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| # 00b_Assigning Dispersals to unknown generation times | ||
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| # Iceberg pre-GAM spatial processing #### | ||
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| # Rscript "01_Iceberg ENM Currents.R" | ||
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| library(tidyverse); library(raster); library(parallel); library(sf); library(Matrix); library(magrittr); library(SpRanger); library(cowplot) | ||
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| CORES <- 45 | ||
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| t1 <- Sys.time() | ||
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| print("Dropping Species!") | ||
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| Method = "MaxEnt" | ||
| # Method = "RangeBags" | ||
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| source("00_Iceberg Species Dropping.R") | ||
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| paste0("Iceberg Input Files/","MaxEnt","/01_Raw/Currents") %>% | ||
| list.files(full.names = T) %>% | ||
| append(paste0("Iceberg Input Files/","RangeBags","/01_Raw/Currents") %>% list.files(full.names = T)) -> | ||
| FullFiles | ||
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| paste0("Iceberg Input Files/","MaxEnt","/01_Raw/Currents") %>% | ||
| list.files() %>% str_remove(".rds$") %>% | ||
| append(paste0("Iceberg Input Files/","RangeBags","/01_Raw/Currents") %>% list.files() %>% str_remove(".rds$")) -> | ||
| names(FullFiles) | ||
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| Species <- SpeciesList %>% unlist %>% sort() | ||
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| Files <- FullFiles[Species] | ||
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| PredReps <- c("Currents", paste0("Futures", 1:4)) | ||
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| # Blanks | ||
| blank <- matrix(0,360*2,720*2) # proper resolution | ||
| blank <- raster(blank) | ||
| extent(blank) <- c(-180,180,-90,90) | ||
| projection(blank) <- CRS("+proj=longlat +datum=WGS84") | ||
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| UniversalBlank <- raster("Iceberg Input Files/UniversalBlank.tif") | ||
| Land = which(raster::values(UniversalBlank)==0) | ||
| Sea = which(is.na(raster::values(UniversalBlank))) | ||
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| # Grid areas | ||
| AreaRaster <- raster("Iceberg Input Files/LandArea.asc") | ||
| AreaValues <- raster::values(AreaRaster) | ||
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| # Land Use Data | ||
| iucndat <- read.csv('Iceberg Input Files/IucnHabitatData.csv') | ||
| convcodes <- read.csv('Iceberg Input Files/IUCN_LUH_conversion_table.csv') | ||
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| iucndat %>% | ||
| left_join(convcodes, by = c("code" = "IUCN_hab")) %>% | ||
| mutate(name = name %>% str_replace(" ", "_")) -> | ||
| Habitats | ||
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| lapply(Species, function(a){ | ||
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| Habitats %>% filter(name == a) %>% pull(LUH) | ||
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| }) -> HabitatList | ||
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| names(HabitatList) <- Species | ||
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| landuse2017 <- brick('Iceberg Input Files/landuse2017.grd') | ||
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| # Continents #### | ||
| print("Continents!") | ||
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| ContinentRaster <- raster("Iceberg Input Files/continents-greenland.tif") %>% | ||
| resample(blank, method = "ngb") | ||
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| ContinentWhich <- lapply(1:6, function(a) which(values(ContinentRaster)==a)) | ||
| names(ContinentWhich) <- c("Africa", "Eurasia", "Greenland", "NAm", "Oceania", "SAm") | ||
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| # IUCN ranges for continent clipping #### | ||
| print("IUCN!") | ||
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| load("~/LargeFiles/MammalStackFullMercator.Rdata") | ||
| load("Iceberg Input Files/IUCNBuffers.Rdata") | ||
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| IUCNSp <- names(MammalStackFull) %>% intersect(Species) | ||
| MammalStackFull <- MammalStackFull[IUCNSp] | ||
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| # Dispersals #### | ||
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| Dispersals <- read.csv("Iceberg Input Files/Data for dispersal.csv", header = T) | ||
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| Dispersals$Scientific_name <- Dispersals$Scientific_name %>% str_replace(" ", "_") | ||
