readAll: Read in All the Data Corresponding to a Specified Reference...
In JVAdams/EchoNet2Fish: Estimate Fish Abundance from Acoustic Echoes and Net Catch

Description Usage Arguments Details Value

Read in all the acoustic and midwater trawl data corresponding to the specified row or a reference csv file. Save the data as objects in an RData file.

readAll(
  refdir,
  keyvals,
  keyvars = c("LAKE", "YEAR"),
  rdat = "ACMT",
  refcsv = "Reference"
)

`refdir`	A character scalar giving the directory in which the reference csv file, `ref`, is located.
`keyvals`	A vector giving the values of `keyvars` to identify a single row of the reference csv file, `ref`.
`keyvars`	A character vector giving the names of columns in the reference csv file, `ref`, that will be used to identify a single row, default c("LAKE", "YEAR").
`rdat`	A character scalar giving the name of the RData file that will be saved containing all of the objects corresponding to the selected row of the reference csv file, `ref`, default "ACMT".
`refcsv`	A character scalar giving the name of the reference csv file, `ref`, default "Reference". The csv file must have the following 10 columns: `subdir` = a subdirectory of `refdir` containing all the other subdirectories and files, `svsubdir` = the Sv subdirectory, `tssubdir` = the TS subdirectory, `optropf` = the midwater trawl operations file, `trcatchf` = the midwater trawl catch file, `trlff` = the midwater trawl lengths file, `keysp1` = the species code for `keyfile1`, `keyfile1` = the age-length csv file for species`keysp1`, `keysp2` = the species code for `keyfile2`, `keyfile2` = the age-length csv file for species`keysp2`. There should also be additional columns for `keyvars`.

The acoustic and midwater trawl data corresponding to the selected row of the reference csv file are read in and saved as objects in the specified RData file, in subdir. Objects include the scalar rdat; the vectors keyvals and keyvars; and the data frames inputs (the selected row from the reference data); sv and ts (acoustic data); optrop, trcatch, and trlf (midwater trawl data); key1 and key2 (age-length keys, if specified).