df.fer <- read.xlsx("../data/data.xlsx",sheet='fermentation')

# adjusting data, creating factors, adjusting data types, etc.
df.fer$`Volume.[Nml]` <- as.numeric(df.fer$`Volume.[Nml]`) # some text artifacts are present so as.numeric has to be used
df.fer$`disintegration.temp.[oC]` <- factor(df.fer$`disintegration.temp.[oC]`,
                                            ordered=TRUE, levels=c('in.','b.d.','45','50','55','60'))
df.fer$`disintegration.time.[h]` <- factor(df.fer$`disintegration.time.[h]`,
                                           ordered=TRUE,levels=c('in.','0','24','48'))

# creating new factor to distinguish between case No and experiment included in a case
df.fer$case.exp <- factor(paste(df.fer$case.No, df.fer$experiment.No,sep='-'))


# changing the column names for simpler manipulation
df.fer.original.col.names <- colnames(df.fer) # just in case
df.fer.simlified.col.names <- c('day','volume','original.column.header','description','composition','inoculum.weight',
                                'co-substrate.weight','dis.temp','dis.time','case','experiment','disintegration.tab','case.exp')

colnames(df.fer) <- df.fer.simlified.col.names

# removing one series - it turned out to be invalid
bad.series_case.exp <- '35-1' # it will be removed in some analyses
df.fer <- df.fer[df.fer$case.exp != bad.series_case.exp,]