.com")) 
 Depends: R (>= 4.0.0)
-Imports: doParallel, dplyr, drc, foreach, geosphere, raster, slam, sp, terra
+Imports: parallel, doParallel, foreach, drc, geosphere, terra
 BugReports: https://github.com/mattmar/dynamAedes
 Description: Generalised model for population dynamics of invasive Aedes mosquitoes. Rationale and model structure are described here: Da Re et al. (2021) <doi:10.1016/j.ecoinf.2020.101180> and Da Re et al. (2022) <doi:10.1101/2021.12.21.473628>.
 VignetteBuilder: knitr
@@ -13,6 +13,6 @@ Language: en-GB
 License: GPL(>=2)
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Suggests: parallel, rmarkdown, knitr, eesim, ggplot2, gstat, spatstat, rgdal
+Suggests: rmarkdown, knitr, eesim, gstat, stats, dplyr, ggplot2, sf
 Config/testthat/edition: 3
 URL: https://mattmar.github.io/dynamAedes/

NAMESPACE

@@ -6,13 +6,9 @@ importFrom("doParallel", "registerDoParallel")
 importFrom("foreach", "%dopar%", "foreach", "%do%")
 importFrom("utils", "setTxtProgressBar", "txtProgressBar")
 importFrom("stats", "dgamma", "dlnorm", "lm", "predict", "rbinom", "rmultinom", "rpois", "sortedXyData", "quantile", "setNames", "glm")
-importFrom("slam", "as.simple_sparse_array")
 importFrom("drc", "drm")
 importFrom("geosphere", "daylength")
-importFrom("raster", "stack", "raster", "rasterFromXYZ")
-importFrom("terra", "distance")
-importFrom("sp", "gridded", "coordinates", "spTransform", "CRS", "SpatialPoints")
-importFrom("dplyr", "%>%", "bind_rows", "as_tibble", "mutate")
+importFrom("terra", "distance","crds","project","vect")
 #####################################
 ##               Export            ##
 #####################################

NEWS.md

@@ -1,16 +1,20 @@
+# dynamAedes 2.2.5
+* Removes definitely rgdal from package
+* Clears NAMESPACE
+
 # dynamAedes 2.2.0
 * Substitutes `fields::rdist` with terra::distance which solves a bug in active dispersal
 * Adds a switch for active dispersal only `pDispersal=FALSE`
-* Removes warnings changing Beta function with polynomial for egg survival in aegypti
-* Raised 0 hatching rate to 15°C
+* Removes warnings changing Beta function with polynomial for egg survival in Aedes aegypti
+* Raised 0 hatching rate to 15°C for aegypti
 * Other minor cosmetic changes
 * Modify verbose option for debugging, now an integer with values 0 (silent), 1 or 2.
 
 # dynamAedes 2.1.2
 * Transitioning from 'rgdal' and 'sp' to 'terra'
 * Transitioning from 'insol' to 'geosphere'
 * Removing block-loading of 'tidyverse' (speeding up loading?)
-* Helper functions not anymore exported
+* Helper functions not exported any more
 
 # dynamAedes 2.1.1
 * Adding rgdal in the description
@@ -19,12 +23,11 @@
 * Adding website with examples for the three scales (pkgdown)
 * Coordinates now internally transformed (if not in lat/long) for the derivation of the photoperiod
 * Adding option **coords.proj4** to specify coordinate projection (in proj4 format)
-* Renaming dynamAedes as dynamAedes
+* Renaming dynamAedes as dynamAedes.m
 
 # dynamAedes 2.0.3
 * At regional scale now diapause derived pixel by pixel using the photoperiod of input coordinates.
-* You can now introduce diapause eggs using dynamAedes argument
- "intro.degg"
+* You can now introduce diapause eggs using dynamAedes argument "intro.degg"
 
