compareData.FleetTimeSeriesABs: Compare time series of abundance or biommass data by fleet...

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

Compare time series of abundance or biommass data by fleet among several model scenarios

Description

Function to compare abundance or biomass time series data by fleet among several model scenarios.

Usage

compareData.FleetTimeSeriesABs(
  objs = NULL,
  fleet.type = c("survey", "fishery"),
  catch.type = c("index", "retained", "discard", "total"),
  data.type = c("abundance", "biomass"),
  fleets = "all",
  sexs = "all",
  maturity_states = "all",
  shell_conditions = "all",
  position = ggplot2::position_dodge(0.2),
  ci = 0.8,
  numRecent = 15,
  ylims = NULL,
  facets = "fleet~x",
  scales = "free_y",
  verbose = FALSE
)

Arguments

objs	object that can be converted into a list of tcsam2013.resLst and/or tcsam02.resLst objects (or dataframe from call to extractMDFR.Data.FleetTimeSeriesABs())
fleet.type	fleet type ('fishery' or 'survey')
catch.type	catch type ('index','retained', 'discard' or 'total')
data.type	data type ('abundance' or 'biomass')
fleets	vector of names of fleets to plot (or 'all')
sexs	vector of sexes to plot (or 'all')
maturity_states	vector of maturity states to plot (or 'all')
shell_conditions	vector of shell conditions to plot (or 'all')
position	indicates ggplot2 position_ to use ('dodge','jitter','identity',)
ci	confidence interval for plots
numRecent	number of years for 'recent' plot
ylims	limits for y axis (default is NULL)
facets	grid faceting formula (as an expresssion for multilevel faceting)
scales	ggplot2 scales option for facet_grid
verbose	flag (T/F) to print diagnostic information

Details

Uses extractMDFR.Data.FleetTimeSeriesABs() to extract the data (if objs is not a dataframe). Uses plotMDFR.Fits.TimeSeries() to make the plots, with plotObs=TRUE and plotMod=FALSE. Only time series with at least one non-zero value will be plotted (to eliminate lots of values along y=0).

Note that facets should be given as an expression, not as a character string, if you want multilevel faceting.

Value

Non-nested list of ggplot2 objects, with captions as names

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