Plot_trait: Plots trait predictions

In James-Thorson/FishLife: Predict Life History Parameters For Any Fish

Plots trait predictions

Description

Plots predictive interval for a given taxon and trait-pair

Usage

Plot_trait(
  Taxon,
  params = c("K", "M"),
  Database = FishLife::FishBase_and_RAM,
  Cov_gjj = Database$Cov_gvv,
  Mean_gj = Database$beta_gv,
  ParentChild_gz = Database$ParentChild_gz,
  Y_ij = Database$Y_ij,
  g_i = Database$g_i,
  SpeciesMatch = NULL,
  prob = 0.95,
  add = FALSE,
  xlim = log(c(0.01, 2)),
  ylim = xlim,
  partial_match = TRUE,
  main = "",
  xlab = "",
  ylab = "",
  lcol = "black",
  plot_lines = FALSE,
  verbose = FALSE,
  ticks = c(0, 5),
  logticks = c(1, 2, 5),
  obsCov_jj = Database$obsCov_jj,
  include_obscov = FALSE,
  lty = "solid",
  xaxt = "s",
  yaxt = "s",
  ...
)

Arguments

Taxon	A taxon (matching row from ParentChild_gz[,'ChildName'])
params	character vector (length of two) of parameters to plot
Database	Whether to use results for both adult and stock-recruit parameters, Database="FishBase_and_RAM", or just adult parameters, Database="FishBase"
Cov_gjj	Array of estimated covariance for each taxonomic group g and trait j
Mean_gj	Matrix of Empirical Bayes predictions of traits for each taxonomic group
ParentChild_gz	Matrix representing taxonomic tree for analyzed data
Y_ij	a data frame of trait values (perhaps log-scaled) with rows for records, and tagged-columns for traits
g_i	Vector that associates every observation with a level of the taxonomic tree
SpeciesMatch	Species for which to plot data
prob	for defining predictive interval
add	Boolean whether to add ellipse to existing plot
xlim	x-limits if add=FALSE
ylim	y-limits if add=FALSE
partial_match	Should Taxon be an partial match or not (exact match)
main	legend for each panel
xlab	x-axis label
ylab	y-axis label
lcol	line color for ellipse
plot_lines	whether to plot lines representing "major axis" and "OLS" regression parameters
verbose	Boolean whether to print name matches or not
ticks	ticks to use if plotting on a natural-scale
logticks	ticks to use if plotting on a log-scale
...	additional arguments passed to shape::plotellipse

James-Thorson/FishLife documentation built on Feb. 29, 2024, 3:47 a.m.