R/save.ord.result.R

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

save.ord.result <-
function (ord.result, use.last.result, type, deleted.plots)
{
if (type == 'dca')
{
dca <- ord.result
cat ('Results of Dentrended correspondence analysis\n\n', sep = '\t', file = 'ordi-result.txt')
if (use.last.result) cat ('PREVIOUSLY SAVED RESULTS USED FOR VISUALIZATION (e.g. as the data are the same as in previous ', type, ' analysis, also the results of previous analysis are used for visualization; this is intendet to save some time for calculation ...)\n\n', append = T, file = 'ordi-result.txt')
cat('           ','DCA1  ', 'DCA2  ','DCA3  ', 'DCA4  ', '\n', sep = '\t', append = T, file = 'ordi-result.txt')
cat('Eigenvalues', formatC(dca$evals, digits = 4, format = 'f'), '\n', sep = '\t', append = T, file = 'ordi-result.txt')
cat('Decorana values', formatC (dca$evals.decorana, digits = 4, format = 'f'),'\n', sep = '\t', append = T, file = 'ordi-result.txt')
cat('Axis length', formatC (apply(dca$rproj, 2, max), digits = 4, format = 'f'), '\n\n', sep = '\t', append = T, file = 'ordi-result.txt')
cat('There are two versions of eigenvalues - the first (Eigenvalues) are the values calculated by the function "decorana" in vegan, the second (Decorana values) are the values calculated by the original DECORANA program of Mark Hill - these are included only for reference and should not be used. For more details see manual of vegan.\n\n', sep = '\t', append = T, file = 'ordi-result.txt')

cat('Species scores\n\n', sep = '\t', append = T, file = 'ordi-result.txt')

cat('        ','DCA1  ', 'DCA2  ','DCA3  ', 'DCA4  ', '\n', sep = '\t', append = T, file = 'ordi-result.txt')
format.cproj <- formatC (dca$cproj, digits = 4, format = 'f')
for (r in seq (1, dim (dca$cproj)[1]))
cat (rownames (dca$cproj)[r], format.cproj[r,], '\n', sep = '\t', append = T, file = 'ordi-result.txt') 

cat('\nSite scores\n\n', sep = '\t', append = T, file = 'ordi-result.txt')
cat('  ','DCA1  ', 'DCA2  ','DCA3  ', 'DCA4  ', '\n', sep = '\t', append = T, file = 'ordi-result.txt')
format.rproj <- formatC (dca$rproj, digits = 4, format = 'f')
for (r in seq (1, dim (dca$rproj)[1]))
cat (formatC(rownames (dca$rproj)[r], format = 'd'), format.rproj[r,], '\n', sep = '\t', append = T, file = 'ordi-result.txt') 

if (!is.null (deleted.plots))
  {
  cat('\nPlots deleted due to incomplete header data:\n\n', sep = '\t', append = T, file = 'ordi-result.txt')
  cat(deleted.plots, append = T, file = 'ordi-result.txt')
  }
}
if (type == 'nmds')
{
nmds <- ord.result
cat ('Results of Nonmetric Multidimensional Scaling using isoMDS (MASS package)\n\n', sep = '\t', file = 'ordi-result.txt')
if (use.last.result) cat ('PREVIOUSLY SAVED RESULTS USED FOR VISUALIZATION (e.g. as the data are the same as in previous ', type, ' analysis, also the results of previous analysis are used for visualization; this is intended to save some time for calculation ...)\n\n', append = T, file = 'ordi-result.txt')

    cat("Distance:", nmds$distance, "\n", append = T, file = 'ordi-result.txt')
    cat("Dimensions:", nmds$dims, "\n", append = T, file = 'ordi-result.txt')
    cat("Stress:    ", nmds$stress, "\n", append = T, file = 'ordi-result.txt')
    if (nmds$converged) cat("Two convergent solutions found after", x$tries, 
            "tries\n", append = T, file = 'ordi-result.txt') else cat("No convergent solutions - best solution after", nmds$tries, "tries\n", append = T, file = 'ordi-result.txt')

