Plot_taxa: Plots trait predictions for taxa
In James-Thorson/FishLife: Predict Life History Parameters For Any Fish

Plot_taxa

R Documentation

Plots trait predictions for taxa

Description

Plots bivariate predictive intervals for specified parameters and taxa

Usage

Plot_taxa(
  Taxa,
  prob = 0.95,
  params = matrix(c("K", "M", "Winfinity", "Loo", "tmax", "tm", "Lm", "Temperature",
    "ln_margsd", "rho", "logitbound_h", "ln_r"), ncol = 2, byrow = TRUE),
  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,
  xlim = log(c(0.01, 2)),
  ylim = xlim,
  ticks = c(0, 5),
  logticks = c(1, 2, 5),
  partial_match = FALSE,
  drop_pred = TRUE,
  mfrow = c(nrow(params), 1),
  legendnum = 2,
  verbose = FALSE,
  plot_lines = FALSE,
  lcol = rainbow(length(Taxa)),
  lty = rep("solid", length(Taxa)),
  xaxt = "s",
  yaxt = "s",
  ...
)

Arguments

`Taxa`	One or more taxonomic names (matching rows from `ParentChild_gz[,'ChildName']`)
`prob`	for defining predictive interval
`params`	matrix (2 columns) of parameters to plot, where each row gives parameter names for a given 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
`xlim`	x-limits if `add=FALSE`
`ylim`	y-limits if `add=FALSE`
`ticks`	ticks to use if plotting on a natural-scale
`logticks`	ticks to use if plotting on a log-scale
`partial_match`	Should `Taxon` be an partial match or not (exact match)
`drop_pred`	Boolean whether to drop "_predictive" from legend
`mfrow`	numeric vector giving number of rows and columns for panel figure
`legendnum`	which panel to use for legend
`verbose`	Boolean whether to print diagnostics to terminal
`plot_lines`	whether to plot lines representing "major axis" and "OLS" regression parameters
`lcol`	line color for ellipse
`...`	additional arguments passed to `shape::plotellipse`