 # dynamAedes 2.0.2
 * Minor bug fix for idci and icci functions

R/adci_sp.R

@@ -53,11 +53,12 @@ adci_sp=function (input_sim = NULL, coords = NULL, eval_date = NULL, stage = 1,
       tmp = rate.sp[, y]
       tmp = as.data.frame(cbind(coords, tmp))
       names(tmp)[1:2] = c("X", "Y")
-      tmp=rasterFromXYZ(tmp)
+      tmp=terra::rast(tmp, type="xyz")
       names(tmp) = paste0("p", breaks[y])
       return(tmp)
         })
-    outr=stack(rb)
+    outr=return(do.call(c,rb))
+
 })
   }
   names(myOut)=paste0("d_", eval_date)

R/dici.R

@@ -38,10 +38,10 @@ dici <- function(input_sim=NULL, coords=NULL, eval_date=NULL, breaks=c(0.25,0.5,
 				coords1$inv <- 0
 				coords1$inv[x[[maxdate]]] <- 1
 				names(coords1)=c("X", "Y", paste0("day",maxdate,"_inv_cells_Iteration"))
-				coords1 <- rasterFromXYZ(coords1)
+				coords1 <- terra::rast(coords1, type="xyz")
 				return(coords1)
 			})
-			return(stack(outs))
+			return(do.call(c,outs))
 		}
 	}
 }

R/dynamAedes.m.R

@@ -28,7 +28,7 @@
 #' @param sparse.output logical. The output matrix is optimised for sparse-matrix algebra (e.g. zeros are indexed).
 #' @param compressed.output logical. Default TRUE, if FALSE provide abundance for each model's subcompartiment; if FALSE abundances are summed per compartment.
 #' @param suffix character. Model output suffix for output RDS. 
-#' @param verbose integer. if 1 then an overview of population dynamics is printed in the console, if 2 more information on population dinamycs are printed out. Default is 0 (silent).
+#' @param verbose integer. if 1 then an overview of population dynamics is printed in the console, if 2 more information on population dynamics are printed out. Default is 0 (silent).
 #' @param seeding logical, default \code{FALSE}, if \code{seeding=TRUE} a fixed seed is applied for result reproducibility.  
 #' @return Matrix or a list of matrices containing, for each iteration, the number of individuals in each life stage per day (and for each grid cell of the study area if scale="lc" or "rg"). If the argument compressed.output=FALSE (default TRUE), the model returns the daily number of individuals in each life stage sub-compartment.	
 #' @example inst/examples/dynamAedes.m.R
@@ -84,7 +84,7 @@ if(scale!="ws") {
 		if( is.na(coords.proj4) ) {
 			stop("No proj4 string for input coordinates. Please set 'coords.proj4' option.")
 			} else {
-				cells.coords.photo <- as.data.frame(coordinates(spTransform(SpatialPoints(cells.coords, proj4string=CRS(coords.proj4)), CRSobj=CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"))))
+				cells.coords.photo <- terra::crds(terra::project(terra::vect(x= cells.coords, type="points", atts=NULL, crs=coords.proj4), "EPSG:4326"), df=TRUE)
 			}
 		}
 		if( maxlat>90 )	{
@@ -116,7 +116,7 @@ if( is.na(avgpdisp) ) {
 if( species!="aegypti" ){
 	doy <- as.numeric(format(seq(as.POSIXct(startd), as.POSIXct(as.Date(startd)+dayspan), by='day'), "%j"))
 	if( scale=="rg" ) {
-		photo.matrix <- lapply(doy, function(x){daylength(lat=cells.coords.photo[,2], doy=x)})
+		photo.matrix <- lapply(doy, function(x){geosphere::daylength(lat=cells.coords.photo[,2], doy=x)})
 		photo.matrix <- do.call(cbind,photo.matrix)
 		} else if( !is.na(lat)&!is.na(long) ) {
 			dl <- daylength(lat,doy)
@@ -135,7 +135,7 @@ if(cluster.type=="PSOCK") {
 	cl <- makeCluster(spec=n.clusters, type=cluster.type, nnodes=n.clusters, outfile="")
 	} else(message("The only supported `cluster.type` is SOCK"))
 ## Register the environment 
-registerDoParallel(cl, cores=n.clusters)
+doParallel::registerDoParallel(cl, cores=n.clusters)
 if(seeding) parallel::clusterEvalQ(cl, set.seed(2021))
 ## Define space dimensionality into which simulations occour
 space <- nrow(temps.matrix)
@@ -145,7 +145,7 @@ pb <- txtProgressBar(char = "%", min = 0, max = iter, style = 3)
 ### End of preamble ###
 #%%%%%%%%%%%%%%%%%%%%%#
 ### Iterations: start parallelised introduction "iteration" ###
-rs <- foreach( iteration=1:iter, .packages="foreach", .export = ls(globalenv()) ) %dopar% {
+rs <- foreach::foreach( iteration=1:iter, .packages="foreach", .export = ls(globalenv()) ) %dopar% {
 ## Condition to satisfy to stop the life cycle: sum(pop) == 0, in case the day before extinction has happened
 stopit <- FALSE
 ## Update progress bar
@@ -471,6 +471,6 @@ if( !is.na(suffix) ) {
 	saveRDS(rs, paste(suffix,".RDS",sep=""))
 	} else message("\n\n\n########################################\n## Iterations concluded.##\n########################################\n\n\n")
 # Close cluster
-stopCluster(cl)
+parallel::stopCluster(cl)
 return(rs)
 }

