WIP

R/density.R

@@ -1,106 +1 @@
-## SSU density
-## @export
-## @description Number of individuals per secondary sampling unit (~177m^2) calculated
-## for each species at the secondary sampling unit level
-## @param x
-## A data.frame including columns: REGION, YEAR, STRAT, PROT, PRIMARY_SAMPLE_UNIT,
-## STATION_NR, SPECIES_CD, NUM
-## @return A data.frame with density per SSU for each SSU
-ssu_density = function(x){
-  ## variables to aggregate by
-  by = .aggBy("ssu")
-  ## Get summarize fn from plyr package
-  summarize = get("summarize", asNamespace("plyr"));
-  ## aggregate by SSU and sum count
-  return(plyr::ddply(x, by, summarize, density = sum(NUM)))
-}
-
-## PSU density per SSU
-## @export
-## @description Number of individuals per secondary sampling unit (~177m^2) calculated
-## for each species at the primary sampling unit level
-## @param x
-## A data.frame of the output from ssu_density
-## @return A data.frame with density per SSU aggregated by PSU and species,
-## variance in density (var), and the number of ssus per psu (m)
-psu_density = function(x) {
-  ## variables to aggregate by
-  by = .aggBy("psu")
-  ## get summarize fn from plyr package
-  summarize = get("summarize", asNamespace("plyr"))
-  ## Aggregate by PSU, sum density and divide by number of SSUs
-  return(plyr::ddply(x, by, summarize,
-                     m = length(STATION_NR),
-                     var = var(density),
-                     density = sum(density)/length(STATION_NR)
-                     ))
-}
-
-## Stratum level density per SSU
-## @export
-## @description Number of individuals per secondary sampling unit (~177m^2) calculated
-## for each species at the stratum level
-## @param x
-## A data.frame which is the output from psu_density
-## @param ntot
-## A data.frame including columns: REGION, YEAR, STRAT, PROT, NTOT, GRID_SIZE
-## @return A data.frame with density per SSU aggregated by stratum and species, its variance (var),
-## the number of SSUs per stratum (nm), the number of PSUs per stratum (n), the total
-## possible number of SSUs (NM), and the total possible number of PSUs (N)
-strat_density <- function(x, ntot) {
-  ## merge with ntot data
-  merged = merge(x, ntot)
-  ## Aggregate by variables
-  by = .aggBy("strat")
-  ## Get the summarize function from the plyr namespace
-  summarize = get("summarize", asNamespace('plyr'))
-  ## Calculate a whole series of statistics while aggregating by stratum
-  strm = plyr::ddply(merged, by, summarize,
-                     v1 = var(density), # Between PSU variance
-                     np = sum(ifelse(m>1,1,0)), # Number of PSUs with replicates
-                     v2 = sum(var, na.rm = TRUE)/np, #Between SSU variance
-                     mtot = mean(GRID_SIZE)^2/(pi*7.5^2),
-                     mbar = mean(m),
-                     n = length(PRIMARY_SAMPLE_UNIT),
-                     nm = sum(m),
-                     fn = n/mean(NTOT), #PSU variance weighting factor
-                     fm = mbar/mtot, #SSU variance weighting factor
-                     var = (1-fn)*v1/n + (fn*(1-fm)*v2)/nm,
-                     density = mean(density),
-                     N = mean(NTOT),
-                     NM = mtot*N
-  )
-
-  ## Clean up output
-  keep = c("YEAR", "REGION", "STRAT", "PROT", "SPECIES_CD", "density", "var", "n",
-           "nm", "N", "NM")
-
-  return(strm[keep])
-}
-
-## Domain level density per SSU
-## @export
-## @description Number of individuals per secondary sampling unit (~177m^2) calculated
-## for each species at the stratum level
-## @param x
-## A data.frame which is the output from the strat_density function
-## @inheritParams strat_density
-## @return A data.frame with density per SSU by species, its variance (var),
-## the number of SSUs in the domain (nm), the number of PSUs in the domain (n), the total
-## possible number of SSUs (NM), and the total possible number of PSUs (N)
-domain_density = function(x, ntot){
-  ## Use ntot data.frame to calculate weighting
-  merged = .getWeight(x, ntot)
-  ## Return weighted statistics
-  by = .aggBy("domain")
-  summarize = get("summarize", asNamespace('plyr'))
-
-  return(plyr::ddply(merged, by, summarize,
-                     density = sum(wh*density),
-                     var = sum(wh^2*var, na.rm = TRUE),
-                     n = sum(n),
-                     nm = sum(nm),
-                     N = sum(N),
-                     NM = sum(NM)
-                     ))
-}
+Hi