indivsInfo_ExtractStartEndByStage: Extract info by individual at start and end of life or model...
In wStockhausen/rDisMELS: Basic functions for dealing with DisMELS IBM model output

View source: R/indivsInfo_ExtractStartEndByStage.R

indivsInfo_ExtractStartEndByStage

R Documentation

Extract info by individual at start and end of life or model run

Description

Function to extract info by individual at start and end of life or model run.

Usage

indivsInfo_ExtractStartEndByStage(
  sf_start = NULL,
  sf_ebs = NULL,
  lst_indivs = NULL,
  startLHS = NULL,
  addVarsStart = "",
  addVarsEnd = "",
  hasSuccessful = FALSE,
  verbose = FALSE,
  checkCalcs = FALSE
)

Arguments

`sf_start`	- (optional) sf dataframe returned by `indivsInfo_ExtractStart`
`sf_ebs`	- (optional) sf dataframe returned by `indivsInfo_ExtractEndByStage`
`lst_indivs`	- (req'd if sf_start or sf_end is NULL) list of sf dataframes by life stage returned by `indivsInfo_ReorderResults`
`startLHS`	- (req'd if sf_start is NULL) life stage in which all individuals start
`addVarsStart`	- character vector with names of additional (non-default) start variables to extract
`addVarsEnd`	- character vector with names of additional (non-default) end variables to extract
`hasSuccessful`	- flag indicating that sf_start, sf_ebs, or lst_indivs include "successful" columns
`verbose`	- flag to print debugging info
`checkCalcs`	- flag (T/F) to check endGeom is correctly assigned (for debugging)

Details

The input sf dataframes sf_start and sf_end should be the output of indivsInfo_ExtractStart and indivsInfo_ExtractEnd, respectively. If both are given as an inputs, addVars is ignored.

If either are NULL, lst_indivs must be given. If sf_start is NULL, startLHS must be given. If sf_start is NULL, it is calculated internally using sf_start = indivsInfo_ExtractStart(lst_indivs[[startLHS]],addVars=addVars).

If sf_end is NULL, it is calculated internally using sf_ebs = indivsInfo_ExtractEndByStage(lst_indivs,addVars=addVars) followed by sf_end = indivsInfo_ExtractEnd(sf_ebs).

Value

sf dataframe with columns:

startTime
origID - original (starting) individual ID
startLHS - starting life stage
startGridCell - ID of starting ROMS grid cell
startLon - starting longitude
startLat - starting latitude
startDepth - starting depth (m)
startBathym - bathymetric depth (m) at starting location
startAge - starting depth
startNum - starting depth
start..AddVarsStart - starting values for additional (non-default) variables
startGeom - starting 2d location as SF_POINT
endTime - ending time
endID - ending individual ID
endLHS - ending life stage
endGridCell - ID of ending ROMS grid cell
endLon - ending longitude
endLat - ending latitude
endDepth - ending depth (m)
endBathym - bathymetric depth (m) at ending location
endAge - ending age(d)
endNum - ending number
end..AddVarsEnd - ending values for additional (non-default) variables
successful - flag indicating "success" (TRUE) or failure (FALSE) (e.g., settlement) [depends on inputs]
endGeom - ending 2d location as SF_POINT