Timeseries_Fn: Generates a summary of model fit by plotting estimated time...

In aaronmberger/Geo_dGLMM_habitat: Package for conducting spatial estimation of CPUE index standardization (fisheries, ecology, etc).

Usage

Timeseries_Fn(Report, FileName, ControlList = list(Width = 4 * 3, Height = 2 * 3, Res = 200, Units = "in"))

Arguments

Report
FileName
ControlList

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (Report, FileName, ControlList = list(Width = 4 * 3, 
    Height = 2 * 3, Res = 200, Units = "in")) 
{
    png(file = FileName, width = ControlList$Width, height = ControlList$Height, 
        res = ControlList$Res, units = ControlList$Units)
    par(mfrow = c(2, 4), oma = c(0, 0, 0, 0), mar = c(3, 3, 2, 
        0), mgp = c(1.5, 0.5, 0), tck = -0.02)
    EntropyFn = function(Vec) {
        sum(Vec * log(Vec + 1e-250)/log(length(Vec)))
    }
    Entropy_t = apply(Report$D_xt, MARGIN = 2, FUN = EntropyFn)
    plot(x = Year_Set, y = Entropy_t, type = "l", main = "Entropy")
    Var_t = apply(Report$D_xt, MARGIN = 2, FUN = var)
    plot(x = Year_Set, y = Var_t, type = "l", main = "Variance", 
        ylim = c(0, max(Var_t)))
    CV_t = apply(Report$D_xt, MARGIN = 2, FUN = function(Vec) {
        sd(Vec)/mean(Vec)
    })
    plot(x = Year_Set, y = CV_t, type = "l", main = "CV", ylim = c(0, 
        max(CV_t)))
    Occup_t = colMeans(R1_it)
    plot(x = Year_Set, y = Occup_t, type = "l", main = "Occup_t", 
        ylim = c(0, 1))
    CondDens_t = colMeans(R2_it)
    plot(x = Year_Set, y = CondDens_t, type = "l", main = "CondDens_t", 
        ylim = c(0, max(CondDens_t)))
    Index_t = colMeans(D_it)
    plot(x = Year_Set, y = Index_t, type = "l", main = "Index_t", 
        ylim = c(0, max(Index_t)))
    Cor_t = sapply(1:length(Year_Set), FUN = function(Num) {
        cor(R1_it[, Num], R2_it[, Num], method = "spearman")
    })
    plot(x = Year_Set, y = Cor_t, type = "l", main = "Cor_t", 
        ylim = c(-1, 1))
    abline(h = 0, lty = "dotted")
    dev.off()
  }

aaronmberger/Geo_dGLMM_habitat documentation built on May 10, 2019, 3:20 a.m.