knitr::opts_chunk$set(echo = TRUE)
library(here) library(lubridate)
This just includes site persistent individuals (individuals that were re-sighted or recapture later w/in the same winter, or that were at some time later reisghted/recaptured)
fi <- "body_condition_mencia_aceitillar_SP_inds_only_CSV_2.csv" fi <- here::here("data-raw", "data-raw-bodymass", "CSV_body_condition_both_sites", fi) body <- read.csv(file = fi, skip = 8, header = TRUE, stringsAsFactors = F, na.strings = c(""))
explore <- TRUE if(explore == TRUE){ head(body) summary(body,15) }
body$sex <- as.character(body$sex) body$sex <- gsub(" ","",body$sex) summary(factor(body$sex )) body$sex <- factor(body$sex)
body$age <- factor(body$age)
body$site.age <- as.character(body$site.age) body$site.age <- gsub("yr","",body$site.age) body$site.age <- gsub("50","mature",body$site.age) body$site.age <- gsub("Aceitillar","mature",body$site.age) body$site.age <- factor(body$site.age ) summary(body$site.age )
summary(factor(body$date.cap.org)) body$dat2 <- NA body$dat3 <- NA body$dat4 <- NA body$dat5 <- NA #Has explicity month i.easy <- grep("[NDJFM][oeaea][vcnbr]",body$date.cap.org) body$dat2[i.easy] <- as.character(dmy(body$date.cap.org[i.easy])) #has slash i.slash <- grep("[//]",body$date.cap.org) body$dat3[i.slash] <- as.character(mdy(body$date.cap.org[i.slash])) #has 6 numbers for date i.xxxxxx <- grep("^[10][213][01-9][01-9][9][67]",body$date.cap.org) body$dat4[i.xxxxxx] <- gsub("^([10][213])([01-9][01-9])([9][67])", "19\\3-\\1-\\2", body$date.cap.org[i.xxxxxx]) body$dat4[i.xxxxxx] <- as.character(body$dat4[i.xxxxxx]) #has 5 numbers for date str.x <- "^[13][1-90][1-90][01-9][01-9]$" i.xxxxx <- grep(str.x,body$date.cap.org) body$date.cap.org[i.xxxxx] body$dat5[i.xxxxx] <- gsub("^([13])([1-90][1-90])([01-9][01-9])$", "19\\3-0\\1-\\2", body$date.cap.org[i.xxxxx]) dats <- body[,c("dat2","dat3","dat4","dat5")] newdat <- rep(NA,dim(dats)[1]) dim(dats) length(newdat) for(i in 1:dim(body)[1]){ #print(i) j <- which(is.na(dats[i,]) == FALSE) if( is.numeric(j) == TRUE){ newdat[i] <- dats[i,j] } else {next} } body$date.cap.org2 <-newdat i.drop <- grep("^dat.$",names(body) ) names(body)[i.drop] body2 <- body[,-i.drop]
summary(body2) body2$date.cap.org2 <- as.Date(body2$date.cap.org2) body2$year <- year(body2$date.cap.org2) body2$month <-month(body2$date.cap.org2) summary(factor(body2$month))
Set nominal year of study
#$year == year captured body2$year.num <- body2$year #subtract one year for birds captured in Jan, Feb, or March i <- which(body2$month< 4) body2$year.num[i] <- body2$year.num[i]-1
Set name of winter
body2$year <-paste(body2$year.num,"-",c(body2$year.num+1), sep = "") body2$year <- as.factor(body2$year)
summary(body2)
source(here::here("R","focal_spp.R")) body2$stat.focals <- NA body2$stat.focals[which(body2$spp.code %in% focal.mig)] <- "mig" body2$stat.focals[which(body2$spp.code %in% focal.res)] <- "res"
body2$spp.code <- gsub(" ", "",body2$spp.code)
condition <- body2 save(condition, file = here::here("data-raw", "data-raw-bodymass", "condition.RData"))
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