ReadADIOS: Get ADIOS! data and prepare for Plan B smooth

In cmlegault/PlanBsmooth: Applies Plan B Smooth Approach to Biomass Index Data

Description

Reads in ADIOS! csv file (ADIOS_SV_speciesitis_stock_sex_strat_mean.csv), standardizes series if desired, computes mean of all or user selected surveys, outputs csv file with Year and Mean Index.

Usage

ReadADIOS(
  data.dir,
  adios.file.name,
  od = ".",
  standardize = FALSE,
  usesurvey = NA,
  shiftfallflag = TRUE,
  narmavgflag = FALSE,
  saveplots = FALSE,
  nameplots = ""
)

Arguments

data.dir	directory with csv file
adios.file.name	name of ADIOS! csv file (without the .csv extension)
od	directory for output (default=working directory)
standardize	true/false flag to divide by mean of time series (default=FALSE)
usesurvey	vector of true/false to select surveys to average (default=NA which means use all)
shiftfallflag	true/falsee flag for shifting fall survey by one year (default=TRUE)
narmavgflag	true/false flag for na.rm setting in average across multiple surveys (default=FALSE)
saveplots	true/false flag to save output to od (default=FALSE)
nameplots	added to start of saved files (default=""), spaces not recommended

cmlegault/PlanBsmooth documentation built on Aug. 31, 2021, 8:48 p.m.