compareResults.Pop.CohortProgression: Function to compare cohort progression by year among several...

In wStockhausen/rCompTCMs: Package to compare TCSAM02, rsimTCSAM, and TCSAM2013 model runs

Function to compare cohort progression by year among several models

Description

This function compares cohort progression by year among several models.

Usage

compareResults.Pop.CohortProgression(
  objs,
  cast = "x+m+s+z",
  scaleToDensity = FALSE,
  aggToCutpts = FALSE,
  cutpts = seq(25, 185, 5),
  facet_grid = NULL,
  facet_wrap = NULL,
  dodge = 0.2,
  years = NULL,
  mxy = 4,
  nrow = 2,
  lnscale = FALSE,
  scales = "fixed",
  types = c("progression", "byyear"),
  plotPoints = FALSE,
  shapes = "s",
  plotLines = TRUE,
  linetypes = "ms",
  showPlot = FALSE,
  pdf = NULL,
  verbose = FALSE
)

Arguments

objs	list of TCSAM02 resLst objects (or a dataframe from extractMDFR.Pop.CohortProgression())
cast	casting formula for excluding x,m,s,z factor levels from sums across the unspecified factors
scaleToDensity	flag to scale abundance to 1-mm size bins
aggToCutpts	flag to aggregate (rebin) to provided cutpts
cutpts	cutpoints to aggregate to
facet_grid	formula for faceting using facet_grid
facet_wrap	formula for faceting using facet_wrap
dodge	width to dodge overlapping series
years	numeric vector of years to include (or NULL for all)
mxy	max number of years per page
nrow	number of rows per page, when facet_wrap'ing
lnscale	use log scale on y axis
scales	scales parameter for facet_grid/facet_wrap
types	types of plots to produce ("progression","byyear")
plotPoints	flag to plot points
shapes	name of column for ggplot shape factors (defaults to 's' for shell condition)
plotLines	flag to plot cohorts as lines
linetypes	name of column for ggplot linetype factors (defaults to 'ms' for maturity + shell condition)
showPlot	flag (T/F) to show plot
pdf	filename for pdf output (or NULL for no pdf)
verbose	flag (T/F) to print diagnostic information

Details

If objs is a list of TCSAM02 resLst objects, model results are extracted using extractMDFR.Pop.CohortProgression(). objs can also be a dataframe output extractMDFR.Pop.CohortProgression(). Plots are made using plotMDFR.XY(). You can an plot cohort abundance as a progression by stage for each model (types="progression" or as size distributions by year with colours indicating different models (types="byyear". Sex-specific cohort progressions are plotted separately. By default, different maturity/shell condition categories are indicated using different linetypes.

Value

a list of ggplot2 objects, with potential captions as element names.

wStockhausen/rCompTCMs documentation built on Sept. 12, 2023, 3:13 p.m.