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Construct an explicitly weighted microbial guild contrast

Source: R/rri_micro_functional_score.R
rri_micro_functional_score.Rd

Summarises supplied guild measurements or proxies. The weights define a contrast, not a universal ordering of microbial resilience. Denitrification, sulfate reduction and methanogenesis may be beneficial or detrimental depending on the specified ecosystem function and disturbance.

Usage

rri_micro_functional_score(micro_traits, weights = NULL, scale = TRUE)

Arguments

micro_traits

Numeric data frame with comparable, justified guild scales. Gene abundance or expression does not by itself measure process rate.

weights

Named finite signed weights. Default legacy weights are illustrative only and trigger a warning; supply scientifically justified weights.

scale

If TRUE, scale finite contrasts within the supplied cohort to [0, 1]. Constants map to 0.5 and wholly unobserved rows remain NA.

Value

Numeric vector with coverage and raw_contrast attributes. The raw contrast is a signed weighted sum divided by the available absolute weight. Missing guilds are not zeros; changing availability changes the estimand.

See also

rri_reference_scores

Examples

x <- data.frame(EET_reduction = c(0.2, 0.4, NA),
                methanogenesis = c(0.3, 0.1, NA))
rri_micro_functional_score(x, weights = c(EET_reduction = 1, methanogenesis = -1))
#> [1]  0  1 NA
#> attr(,"coverage")
#> [1] 1 1 0
#> attr(,"raw_contrast")
#> [1] -0.05  0.15    NA