cat('\nSpecies scores\n\n', sep = '\t', append = T, file = 'ordi-result.txt')
if (nmds$dims == 2)  cat('        ','NMDS1 ', 'NMDS2 ', '\n', sep = '\t', append = T, file = 'ordi-result.txt') else
  cat('        ','NMDS1 ', 'NMDS2 ', 'NMDS3 ', '\n', sep = '\t', append = T, file = 'ordi-result.txt')
  format.cproj <- formatC (nmds$species, digits = 4, format = 'f')
for (r in seq (1, dim (nmds$species)[1])) cat (rownames (nmds$species)[r], format.cproj[r,], '\n', sep = '\t', append = T, file = 'ordi-result.txt') 

cat('\nSite scores\n\n', sep = '\t', append = T, file = 'ordi-result.txt')
if (nmds$dims == 2)  cat('       ','NMDS1 ', 'NMDS2 ', '\n', sep = '\t', append = T, file = 'ordi-result.txt') else
  cat('    ','NMDS1 ', 'NMDS2 ', 'NMDS3 ', '\n', sep = '\t', append = T, file = 'ordi-result.txt')
  format.rproj <- formatC (nmds$points, digits = 4, format = 'f')
for (r in seq (1, dim (nmds$points)[1])) cat (rownames (nmds$points)[r], format.rproj[r,], '\n', sep = '\t', append = T, file = 'ordi-result.txt') 

if (!is.null (deleted.plots))
  {
  cat('\nPlots deleted due to incomplete header data:\n\n', sep = '\t', append = T, file = 'ordi-result.txt')
  cat(deleted.plots, append = T, file = 'ordi-result.txt')
  }
}

if (type == 'pca')
{
pca <- ord.result
cat ('Results of Principal Components Analysis\n\n', sep = '\t', file = 'ordi-result.txt')
if (use.last.result) cat ('PREVIOUSLY SAVED RESULTS USED FOR VISUALIZATION (e.g. as the data are the same as in previous ', type, ' analysis, also the results of previous analysis are used for visualization; this is intended to save some time for calculation ...)\n\n', append = T, file = 'ordi-result.txt')
    cat('                  ','PC1   ', 'PC2   ', 'PC3   ', 'PC4   ', '\n', sep = '\t', append = T, file = 'ordi-result.txt')
    cat("Standard deviation:", formatC (pca$sdev[1:4], digits = 4, format = 'f'), "\n", sep = '\t', append = T, file = 'ordi-result.txt')

cat('\nSpecies scores\n\n', sep = '\t', append = T, file = 'ordi-result.txt')
cat('        ','PC1 ', 'PC2 ', 'PC3', 'PC4', '\n', sep = '\t', append = T, file = 'ordi-result.txt')
format.cproj <- formatC (pca$rotation[,1:4], digits = 4, format = 'f')
for (r in seq (1, dim (format.cproj)[1])) cat (rownames (format.cproj)[r], format.cproj[r,], '\n', sep = '\t', append = T, file = 'ordi-result.txt') 

cat('\nSite scores\n\n', sep = '\t', append = T, file = 'ordi-result.txt')
cat('      ','PC1   ', 'PC2   ', 'PC3   ', 'PC4   ', '\n', sep = '\t', append = T, file = 'ordi-result.txt')
format.rproj <- formatC (scores (pca, display = 'sites')[,1:4], digits = 4, format = 'f')
for (r in seq (1, dim (format.rproj)[1])) cat (rownames (format.rproj)[r], format.rproj[r,], '\n', sep = '\t', append = T, file = 'ordi-result.txt') 

if (!is.null (deleted.plots))
  {
  cat('\nPlots deleted due to incomplete header data:\n\n', sep = '\t', append = T, file = 'ordi-result.txt')
  cat(deleted.plots, append = T, file = 'ordi-result.txt')
  }
}
}