R/draw.dca.R

In zdealveindy/ordijuice: Unconstrained ordinations of vegetation data in JUICE program

draw.dca <-
function(display.in.diagram = c('sites'),
                     display.species = c('none'),
                     display.sites = c('points'),
                     axes.shown = c(1,2),
                     down.rare.spec = 0,
                     display.EIV = FALSE,
                     display.header = FALSE,
                     display.envelope = FALSE,
                     header.name = 'env',
                     display.header.style = c('arrow'),
                     display.spider,
                     display.group.center = FALSE,
                     three.dim = FALSE,
                     resolution = c(1280, 768),
                     bw = FALSE,
                     ...)
{
newRversion <- check.install (display.spider)
open.r.window(three.dim, resolution)
if (newRversion) pb <- myTkProgressBar (paste (ifelse (three.dim, '3D', '2D'),'DCA - Analysis progress'), 'Importing data from JUICE', 0, 100, 20) else pb <- NULL
write ('End of ordination', file='result.txt')
library (vegan)
input.data <- read.check.data (display.sites = display.sites, display.EIV = display.EIV, display.header = display.header, display.envelope = display.envelope, display.spider = display.spider, display.group.center = display.group.center)

# 2. update progress bar
if (newRversion) setTkProgressBar (pb, label = 'Calculation of ordination', value = 40)

# calculation of ordination
last.result <-  use.last (input.data, 'dca', setting = list (down.rare.spec = down.rare.spec))
if (last.result$use.last.result) spec.data.ord <- last.result$last.data.result  else
  spec.data.ord <- decorana(input.data$spec.data, iweigh=down.rare.spec)

# 3. update progress  bar
if (newRversion) setTkProgressBar (pb, label = 'Saving results', value = 60)

save.ord.result (spec.data.ord, last.result$use.last.result, 'dca', input.data$deleted.plots)  

# 3. update progress  bar
if (newRversion) setTkProgressBar (pb, label = 'Drawing the figure', value = 80)

  
if (three.dim)  
  draw.3d(input.data = input.data, spec.data.ord = spec.data.ord, display.in.diagram = display.in.diagram, display.species = display.species, display.sites = display.sites, axes.shown = axes.shown, display.EIV = display.EIV, display.header = display.header, display.envelope = display.envelope, header.name = header.name, display.header.style = display.header.style, display.spider = display.spider, display.group.center = display.group.center, pb = pb) else
  draw.2d(input.data = input.data, spec.data.ord = spec.data.ord, display.in.diagram = display.in.diagram, display.species = display.species, display.sites = display.sites, axes.shown = axes.shown, display.EIV = display.EIV, display.header = display.header, display.envelope = display.envelope, header.name = header.name, display.header.style = display.header.style, display.spider = display.spider, display.group.center = display.group.center, bw = bw, pb = pb)

if (!last.result$use.last.result)
  {
  last.data <- list (last.matrix.sum = sum(input.data$spec.data), last.matrix.species = colnames (input.data$spec.data), last.matrix.sites = rownames (input.data$spec.data), last.result = spec.data.ord)
  save (last.data, file = 'dca_lfa.r')
  last.data.quick <- list (type.of.analysis = 'dca', size.of.matrix = dim (input.data$spec.data), setting = list (down.rare.spec = down.rare.spec))
  save (last.data.quick, file = 'dca_lfq.r')
  }
}