getMDFR.SurveyQuantities: Get estimated/predicted survey-related quantities from...

In wStockhausen/rTCSAM2013: Functions to run and plot output from TCSAM2013 models.

Description

Function to get estimated/predicted survey-related quantities from several model runs.

Usage

getMDFR.SurveyQuantities(obj, type = c("MB_yx", "lglN_y", "lglB_y", "N_yxmsz",
  "N_yxmz", "N_yxz", "N_yxms", "N_yxm", "N_yx", "B_yxmsz", "B_yxmz", "B_yxz",
  "B_yxms", "B_yxm", "B_yx", "prNatZ_yxmsz", "prNatZ_yxmz", "prNatZ_yxz",
  "PRs_yxmsz", "PRs_yxmz", "PRs_yxz", "mnPrNatZ_xmz", "mnPrNatZ_xz", "qSrv_xy",
  "selSrv_cxz", "selSrv_yxz", "zscores", "effSS_y"), pdfType = c("lognormal",
  "normal"), ci = 0.8, verbose = FALSE)

Arguments

obj	- object that can be converted into a list of tcsam2013.resLst objects
type	- survey-related quantity to retrieve
pdfType	- type of error distribution for observations
ci	- confidence interval for error bars on observations
verbose	- flag (T/F) to print debug info

Details

Potential values for 'type' are:

• 'MB_yx' - mature biomass at survey time, by sex (1000's t)

• 'B_yx' - total biomass at survey time, by sex (1000's t)

• 'N_yxmsz' - annual survey abundance-at-size by x,m,s (millions)

• 'N_yxmz' - annual survey abundance-at-size by x,m (millions)

• 'N_yxz' - annual survey abundance-at-size by x (millions)

• 'N_yxms' - annual survey abundance by x,m,s (millions)

• 'N_yxm' - annual survey abundance by x,m (millions)

• 'N_yx' - annual survey abundance by x (millions)

• 'B_yxmsz' - annual survey biomass-at-size by x,m,s,z (1000's t)

• 'B_yxms' - annual survey biomass by x,m,s (1000's t)

• 'B_yxm' - annual survey biomass by x,m (1000's t)

• 'B_yx' - annual survey biomass by x (1000's t)

• 'lglN_y' - legal male annual survey abundance (millions)

• 'lglB_y' - legal male annual survey biomass (1000's t)

• 'prNatZ_yxmsz' - annual proportions-at-size by x,m,s

• 'prNatZ_yxmz' - annual proportions-at-size by x,m

• 'prNatZ_yxz' - annual proportions-at-size by x

• 'PRs_yxmsz' - pearsons residuals for annual proportions-at-size by x,m,s

• 'PRs_yxmz' - pearsons residuals for annual proportions-at-size by x,m

• 'PRs_yxz' - pearsons residuals for annual proportions-at-size by x

• 'mnPrNatZ_xmz' - mean proportions-at-size by x,m

• 'mnPrNatZ_xz' - mean proportions-at-size by x

• 'qSrv_yxz' - survey catchability, by survey, year and sex

• 'selSrv_cxz' - survey selectivity, by time period and sex

• 'selSrv_yxz' - survey selectivity, by survey, year and sex

• 'zscores' - annual z-scores for fit to mature survey biomass, by sex

• 'effSS_y' - effective (and input) sample sizes for multinomial fits

Requires sqldf package.

Value

dataframe with columns in canonical format

wStockhausen/rTCSAM2013 documentation built on May 3, 2019, 7:13 p.m.