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Read-in dataframes from downloaded RAM Legacy Database

Source: R/load_ramlegacy.R
load_ramlegacy.Rd

Returns a list of specific dataframes or a list of all the dataframes present in the requested version of the database.

Usage

load_ramlegacy(version = NULL, tables = NULL, ram_path = NULL)

Arguments

version

A character vector of length 1 specifying the version number of the database. As of writing this package, the available versions are "1.0", "2.0", "2.5", "3.0", "4.3", "4.40", "4.41" and "4.44". If version argument is not specified then it defaults to newest version (v4.44).

tables

A character vector specifying the names of particular dataframes to load from a specified version. If not specified then a list containing all the dataframes within the requested version is returned. For a description of the different tables present in the database please see below.

ram_path

path to the local directory where the specified version of the RAM Legacy Stock Excel Assessment Database was downloaded. By default this path is set to within the rappdirs directory and can be viewed using calling the function ram_dir and specifying the version number inside the function call. Although this is not the recommended approach load_ramlegacy supports reading in the database's dataframes from a user-specified path provided that the database is present at the specified path as an rds object.

Description of the dataframes present in the database

  • metadata: Table with summarized metadata (only available in newer versions starting from v4.40)

  • stock: This stores the stock database table

  • assessment: This stores the assessment database table

  • taxonomy: This stores the taxonomy database table

  • management: This stores the management database table

  • assessor: This stores the assessor database table

  • assessmetod: This stores the assessmetod database table

  • area: This stores the area database table

  • biometrics: This stores the biometrics database table

  • tsmetrics: This stores the tsmetrics database table

  • timeseries: The time series data is a matrix object with the following headers/columns: (1) assessid (2) stockid (3) stocklong (4) tsid (5) tsyear (6) tsvalue

  • bioparams: The parameter data is a matrix object with the following headers/columns: (1) assessid (2) stockid (3) stocklong (4) bioid (5) biovalue (6) bioyear (7) bionotes

  • timeseries_values_views: This stores the timeseries values with timeseries type along the columns and stocks along the rows

  • timeseries_units_views: This stores the timeseries values with timeseries type along the columns and stocks along the rows

  • timeseries_ids_views: This stores the timeseries IDs with timeseries type along the columns and stocks along the rows

  • timeseries_assessments_views: This stores the timeseries assessments with timeseries type along the columns and stocks along the rows

  • timeseries_notes_views: This stores the timeseries notes with timeseries type along the columns and stocks along the rows

  • timeseries_sources_views: This stores the timeseries sources with timeseries type along the columns and stocks along the rows

  • timeseries_years_views: This stores the timeseries years with timeseries type along the columns and stocks along the rows

  • bioparams_values_views: This stores the reference point values, with reference point type along the columns and stocks along the rows

  • bioparams_units_views: This stores the reference point units, with reference point type along the columns and stocks along the rows

  • bioparams_ids_views: This stores the reference point IDs, with reference point type along the columns and stocks along the rows

  • bioparams_assessments_views: This stores the reference point assessments, with reference point type along the columns and stocks along the rows

  • bioparams_sources_views: This stores the reference point sources, with reference point type along the columns and stocks along the rows

  • bioparams_notes_views: This stores the reference point notes, with reference point type along the columns and stocks along the rows

Newer versions (v4.40 onwards) also contains tables of individual most-used time series

  • tb.data: Total Biomass

  • ssb.data: Spawning Stock Biomass

  • tn.data: Total Abundance

  • r.data: Recruits

  • tc.data: Total Catch

  • tl.data: Total Landings

  • recc.data: Recreational Catch

  • f.data: Fishing Mortality

  • er.data: Exploitation Rate

  • divtb.data: TB/TBmsy

  • divssb.data: SSB/SSBmsy

  • ivf.data: F/Fmsy

  • diver.data: ER/ERmsy

  • divbpref.data: B/Bmsypref

  • divupref.data: U/Umsypref

  • tbbest.data: TBbest

  • tcbest.data: TCbest

  • erbest.data: ERbest

  • divtb.mgt.data: TB/TBmgt

  • divssb.mgt.data: SSB/SSBmgt

  • divf.mgt.data: F/Fmgt

  • diver.mgt.data: ER/ERmgt

  • divbpref.mgt.data: B/Bmgtpref

  • divupref.mgt.data: U/Umgtpref

  • cpair.data: Cpair

  • tac.data: TAC

  • cadv.data: Cadvised

  • survb.data: survB

  • cpue.data: CPUE

  • effort.data: EFFORT

See also

Other ramlegacy functions: download_ramlegacy, ram_dir

Examples

# \donttest{
Sys.setenv(RAM_HOME = tempfile())
# first download version 4.44 of the database
download_ramlegacy(version = "4.44")
#> ★ Downloading...this may take a while
#> ★ Finished Downloading. Now unzipping it...
#> ★ Saving the unzipped database as RDS object...
#> ✔ Version 4.44 successfully downloaded.

# get a list containing area and bioparams tables
# from version 4.44 database
load_ramlegacy(version = "4.44", tables = c("area", "bioparams"))
#>  Number of tables:  2 
#> ====================================== 
#> 'area':  821 obs. of 6 variables 
#> 'bioparams':  16204 obs. of 7 variables 
# }