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PalEON_arctic_project_aby.R
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PalEON_arctic_project_aby.R
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library(neotoma)
library('mapdata')
library(maps)
map("world", c("Alaska"), boundary=TRUE, col=8, add=TRUE, fill=TRUE)
map("state", c("hawaii"), boundary = TRUE, col=8, add = TRUE, fill=TRUE )
#---------------------- download data ----------------------#
# get arctic sites pollen datasets
# surface sample
arctic_surface_pollen_sites <- get_dataset(datasettype = "pollen surface sample", loc=c(-170, 66, -135, 72))
# pollen
arctic_pollen_sites <- get_dataset(datasettype = "pollen", loc=c(-170, 66, -135, 72))
print(arctic_surface_pollen_sites)
print(arctic_pollen_sites)
# download arctic pollen data
arctic_surface_pollen_data <- get_download(arctic_surface_pollen_sites)
arctic_pollen_data <- get_download(arctic_pollen_sites)
print(arctic_surface_pollen_data)
print(arctic_pollen_data)
#---------------------- reformat surface pollen data ----------------------#
# site.name - lat -lon age Alnus Betula Ericales Populus Salix Total
# site.id - lat -lon age Alnus Betula Ericales Populus Salix Total
names(arctic_surface_pollen_data[[1]])
head(arctic_surface_pollen_data[[1]]$taxon.list)
head(arctic_surface_pollen_data[[1]]$counts)
head(arctic_pollen_data[[1]]$counts)
head(arctic_pollen_data[[1]]$ecological)
head(arctic_pollen_data[[39]]$counts)
surface_pollen_taxons <- pollen_taxons <- list()
surface_pollen_counts <- pollen_counts <- list()
# lat - lon - elev - taxon.list -
foseq_along(arctic_surface_pollen_data)
arctic_pollen_data[[1]]$dataset$site.data$lat
n<-c("Alnus", "Betula", "Ericales", "Populus", "Salix")
sites<-names(arctic_surface_pollen_data)
d<-NULL
sites<-print(arctic_surface_pollen_data$Datasets[,c(2:5)])
df<-data.frame(n,sites, d)
setwd("../PalEON/")
imported_image <- raster("AllShrubMap_masked.img")
# site.name - lat -lon age Alnus Betula Ericales Populus Salix Total
sites.id<-names(arctic_surface_pollen_data)
site.lat<- rep(NA, 148)
site.long<-rep(NA, 148)
site.total<-rep(NA,148)
shrub.total <- rep(NA,148)
shrub.taxa <- c("Alnus", "Betula", "Salix" )
for(i in 1:length(arctic_surface_pollen_data)){
site.lat[i]<-arctic_surface_pollen_data[[i]]$dataset$site.data$lat
site.long[i]<-arctic_surface_pollen_data[[i]]$dataset$site.data$long
site.total[i]<-sum(arctic_surface_pollen_data[[i]]$count)
shrub.total[i] <- sum(arctic_surface_pollen_data[[i]]$count[which(colnames(arctic_surface_pollen_data[[i]]$counts) %in% shrub.taxa)])
}
surface_pollen <- data.frame(site.id = sites.id,site.lat = site.lat, site.long = site.long, site.total = site.total, shrub.total = shrub.total)
head(arctic_pollen_data[[39]]$counts)
pollen.id<-arctic_pollen_data[[39]]$counts
pollen.shrub<-rep(NA, 24)
pollen.total<-rep(NA, 24)
pollen.shrub <- apply(pollen.id[,which(colnames(pollen.id)%in% shrub.taxa)],1,sum)
pollen.total<- apply(pollen.id,1,sum)
pollen.all<-data.frame(pollen.id=pollen.id, pollen.shrub=pollen.shrub, pollen.total=pollen.total)
pollen.all$prop<-(pollen.all$pollen.shrub/pollen.all$pollen.total)*100
pollen.all$rownames<-