#__________________________________________________________________________
# Info Flora Online-Feldbuch in Kreuztabelle formatieren
# Stefan Widmer, Forschungsgruppe Vegetationsoekologie
# Daten_InfoFlora_Feldbuch_formatieren_v.04.R | Version 0.4, 30.11.2021
#__________________________________________________________________________

# Set working directory
setwd("C:/Users/name/Documents/VegA") # Example

# Import dataset (Replace file name "my.Data.csv", change "sep =" if required)
SpxPlot <- read.delim("myData.csv", sep = ";") 

# If the layers of the taxa were (partially) defined, choose the layer of 
# interest below (remove # to run code); otherwise, continue with code in line 27
# ? = herb layer / v = shrub layer / Y = Tree layer / "" = not defined

# SpxPlot <- SpxPlot[SpxPlot$supplements.releve_stratum == "?" | 
#                              SpxPlot$supplements.releve_stratum == "",] # herb & not defined
# SpxPlot <- SpxPlot[SpxPlot$supplements.releve_stratum == "?",] # herb
# SpxPlot <- SpxPlot[SpxPlot$supplements.releve_stratum == "v",] # shrub
# SpxPlot <- SpxPlot[SpxPlot$supplements.releve_stratum == "Y",] # tree
# SpxPlot <- SpxPlot[SpxPlot$supplements.releve_stratum == "",] # not defined


# load and attach package tydyr for data transformation
if(!require(tidyr)){install.packages("tidyr")}
library("tidyr")

# Data Transformation
spxplot <- SpxPlot[,c("releve_id","taxon.taxon_name", "supplements.cover_abs")] # select relevant colums
spxplot <- spread(spxplot, releve_id, supplements.cover_abs) # if error: "doppelte Eintraege" -> Correct in "Online-Feldbuch"
spxplot[is.na(spxplot)] <- 0 # replace empty entries with  0

rownames(spxplot) <- spxplot[,1 ] # the first column will be the row name
spxplot <- spxplot[,-1] 

# Export Species x Plot data
write.table(spxplot, file = "spxplot.csv", sep = ";", col.names = NA)

# Transpose Species x Plot data for further analysis in R
spxplot <- t(spxplot)