plotRMSE: plotRMSE

In mcalgaro93/benchdamic: Benchmark of differential abundance methods on microbiome data

plotRMSE

Description

A function to plot RMSE values computed for mean difference (MD) and zero probability difference (ZPD) values between estimated and observed values.

Usage

plotRMSE(data, difference = NULL, plotIt = TRUE)

Arguments

data	a list, output of the fitModels function. Each element of the list is a 'data.frame' object with Model, Y, Y0, MD, and ZPD columns containing the model name, the observed values for the mean and the zero proportion and the differences between observed and estimated values.
difference	character vector, either MD or ZPD to plot the differences between estimated and observed mean counts or the differences between estimated zero probability and observed zero proportion.
plotIt	logical. Should plotting be done? (default plotIt = TRUE)

Value

a ggplot object.

See Also

fitModels and RMSE for the model estimations and the RMSE computations respectively. plotMD for the graphical evaluation.

Examples

# Generate some random counts
counts = matrix(rnbinom(n = 600, size = 3, prob = 0.5), nrow = 100, ncol = 6)

# Estimate the counts assuming several distributions
GOF <- fitModels(
    object = counts, models = c(
        "NB", "ZINB",
        "DM", "ZIG", "HURDLE"
    ), scale_HURDLE = c("median", "default")
)

# Plot the RMSE results
plotRMSE(data = GOF, difference = "MD")
plotRMSE(data = GOF, difference = "ZPD")

mcalgaro93/benchdamic documentation built on March 10, 2024, 10:40 p.m.