| Dispersals <- Dispersals %>% filter(!is.na(Scientific_name)) | ||
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| ToBuffer <- intersect(Species, Dispersals %>% filter(!is.na(disp50)) %>% pull(Scientific_name)) | ||
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| ToFill <- setdiff(Species, ToBuffer) | ||
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| write.csv(ToFill, file = "Iceberg Input Files/ImputedDispersals.csv") | ||
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| # Assigning generation times #### | ||
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| Dispersals[Dispersals$Scientific_name%in%ToFill,"Carnivore"] # All there | ||
| Dispersals[Dispersals$Scientific_name%in%ToFill,"BodyMass.Value"] # All there | ||
| Dispersals[Dispersals$Scientific_name%in%ToFill,"GenerationLength_d"] # All NA's | ||
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| # Importing nearest phylogenetic neighbour #### | ||
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| if(!file.exists("Iceberg Input Files/FullSTMatrix.csv")){ | ||
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| library(geiger);library(ape);library(picante);library(dplyr) | ||
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| STFull <- read.nexus("data/ele_1307_sm_sa1.tre")[[1]] | ||
| FullSTMatrix <- as.data.frame(cophenetic(STFull)) %>% as.matrix | ||
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| write.csv(FullSTMatrix, file = "Iceberg Input Files/FullSTMatrix.csv", row.names = F) | ||
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| } else{FullSTMatrix <- as.matrix(read.csv("Iceberg Input Files/FullSTMatrix.csv", header = T)) } | ||
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| colnames(FullSTMatrix) %>% setdiff(ToFill, .) | ||
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| rownames(FullSTMatrix) <- colnames(FullSTMatrix) | ||
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| ThinSTMatrix <- FullSTMatrix[,intersect(colnames(FullSTMatrix), | ||
| Dispersals %>% filter(!is.na(disp50)) %>% pull(Scientific_name))] | ||
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| for(a in 1:length(ToFill)){ | ||
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| Sp <- ToFill[a] | ||
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| Vector <- ThinSTMatrix[Sp,] | ||
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| MinVector <- which(Vector==min(Vector)) | ||
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| if(length(MinVector)>1){ | ||
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| MinVector %>% sample(1) %>% names -> | ||
| Sp2 | ||
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| }else{ | ||
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| MinVector %>% names -> | ||
| Sp2 | ||
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| } | ||
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| FillGenerationLength <- Dispersals[Dispersals$Scientific_name == Sp2, "GenerationLength_d"] -> | ||
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| Dispersals[Dispersals$Scientific_name == Sp, "GenerationLength_d"] | ||
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| } | ||
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| Dispersals[Dispersals$Scientific_name%in%ToFill,"GenerationLength_d"] # it worked! | ||
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| # Colin's loop #### | ||
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| for(i in 1:nrow(Dispersals)){ | ||
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| if(is.na(Dispersals$Carnivore[i])) {} else { | ||
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| if(Dispersals$Carnivore[i]==1) { | ||
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| Dispersals$disp[i] <- (40.7*(Dispersals$BodyMass.Value[i]/1000)^0.81)/(as.numeric(Dispersals$GenerationLength_d[i])/365.25) | ||
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| } else { | ||
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| Dispersals$disp[i] <- (3.31*(Dispersals$BodyMass.Value[i]/1000)^0.65)/(as.numeric(Dispersals$GenerationLength_d[i])/365.25) | ||
| } | ||
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| } | ||
| } | ||
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| Dispersals$disp50 <- 50*Dispersals$disp | ||
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| write.csv(Dispersals,'Iceberg Input Files/Data for dispersal_Corrected.csv') | ||
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| paste0("Iceberg Input Files/GretCDF/Currents/", ToFill,".rds") %>% file.remove() | ||
| paste0("Iceberg Input Files/GretCDF/Futures/", ToFill,".rds") %>% file.remove() |
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