transitioned to and ; modified exported functions

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.1.1
-Date: 2022-11-22 10:49:33.969 UTC
-SHA: 67c7b4227692e8479fe385b11fbe8cb4a59ca98d
+Version: 2.1.2
+Date: 2023-03-30 10:19:09.372 UTC
+SHA: 119640b3cb69afd00649a6f5c304c3c4ac5e882b

DESCRIPTION

@@ -1,18 +1,18 @@
 Package: dynamAedes
-Version: 2.1.1
-Date: 2022-11-21
+Version: 2.1.2
+Date: 2023-03-23
 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 (>= 3.6.0), raster
-Imports: drc, fields, foreach, insol, slam, doParallel, sp
+Depends: R (>= 4.0.0)
+Imports: doParallel, dplyr, drc, fields, foreach, geosphere, raster, slam, sp
 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, ..., Marcantonio (2021) <doi:10.1016/j.ecoinf.2020.101180> and Da Re, ..., Marcantonio (2022) <doi:10.1101/2021.12.21.473628>.
+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
 Encoding: UTF-8
 Language: en-GB
 License: GPL(>=2)
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
-Suggests: parallel, rmarkdown, knitr, eesim, geosphere, ggplot2, gstat, rgeos, spatstat, rgdal, tidyverse
+RoxygenNote: 7.2.3
+Suggests: terra, parallel, rmarkdown, knitr, eesim, ggplot2, gstat, spatstat, rgdal
 Config/testthat/edition: 3
 URL: https://mattmar.github.io/dynamAedes/

NAMESPACE

@@ -9,17 +9,12 @@ importFrom("stats", "dgamma", "dlnorm", "lm", "predict", "rbinom", "rmultinom",
 importFrom("fields", "rdist")
 importFrom("slam", "as.simple_sparse_array")
 importFrom("drc", "drm")
-importFrom("insol", "JD", "daylength")
+importFrom("geosphere", "daylength")
 importFrom("raster", "stack", "raster", "rasterFromXYZ")
 importFrom("sp", "gridded", "coordinates", "spTransform", "CRS", "SpatialPoints")
-
+importFrom("dplyr", "%>%", "bind_rows", "as_tibble", "mutate")
 #####################################
 ##               Export            ##
 #####################################
-export(dynamAedes.m, .beta.fun, .DRC.beta, .beta.init)
-export(.a.a_disp.f, .a.gono_rate.f, .a.ovi_rate.f, 
-.a.surv_rate.f, .i.emer_rate.f, .e.surv_rate.f,
-.i.surv_rate.f, .e.hatch_rate.f, .e.dia_rate.f, 
-.d.surv_rate.f, .i.ddmort_rate.f, psi, psi_sp, 
-icci, adci, adci_sp, dici, 
-.returndis, .euc, .meuc)
+export(dynamAedes.m)
+export(psi, psi_sp, icci, adci, adci_sp, dici)

NEWS.md

@@ -1,3 +1,9 @@
+# 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
+
 # dynamAedes 2.1.1
 * Adding rgdal in the description
 

R/dici.R

@@ -44,27 +44,4 @@ dici <- function(input_sim=NULL, coords=NULL, eval_date=NULL, breaks=c(0.25,0.5,
 			return(stack(outs))
 		}
 	}
-}
-
-# Ad-hoc functions
-.returndis <- function(distl=NA, days=NA, breaks=breaks) {
-	out <- do.call(rbind.data.frame, 
-		lapply(days, function(x) {
-			round(quantile(unlist(sapply(1:length(distl),
-				function(y) {mean(if(x<=length(distl[[y]])) as.integer(distl[[y]][[x]]) else NA, na.rm=T)})), probs=breaks, na.rm=T),1)
-		}))
-	names(out) <- breaks
-	return(out)
-}
-
-.euc <- function(xs, ys) { sqrt((xs[1]-xs[2])^2 + (ys[1]-ys[2])^2) }
-.meuc <- function(c1, c2, coords) {
-	c3 <- coords[unlist(c1[,1])[1],]
-	outd <- list(NA)
-	for ( rw in 1:length(c2) ) {
-		outd[[rw]] <- sapply(unlist(c2[rw]), function(x) {
-			.euc(c(as.numeric(c3[1]), as.numeric(coords[x,1])), c(as.numeric(c3[2]), as.numeric(coords[x,2])))
-		})
-	}
-	return(outd)
-}
+}

R/dynamAedes.m.R

@@ -44,18 +44,18 @@ dynamAedes.m <- function(species="aegypti", intro.eggs=0, intro.deggs=0, intro.a
     ### Initial checks
 	#Species
 	if( !species%in%c("aegypti","albopictus","koreicus","japonicus") ) {
-		stop("Species not supported, exiting..." )
+		stop("Mosquito species not supported, exiting..." )
 	}
 	#Dayspan
 	if( is.na(endd) ) {
 		if( nchar(strsplit(as.character(startd),"-")[[1]][1])<4 ) {
-			stop("Dates in the wrong format: change them to %Y-%m-%d")
+			stop("Dates in the wrong format: change them to '%Y-%m-%d'.")
 		}
 		dayspan <- as.integer(ncol(temps.matrix)-1)
 	} 
 	else {
 		if( nchar(strsplit(as.character(startd),"-")[[1]][1])<4|nchar(strsplit(as.character(endd),"-")[[1]][1])<4 ) {
-			stop("Dates in the wrong format: change them to %Y-%m-%d")
+			stop("Dates in the wrong format: change them to '%Y-%m-%d'.")
 		}
 		dayspan <- as.integer(as.Date(endd)-as.Date(startd))
 	}
@@ -68,7 +68,6 @@ dynamAedes.m <- function(species="aegypti", intro.eggs=0, intro.deggs=0, intro.a
 		if( is.na(coords.proj4) ) {
 			stop("No proj4 string for input coordinates. Please set 'coords.proj4' option.")
 			} else {
-				message("inside")
 				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"))))
 			}
 		}
@@ -95,12 +94,13 @@ dynamAedes.m <- function(species="aegypti", intro.eggs=0, intro.deggs=0, intro.a
 									} else (stop("avgpdisp not supported yet..."))
 	## Derive daylength for laying of diapausing eggs in albopictus/koreicus/japonicus
 	if( species!="aegypti" ){
-		jd <- JD(seq(as.POSIXct(startd), as.POSIXct(as.Date(startd)+dayspan), by='day'))
+		doy <- as.numeric(format(seq(as.POSIXct(startd), as.POSIXct(as.Date(startd)+dayspan), by='day'), "%j"))
 		if( scale=="rg" ) {
-			photo.matrix <- lapply(jd, function(x){insol::daylength(long = cells.coords.photo[,1], lat=cells.coords.photo[,2], jd=x, 1)[,3]})
+			photo.matrix <- lapply(doy, function(x){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,long,jd,1)[,3]
+				dl <- daylength(lat,doy)
 				photo.matrix <- matrix(dl, nrow=1)
 				} else (stop("Something's wrong with scale or lat and long"))
 				} else{