CHNOSZ (version 2.1.0)

rank.affinity: Average Ranks of Chemical Affinities

Description

Affinity rankings for groups of species.

Usage

rank.affinity(aout, groups, percent = TRUE)

Value

The average rankings are inserted into the values element of aout, and the names of the groups are inserted into the species element. The result can be used by diagram to make line plots or predominance diagrams (the predominance fields correspond to the groups with highest average ranking of affinity).

Arguments

aout

list, output of affinity

groups

named list of indices (integer or numeric) for species in each group

percent

return average rank percentage for each group

Details

The affinities for all species are ranked, then the mean ranking for the species in each group is calculated. The mean rankings of groups are converted to a percentage, or returned as-is if percent is FALSE. Note that the calculations are applied to each set of conditions individually (i.e., each grid point in the affinity affinity calculation).

See Also

demo("rank.affinity")

Examples

reset()# Compare Rubisco proteins from three domains
datfile <- system.file("extdata/cpetc/rubisco.csv", package = "CHNOSZ")
fastafile <- system.file("extdata/protein/rubisco.fasta", package = "CHNOSZ")
dat <- read.csv(datfile)
aa <- read.fasta(fastafile)
groups <- sapply(c("A", "B", "E"), "==", dat$domain, simplify = FALSE)
names(groups) <- c("Archaea", "Bacteria", "Eukaryota")
ip <- add.protein(aa, as.residue = TRUE)
basis("QEC")
aout <- affinity(O2 = c(-74, -66, 100), H2O = c(-4, 4, 100), iprotein = ip)
arank <- rank.affinity(aout, groups = groups)
nspecies <- sapply(groups, sum)
names <- paste0(names(groups), " (", nspecies, ")")
diagram(arank, fill = "terrain", font = 2, names = names, format.names = FALSE)
title("Average affinity ranking of Rubisco proteins")