knitr::opts_chunk$set(echo = TRUE)
Note that for aceitillar sampling only ever occured in Nov, Jan and March, and that this only occured in 1996-1997, and 1997-1998. In 1999 and beyond all sampling occurred in January. Note that sampling in January 1999 is coded as "1998-1999" for consistency witht he prior years and the Mencia data.
In contrast, Mencia sampling occurred in Nov, Jan and Feb (never March) in all years except 2008, when not sampling is indicate in March.
filename <- "mencia_cleaned.csv" filename <- here::here("data-raw", "data-raw-mencia", "mencia_all_captures_by_year", filename) mencia.ann <- read.csv(file = filename, stringsAsFactors = F)
Annual data was created by melting the site persistence capture histories that were originally provided to NLB
filename <- "aceit_annual.csv" filename <- here::here("data-raw", "data-raw-aceitillar_96-02", filename) aceit.ann <- read.csv(file = filename, stringsAsFactors = F)
names(aceit.ann) <- gsub("bnd","band",names(aceit.ann)) names(aceit.ann) <- gsub("col","colors",names(aceit.ann)) names(aceit.ann) <- gsub("nts","notes",names(aceit.ann)) names(aceit.ann) <- gsub("ag","age",names(aceit.ann)) names(aceit.ann) <- gsub("sx","sex",names(aceit.ann)) names(aceit.ann) <- gsub("stat.focals","status.focals",names(aceit.ann)) aceit.ann$site.age <- NA aceit.ann$site.age.init <- NA
m <- names(mencia.ann)[order(names(mencia.ann))] a <- names(aceit.ann)[order(names(aceit.ann))] intersect(m,a) setdiff(m,a) setdiff(a,m)
some issues downstream occured w/ these columns. Ended up being an excel error while saving the data. See https://twitter.com/lobrowR/status/958418038705082369
# head(mencia.ann$band) # head(aceit.ann$band) # # # summary(factor(mencia.ann$band)) # # summary(factor(aceit.ann$band))
# head(aceit.ann$band) # head(mencia.ann$band) # summary(factor(aceit.ann$year)) # summary(factor(mencia.ann$year)) # summary(factor(aceit.ann$year.num)) # summary(factor(mencia.ann$year.num)) # # head(aceit.ann[,c("year","year.num")]) # # head(mencia.ann[,c("year","year.num")])
ann_caps <- merge(mencia.ann, aceit.ann, all = TRUE) dim(mencia.ann) dim(aceit.ann) dim(mencia.ann)[1] + dim(aceit.ann)[1] dim(ann_caps)
ID is unique for each individual some individuals captured multiple times w/in years some re-captured between years. Make unique ID to seperate out w/in year recaps
ann_caps$ID.yr <- with(ann_caps, paste(band, year,sep = "_"))
447 re-captured in different sites
length(unique(ann_caps$band)) #3143 length(unique(ann_caps$ID.yr)) #3590 length(unique(ann_caps$ID.yr)) - length(unique(ann_caps$band))
161 re-captured in different sites (w/in yr OR between yr)
ann_caps$ID.site <- with(ann_caps, paste(band, site), sep = ".") length(unique(ann_caps$ID.site))-length(unique(ann_caps$band))
#create unique spp-site combo ann_caps$spp_site <- with(ann_caps,paste(spp.code, site)) #center site age variable ann_caps$site.age.cent <- scale(ann_caps$site.age,scale = F)
Change NA to "U"
ann_caps$sex[is.na(ann_caps$sex)] <- "U"
Combine all AHY and beyond catetories
Has to be aged to count
summary(ann_caps$age) ann_caps$age <- as.character(ann_caps$age) #HY and SY = "age1" ann_caps$age.AHY.01 <- gsub("^HY","age1", ann_caps$age) ann_caps$age.AHY.01 <- gsub("^SY","age1",ann_caps$age.AHY.01) ann_caps$age.AHY.01 <- gsub("^AHY","age2",ann_caps$age.AHY.01) ann_caps$age.AHY.01 <- gsub("^ASY","age2",ann_caps$age.AHY.01) ann_caps$age.AHY.01 <- factor(ann_caps$age.AHY.01 ) summary(ann_caps$age.AHY.01 )
summary(factor(ann_caps$sex)) summary(factor(ann_caps$age)) summary(factor(ann_caps$site)) summary(factor(ann_caps$age.AHY.01))
This should extract the 1st instance that a unique band-year combo occurs within a dataset. Datasets are ordered by data so this will grab the 1st capture per year.
#ann_caps$ID.yr i.within.yr <- match(unique(ann_caps$ID.yr), ann_caps$ID.yr) length(i.within.yr) dim(ann_caps)
ann_caps <- ann_caps[i.within.yr,]
saved to "data" folder where working data for real analyses is stored
filename <- "ann_caps.RData" filename <-here::here("data", filename) save(ann_caps, file = filename,row.names = F)
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