rank.affinity: Average ranks of chemical affinities

In CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

Average ranks of chemical affinities

Description

Affinity rankings for groups of species.

Usage

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

Arguments

aout	list, output of affinity
groups	named list of indices (integer or logical) for species in each group
rescale	logical, rescale average ranks for each group to have the same bounds?
percent	logical, take percentages of average ranks for each group (after rescaling)?

Details

The affinities for all species are ranked, then the average rank for the species in each group is calculated. The calculations are applied to each set of conditions individually (i.e., each grid point in the affinity affinity calculation).

Unless rescale is FALSE, the average rank of each group is rescaled to have the same bounds (from 1 to the total number of species). If percent is TRUE, the average ranks of groups (after rescaling) are converted to percentages.

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).

Note

The reaction coefficients in the species element of the returned value of aout are not valid. Because balancing on a basis species (i.e., dividing by its reaction coefficient) would be incorrect, diagram enforces balance = 1 so that that average rankings are used without further modification.

See Also

demo("rank.affinity")

Examples

# Compare Rubisco proteins from three domains
datfile <- system.file("extdata/protein/rubisco.csv", package = "CHNOSZ")
aafile <- system.file("extdata/protein/rubisco_aa.csv", package = "CHNOSZ")
dat <- read.csv(datfile)
aa <- read.csv(aafile)
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 rank of affinity for Rubisco in different domains")

CHNOSZ documentation built on Oct. 27, 2025, 3 p.m.