syntab | R Documentation |
Calculate and display relative or absolute frequency tables with or without use of function multipatt from package indicspecies
syntab(veg, clust, type = c('rel','abs','mean.cover'), mupa, dec=0, refl, ...) print.syntab(x, zero.print = ".", trait, limit = 1, minstat = 0, alpha = 0.05, ...)
veg |
Vegetation dataframe |
clust |
Vector with cluster information with length equal to number of rows of veg |
type |
Relative or absolute frequency, mean species response values or strength of association. |
mupa |
Either logical for (not) using multipatt from package indicspecies to detect significance of cluster association strength or supply output from previous use of multipatt. |
dec |
Number of decimals in result. |
refl |
Name of Turboveg taxonomic reference list to use for fullnames. |
... |
additional arguments |
x |
Object from function syntab |
zero.print |
Replacement for zero values. |
trait |
Optional vector of trait values to be plotted behind the species. |
limit |
Minimum value to display. |
minstat |
Minimal indicator value |
alpha |
Significance threshold. |
Florian Jansen florian.jansen@uni-rostock.de
Package indicspecies with function multipatt for indicator species analysis along multiple cluster combinations
## Not run: elbaue <- tv.veg('elbaue') elbaue.env <- tv.site('elbaue') clust <- vector('integer', nrow(elbaue.env)) clust[elbaue.env$MGL < -50 & elbaue.env$SDGL < 50] <- 1 clust[elbaue.env$MGL < -50 & elbaue.env$SDGL >= 50] <- 2 clust[elbaue.env$MGL >= -50 & elbaue.env$SDGL >= 50] <- 3 clust[elbaue.env$MGL >= -50 & elbaue.env$SDGL < 50] <- 4 levels(clust) <- c('dry.ld','dry.hd', 'wet.hd','wet.ld') traits <- tv.traits() m <- match(rownames(st$syntab), traits$LETTERCODE, nomatch = 0) trait <- traits[m, c("OEK_F","OEK_N")] rownames(trait) <- traits$LETTERCODE[m] st <- syntab(elbaue, clust, mupa=TRUE) print(st, limit=30, trait=trait) #' Manipulation of the syntaxonomic table sttable <- st$syntab sttable <- sttable[sttable$p.value < 0.05 & !is.na(sttable$p.value), !names(sttable) %in% c('stat')] taxa <- tax(rownames(sttable)) rownames(sttable) <- taxa[match(rownames(sttable), taxa$LETTERCODE, nomatch = 0),'TaxonName'] write.csv(sttable, 'sttable.csv') ## End(Not run)
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