## ----prep, echo=FALSE, results='hide'-------------------------------------------------------------
library(knitr)
options(stringsAsFactors=FALSE, width=100)
knitr::opts_chunk$set(engine.opts = list(use_tcolorbox = TRUE), concordance = TRUE, comment = "", warning = FALSE, message = TRUE, echo = TRUE, results = 'tex', size="footnotesize")

## ----packages, results='hide', echo=FALSE---------------------------------------------------------
suppressPackageStartupMessages(library(vegdata))
suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(forcats))

## ----load, results='hide', eval=FALSE-------------------------------------------------------------
# library(vegdata)

## ----eval=TRUE------------------------------------------------------------------------------------
tv_home <- tv.home()

## ----eval=FALSE-----------------------------------------------------------------------------------
# options(tv_home="path_to_your_Turboveg_root_directory")

## ----dblisting------------------------------------------------------------------------------------
tv.db()

## -------------------------------------------------------------------------------------------------
tv.home()
getOption('tv_home')
list.dirs(path = file.path(getOption('tv_home'), "Species"), recursive = FALSE, full.names = FALSE)
tax.refl('TaxRefExample')

## ----eval=FALSE-----------------------------------------------------------------------------------
# tax.refl('your_preferred_list')

## ----syn------------------------------------------------------------------------------------------
tax('Elytrigia repens')$TaxonName
syn('Elytrigia repens')

## ----childs, eval=TRUE----------------------------------------------------------------------------
parent(32)
parent(32, rank = 'FAM')

## ----db-------------------------------------------------------------------------------------------
db <- 'taxatest'

## ----obs------------------------------------------------------------------------------------------
getOption('tv_home')
obs <- tv.obs(db)
# Adding species names
species <- tax('all', refl=tax.refl(db=db))
obs$TaxonName <-  species$TaxonName[match(obs$TaxonUsageID, species$TaxonUsageID)]
head(obs[,c('PlotObservationID','TaxonUsageID','COVER_CODE','LAYER','TaxonName')])

## ----data-----------------------------------------------------------------------------------------
obs <- tv.obs('taxatest')
sort(tax(unique(obs$TaxonUsageID))$TaxonName)

## ----adapt----------------------------------------------------------------------------------------
obs.tax <- taxval(obs, ag='adapt', rank='SPE', check.critical = FALSE, mono = 'pre')
sort(tax(unique(obs.tax$TaxonUsageID))$TaxonName)

## ----conflict-------------------------------------------------------------------------------------
obs.tax <- taxval(obs, ag='conflict', check.critical = FALSE)
sort(tax(unique(obs.tax$TaxonUsageID))$TaxonName)

## ----maxtax---------------------------------------------------------------------------------------
obs.tax <- taxval(obs, ag='conflict', maxtaxlevel = 'AGG', check.critical = FALSE, interactive = TRUE)
obs.tax <- taxval(obs.tax, ag='adapt', rank='SPE', check.critical = FALSE)
sort(tax(unique(obs.tax$TaxonUsageID))$TaxonName)

## ----coverperc, echo=2:4, eval=TRUE---------------------------------------------------------------
obs <- tv.obs(db)
obs <- tv.coverperc(db, obs)
tail(obs)

## ----pseudo1--------------------------------------------------------------------------------------
data(lc.0)
obs <- tv.obs(db)
tv.veg(db, obs=obs)   # , pseudo = list(lc.0, c("LAYER")), lc = "layer")

## ----lc0, warning=FALSE, eval=FALSE---------------------------------------------------------------
# tmp <- tv.veg(db, tax=FALSE, pseudo = list(lc.0, "LAYER"), lc = "layer")
# names(tmp)

## ----Season, eval=FALSE---------------------------------------------------------------------------
# comb <- list(data.frame(SEASON=0:4, COMB=c(0,'Spring','Summer','Autumn','Winter')),'SEASON')
# names(tv.veg(db, tax=FALSE, pseudo=comb))

## ----layer, results='hide', warning=FALSE, eval=FALSE---------------------------------------------
# data(lc.1)
# veg <- tv.veg(db, lc = "sum", pseudo = list(lc.1, 'LAYER'), dec = 1, check.critical = FALSE)
# veg[,1:10]