R/psi_sp.R

@@ -39,11 +39,14 @@ psi_sp = function(input_sim=NULL,coords=NULL, eval_date=NULL, n.clusters=1) {
 			my.out=Reduce('+', mylist)/length(input_sim)
   		#rasterize
 		}
-		return(stack(apply(my.out, 2, function(x) {
+		rateList <- apply(my.out, 2, function(x) {
 			rate.sp=as.data.frame(cbind(coords, data.frame(x)))
-			names(rate.sp)=c("X", "Y", "ProbIntro")
-			rate.sp<-rasterFromXYZ(rate.sp)
-			return(rate.sp)
-		})))
+			#names(rate.sp)=c("X", "Y", "ProbIntro")
+			rate.sp<-terra::rast(rate.sp, type="xyz")
+			#return(rate.sp)
+		})
+		rateList <-do.call(c, unname(rateList))
+		names(rateList) <- my_names
+		return(rateList)
 	}
 }

TODO

@@ -1,7 +1,10 @@
 ## 2.1.*
-# Multiple introductions for punctual scale: Eva?;
-# Implement evaporation function and precipitation input;
-# dynamAedes object to store attributes of the scenario;
+# Remove gdal from DESCRIPTION and thus vignettes
+# Multiple introductions for punctual scale: Emma?
+# Implement evaporation function and precipitation input
+# dynamAedes object to store attributes of the scenario
+# Add new function for adci made by Daniele
+# Check if dplyr can be just in suggested
 
 # dynamAedes.m 1.0.0
 ## package: Add vignettes

docs/pkgdown.yml

@@ -2,8 +2,8 @@ pandoc: 2.9.2.1
 pkgdown: 2.0.7.9000
 pkgdown_sha: 7b810a790f04971c32c9fb33b6ed6eab0e5d16a4
 articles:
-  dynamAedes_local: dynamAedes_local.html
-  dynamAedes_punctual: dynamAedes_punctual.html
-  dynamAedes_regional: dynamAedes_regional.html
-last_built: 2023-07-28T11:29Z
+  dynamAedes_01_punctual: dynamAedes_01_punctual.html
+  dynamAedes_02_local: dynamAedes_02_local.html
+  dynamAedes_03_regional: dynamAedes_03_regional.html
+last_built: 2023-10-05T11:15Z