In brouwern/DRmencia: Data and code to replicate analyses for Latta, Brouwer, et al. 2018. PeerJ.

knitr::opts_chunk$set(echo = TRUE)

Libraries

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)

Load data

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(""))

Look at it

explore <- TRUE
if(explore  == TRUE){
  head(body)

  summary(body,15)
}

Clean data

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  )

Work on dates

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)

Code focal spp

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"

Fix spp name

body2$spp.code  <- gsub(" ", "",body2$spp.code)

Save data

condition <- body2

save(condition, file = here::here("data-raw",
                                  "data-raw-bodymass",
                                  "condition.RData"))

brouwern/DRmencia documentation built on May 6, 2019, 12:24 p.m.