doc/abundance-null-models.R

In irhoppe/cooccur: Abundance Matrix Randomizations

## ---- echo=FALSE, results="asis"----------------------------------------------
alg.table <- data.frame(rbind(
              Functions=paste0("asim",c(1:14)), 
              Algorithm=c("PM","PR","PC","OS","OF","IR","IS","ISR","ISC","IT","ITR","ITC","IA","IF"),
      `Total abundance`=c(T,T,T,T,NA,F,NA,F,F,T,T,T,T,NA), 
    `Total occurrences`=c(T,T,T,T,NA,F,NA,T,T,F,F,F,T,NA), 
            Occurrences=c(T,T,T,T,NA,F,NA,F,F,F,F,F,T,NA), 
   `Species abundances`=c(F,T,T,F,NA,F,NA,F,F,T,T,F,T,NA), 
  `Species occurrences`=c(T,T,T,T,NA,F,NA,T,F,F,F,F,T,NA), 
      `Site abundances`=c(F,F,T,F,NA,F,NA,F,F,T,F,T,T,NA), 
     `Site occurrences`=c(T,T,T,T,NA,F,NA,F,T,F,F,F,T,NA)
), stringsAsFactors=FALSE )

names(alg.table) <- matrix(alg.table[1,])
alg.table <- alg.table[-1,]
alg.table[which(alg.table=="TRUE",arr.ind=T)] <- "X"
alg.table[which(alg.table=="FALSE",arr.ind=T)] <- ""
alg.table[which(is.na(alg.table),arr.ind=T)] <- "?"

knitr::kable(alg.table, format="html", caption="Metrics preserved by different randomization algorithms.", align=c("r",rep("c",14)), excape=FALSE )