inst/doc/glades.TITAN.R

## ------------------------------------------------------------------------
library(TITAN2)

## ------------------------------------------------------------------------
data(glades.taxa)
str(glades.taxa, list.len = 5)

## ------------------------------------------------------------------------
data(glades.env)
str(glades.env)

## ---- eval = F-----------------------------------------------------------
#  glades.titan <- titan(glades.env, glades.taxa)

## ---- eval = F-----------------------------------------------------------
#  glades.titan <- titan(glades.env, glades.taxa, minSplt = 5, numPerm = 250, boot = TRUE, nBoot = 500,
#    imax = FALSE, ivTot = FALSE, pur.cut = 0.95, rel.cut = 0.95, ncpus = 1, memory = FALSE)

## ------------------------------------------------------------------------
data(glades.titan)

## ---- echo = FALSE-------------------------------------------------------
message("100% occurrence detected 1 times (0.8% of taxa), use of TITAN less than ideal for this data type")
message("Taxa frequency screen complete")

## ---- echo = FALSE-------------------------------------------------------
message("Determining partitions along gradient")
message("Calculating observed IndVal maxima and class values")
message("Calculating IndVals using mean relative abundance")
message("Permuting IndVal scores")
message("IndVal $z$ score calculation complete")
message("Summarizing Observed Results")
message("Estimating taxa change points using z-score maxima")

## ---- echo = FALSE-------------------------------------------------------
message("Bootstrap resampling in sequence...")
message(1*1)
message(2*1)
message(3*1)

## ---- echo = FALSE-------------------------------------------------------
message("Bootstrap resampling in parallel using 2 CPUs...no index will be printed to screen")

## ------------------------------------------------------------------------
glades.titan$sumz.cp

## ------------------------------------------------------------------------
head(glades.titan$sppmax)

## ------------------------------------------------------------------------
str(glades.titan, max.level = 1, give.attr = FALSE)

## ---- echo = FALSE-------------------------------------------------------
graphics.off()

## ---- fig.height = 6,fig.width = 8---------------------------------------
plotSumz(glades.titan, filter = FALSE)

## ---- echo = FALSE-------------------------------------------------------
graphics.off()

## ---- fig.height = 6,fig.width = 8---------------------------------------
plotSumz(glades.titan, filter = TRUE)

## ---- echo = FALSE-------------------------------------------------------
graphics.off()

## ---- fig.height = 8,fig.width = 8---------------------------------------
plotTaxa(glades.titan, xlabel = "Surface Water TP (ug/l)")

## ---- echo = FALSE-------------------------------------------------------
graphics.off()

## ---- fig.height = 8,fig.width = 8---------------------------------------
plotTaxa(glades.titan,xlabel = "Surface Water TP (ug/l)",z.med = T)

## ---- echo = FALSE-------------------------------------------------------
graphics.off()

## ---- fig.height = 8,fig.width = 8---------------------------------------
plotTaxa(glades.titan, xlabel = "Surface Water TP (ug/l)", z.med = F, prob95 = T)

## ---- fig.height = 10,fig.width = 10-------------------------------------
plotCPs(glades.titan)

## ---- echo = FALSE-------------------------------------------------------
graphics.off()

## ---- fig.height = 5,fig.width = 8---------------------------------------
plotCPs(glades.titan, taxaID = "ENALCIVI", xlabel = "Surface Water TP (ug/l)")

## ---- echo = FALSE-------------------------------------------------------
graphics.off()

## ---- fig.height = 5,fig.width = 8---------------------------------------
plotCPs(glades.titan, taxaID = "ENALCIVI", cp.trace = TRUE, xlabel = "Surface Water TP (ug/l)")

## ---- echo = FALSE-------------------------------------------------------
graphics.off()

## ---- fig.height = 5,fig.width = 8---------------------------------------
plotCPs(glades.titan, taxaID = "OSTRASP5", cp.trace = TRUE, xlabel = "Surface Water TP (ug/l)")

## ---- echo = FALSE-------------------------------------------------------
graphics.off()

## ---- fig.height = 6,fig.width = 8---------------------------------------
plotCPs(glades.titan, taxa.dist = FALSE, xlabel = "Surface Water TP (ug/l)")

## ---- echo = FALSE-------------------------------------------------------
graphics.off()

## ---- fig.height = 6,fig.width = 8---------------------------------------
plotCPs(glades.titan, taxa.dist = FALSE, xlabel = "Surface Water TP (ug/l)", stacked = TRUE)

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TITAN2 documentation built on May 30, 2017, 1:15 a.m.