R/data wrangling/fridley_2009.r

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

## fridley_2009
library(data.table)

dataset_id <- 'fridley_2009'
load(file = 'data/raw data/fridley_2009/ddata')
setDT(ddata)

setnames(ddata, c('block', 'plot', 'contacts'),
         c('site', 'block', 'value'))

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

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

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

ddata[, ':='(
   singletons = sum(value == 1),
   doubletons = sum(value == 2)
), by = .(site, block, year)
][,
  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[, ':='(
   dataset_id = dataset_id,
   treatment_type = "manipulated climate",
   grain_m2 = 2.5^2,
   grain_comment = "'Each year we record the number of contacts with living shoots of each vascular plant species when 25 steel pins of diameter 2.5 mm are lowered vertically into the vegetation occupying the central (2.5*2.5 m) area of each plot.'",
   design = paste0('A', fifelse(treatment == 'control', 'C', 'I')),
   timepoints = paste0('T', seq_along(unique(year))[match(year, sort(unique(year)))]),
   time_since_disturbance = fifelse(treatment == 'control', NA_integer_,
                                    fifelse(treatment %like% 'warm', year - 1993, year - 1994)
   ),

   realm = 'terrestrial',
   taxon = 'plants',
   species = NULL,
   value = NULL,

   comment = 'Artificial temperature increase in winter began in November 1993 (warm treatment). Artificial drought began in summer 1994. Artificial increase of water input began in summer 1994. See metadata for full setup. No standardisation needed, one sampling per year.'

)]

ddata <- unique(ddata)

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