calcCMs: Calculate connectivity matrices for a set of DisMELS model...

In wStockhausen/wtsDisMELSConn: Functions for dealing with DisMELS IBM model output, including calculating and analyzing connectivity matrices

Description

Function to calculate a set of connectivity matrices corresponding to a set of DisMELS model runs.

Usage

  calcCMs(resDir = "C:\\Projects\\GOA_IERP\\IBM_Runs\\ATF\\FullSeries",
  connResBase = "ConnYYYYMMDD.csv", cellsTbl = file.path(resDir,
  "ATF_ClassifiedCGOAGridCells.csv"), years = as.character(1996:2011),
  months = c("01"), days = c("01"),
  spawningZones = c("SpawningArea_300to600m"),
  nurseryZones = c("NurseryArea_000to050m", "NurseryArea_050to150m"),
  lhsTypeInfo = getLifeStageInfo.ATF(), where_clause = "",
  writeCSVs = TRUE, folder = getwd(), basename = "")

Arguments

resDir	- path to base directory for DisMELS results files
connResBase	- file name template for connectivity results files from DisMELS (e.g., "ConnYYYYMMDD.csv")
cellsTbl	- name of classified grid cells file or dataframe based on classified grid cells file (can be NULL)
years	- vector of years corresponding to model simulation names (YYYY)
months	- vector of months corresponding to model simulation names (MM)
days	- vector of days corresponding to model simulation names (DD)
spawningZones	- vector of names of zones used as spawning areas in the IBM
nurseryZones	- vector of names of zones used as nursery areas in the IBM
lhsTypeInfo	- list object with life stage info
where_clause	- sql "where" clause to determine final state for individuals included in connectivity calculations
writeCSVs	- flag (T/F) to write concatenated dataframes to csv
folder	- folder to write csv files to
basename	- base name for output csv files

Details

If the 'cellsTbl' is a filename,it will be read to create an associated dataframe. If cellsTbl is null, the user can select the classified grid cells file using a file dialog.

Connectivity results files from the DisMELS model runs should be of the form "ConnYYYYMMDD.csv", where "Conn" is arbitrary (but consistent among results files) and YYYY indicates the year (if applicable), MM the month (if applicable), and DD the day (if applicable) for a particular model run. If YYYY, MM, or DD is **not** part of the file name, use "" as the function input for the corresponding years, months, or days.

Value

list w/ 3 elements:

• dfrCMs - dataframe with connectivity matrices results

• dfrICs - dataframe with individual connectivity results

• dfrNRs - dataframe with numbers released

wStockhausen/wtsDisMELSConn documentation built on May 3, 2019, 7:36 p.m.