R/data wrangling/hershey_2016.r

In chase-lab/BioTIMEx: Aggregating long-term ecological communities data

## hershey_2016
library(data.table)

dataset_id <- 'hershey_2016'
load(file = paste0('data/raw data/',dataset_id, '/ddata'))
setDT(ddata)

setnames(ddata, c('station.m', 'Trial', 'Date'),
         c('site', 'block', 'date'))
# reshaping the data
ddata <- melt(ddata,
              measure.vars = c('RHYAC','BRACHY','NATARSIA','ORTHO','OTHCHIR','CHIPUPA','BLACK','BLKPUPA','BAETIS','BAETSP3','EPHEM','CINYG','NEMOURA','TIPULA','SNAILS'),
              variable.name = 'species',
              value.name = 'value')[value > 0 & !is.na(value)]

ddata <- ddata[species != 'SNAILS']

ddata[, ':='(
  year = as.integer(format(as.Date(date, '%d-%b-%y'), '%Y')),
  site =  fifelse(abs(as.numeric(trimws(gsub(x = site, pattern = 'K|k', replacement = '')))) < 10,
                  as.numeric(trimws(gsub(x = site, pattern = 'K|k', replacement = ''))) * 1000,
                  as.numeric(trimws(gsub(x = site, pattern = 'K|k', replacement = ''))))
)]

# Community
ddata[, ':='(
  N = sum(value),
  S = length(unique(species)),
  ENSPIE = vegan::diversity(x = value, index = 'invsimpson')
),
by = .(site, block, year, date)
]

ddata[, minN := min(N), by = .(site, block)] # No minN < 6

ddata[, Sn := vegan::rarefy(value, sample = minN), by = .(site, block, year, date)]

ddata[, ':='(
  singletons = sum(value == 1),
  doubletons = sum(value == 2)
), by = .(site, block, year, date)
][,
  coverage := fifelse(
    doubletons > 0,
    1 - (singletons/N) * (((N - 1)*singletons)/((N - 1)*singletons + 2*doubletons)),
    1 - (singletons/N) * (((N - 1)*singletons)/((N - 1)*singletons + 2))
  )][, ':='(singletons = NULL, doubletons = NULL)]


ddata[, effort := length(unique(date)), by = .(site, block, year)]

ddata <- ddata[,
               lapply(.SD, mean),
               by = .(site, block, year),
               .SDcols = c('effort','N','minN','S','Sn','ENSPIE')
]


ddata[,
      ':='(
        dataset_id = dataset_id,
        treatment = paste(fifelse(site < 0, 'control', 'impact'), site, sep = '_'),
        treatment_type = "eutrophication",
        grain_m2 = 1 * 3,
        grain_comment = "'A rock-scrubbing technique was used to collect bottom samples at several different stations with three replicates at each station in the Kuparuk River.' - estimated",
        design = paste0('A', fifelse(site < 0, 'C', 'I')),
        timepoints = paste0('T', seq_along(unique(year))[match(year, sort(unique(year)))]),
        time_since_disturbance = fifelse(site < 0, NA_integer_, year - 1984),

        realm = 'freshwater',
        taxon = 'invertebrates',

        comment = 'Treatment variable shows the distance above (negative values) and downstream (positive values) of a nutrient source.'
      )
][,
  site := paste0('site_', site)
]

dir.create(paste0('data/wrangled data/', dataset_id), showWarnings = FALSE)
fwrite(ddata, paste0('data/wrangled data/', dataset_id, "/", dataset_id, '.csv'), row.names = FALSE)