## -------------------------------------------------------------------------------------------------
obs.tax$TaxonUsageID[obs.tax$TaxonUsageID == 27] <- 31

## ----replace--------------------------------------------------------------------------------------
taxon.repl <- data.frame(old=c(27), new=c(31))
obs.tax$TaxonUsageID <- replace(obs.tax$TaxonUsageID,
                                match(taxon.repl$old, obs.tax$TaxonUsageID), taxon.repl$new)

## ----site.echo, eval=TRUE-------------------------------------------------------------------------
site <- tv.site(db)

## ----elbaue, results='hide'-----------------------------------------------------------------------
elbaue <- tv.veg('elbaue', check.critical = FALSE)

## ----cluster--------------------------------------------------------------------------------------
elbaue.env <- tv.site('elbaue')
clust <- vector('integer', nrow(elbaue.env))
clust[elbaue.env$MGL < -50 & elbaue.env$SDGL < 50] <- 1		# dry sites, low deviation
clust[elbaue.env$MGL < -50 & elbaue.env$SDGL >= 50] <- 2	# dry sites, high deviation
clust[elbaue.env$MGL >= -50 & elbaue.env$SDGL >= 50] <- 3	# wet sites, high deviation
clust[elbaue.env$MGL >= -50 & elbaue.env$SDGL < 50] <- 4	# wet sites, low deviation
#levels(clust) <- c('dry.ld','dry.hd', 'wet.hd','wet.ld')

## ----syntab.mupa----------------------------------------------------------------------------------
synt <- syntab(elbaue, clust, mupa = TRUE)
synt

## ----nmds, eval=TRUE------------------------------------------------------------------------------
## Data analyses
if (requireNamespace('vegan', quietly = TRUE) ) {
 library(vegan)
 veg.nmds <- metaMDS(elbaue, distance = "bray", trymax = 5, autotransform =FALSE,
                    noshare = 1, expand = TRUE, trace = 2)
} else
  message("package vegan not available")

## -------------------------------------------------------------------------------------------------
# eco <- tv.traits()
F <- cwm(veg = elbaue, trait.db = 'ecodbase.dbf', ivname = 'OEK_F', method = 'mean')
N <- cwm(veg = elbaue, trait.db = 'ecodbase.dbf', ivname = 'OEK_N', method = 'mean')
env <- envfit(veg.nmds, env = data.frame(F, N))

## ----nmdsplot, quiet=TRUE, results='hide', warning=FALSE, eval=TRUE-------------------------------
if (requireNamespace('interp', quietly = TRUE) & requireNamespace('labdsv', quietly = TRUE) & requireNamespace('vegan', quietly = TRUE) ) {
  suppressPackageStartupMessages(library(labdsv))
  library(interp)
color = function(x)rev(topo.colors(x))
nmds.plot <- function(ordi, site, var1, var2, disp, plottitle =  'NMDS', env = NULL, ...) {
lplot <- nrow(ordi$points);  lspc <- nrow(ordi$species)
filled.contour(interp(ordi$points[, 1], ordi$points[, 2], site[, var1], duplicate = 'strip'),
           ylim = c(-1, 1.1), xlim = c(-1.4, 1.4),
           color.palette = color, xlab = var1, ylab = var2, main = plottitle,
           key.title = title(main = var1, cex.main = 0.8, line = 1, xpd = NA),
           plot.axes = { axis(1);  axis(2)
             points(ordi$points[, 1], ordi$points[, 2], xlab = "", ylab = "", cex= .5, col = 2, pch = '+')
             points(ordi$species[, 1], ordi$species[, 2], xlab = "", ylab = "", cex=.2, pch = 19)
             ordisurf(ordi, site[, var2], col = 'black', choices = c(1, 2), add = TRUE)
             orditorp(ordi, display = disp, pch = " ")
             legend("topright", paste("GAM of ", var2), col = 'black', lty = 1)
             if(!is.null(env)) plot(env, col='red')
           }
           ,...)
}

nmds.plot(veg.nmds, elbaue.env, disp='species', var1="MGL", var2="SDGL", env=env, plottitle = 'Elbaue floodplain dataset')
} else {
  message("packages interp and/or labdsv not available")
}