evalplot.nulls: ENMnulls statistics plot

In jamiemkass/ENMeval: Automated Tuning and Evaluations of Ecological Niche Models

ENMnulls statistics plot

Description

Plot histogram of evaluation statistics for null ENM simulations

Usage

evalplot.nulls(
  e.null,
  stats,
  plot.type,
  facet.labels = NULL,
  metric.levels = NULL,
  return.tbl = FALSE
)

Arguments

e.null	ENMnull object
stats	character vector: metrics from results table to be plotted; examples are "auc.val" or "or.10p"; if more than one statistic is specified, the histogram plot will be faceted
plot.type	character: either "violin" or "histogram"
facet.labels	named list: custom names for the metric facets, in the form list(old_name = "new_name", ...)
metric.levels	character vector: custom factor levels for metrics; this controls the order that metric statistics are plotted
return.tbl	boolean: if TRUE, return the data frames of null results used to make the ggplot instead of the plot itself

Details

There are two variations for this plot, but both show null quantiles (0.01, 0.05, 0.5, 0.95, 0.99). For violin plots, the null distribution is displayed as a vertical shape (i.e., the violin) with horizontal lines showing the quantiles and the empirical value is plotted as a red point along the vertical axis. For histogram plots, the null distribution is displayed as a histogram with vertical lines showing the quantiles and the empirical value as a vertical red line on the distribution.

Value

A ggplot of null model statistics.

Examples

## Not run: 
# first, let's tune some models
occs <- read.csv(file.path(system.file(package="predicts"), 
                           "/ex/bradypus.csv"))[,2:3]
envs <- rast(list.files(path=paste(system.file(package="predicts"), 
                                   "/ex", sep=""), pattern="tif$", full.names=TRUE))
bg <- as.data.frame(predicts::backgroundSample(envs, n = 10000))
names(bg) <- names(occs)

ps <- list(orientation = "lat_lat")

e <- ENMevaluate(occs, envs, bg, 
                 tune.args = list(fc = c("L","LQ","LQH"), rm = 2:4), partitions = "block", 
                 partition.settings = ps, algorithm = "maxnet", categoricals = "biome",
                 parallel = TRUE)

d <- eval.results(e)

# here, we will choose an optimal model based on validation CBI, but you can
# choose yourself what evaluation statistics to use
opt <- d |> filter(cbi.val.avg == max(cbi.val.avg))

# now we can run our null models 
# NOTE: you should use at least 100 iterations in practice -- this is just an
# example
nulls <- ENMnulls(e, mod.settings = list(fc = opt$fc, rm = opt$rm), no.iter = 10)

# let's plot the null model results
evalplot.nulls(nulls, stats = c("cbi.val", "auc.val"), plot.type = "violin")

## End(Not run)

jamiemkass/ENMeval documentation built on Jan. 19, 2025, 4:33 a.m.