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ramlegacy

CRAN status Travis Build Status AppVeyor Build Status Coverage status Project Status: Active – The project has reached a stable, usable state and is being actively developed.

ramlegacy is an R package that supports caching and reading in different versions of the RAM Legacy Stock Assessment Data Base, an online compilation of stock assessment results for commercially exploited marine populations from around the world. More information about the database can be found here.

What does ramlegacy do?

  • Provides a function download_ramlegacy(), to download all the available versions of the RAM Legacy Stock Assessment Excel Database and cache them on the user’s computer as serialized RDS objects. This way once a version has been downloaded it doesn’t need to be re-downloaded for subsequent analysis.
  • Supports reading in specified tables or all tables from a cached version of the database through a function load_ramlegacy()
  • Provides a function ram_dir() to view the path of the location where the downloaded database was cached.

Installation

You can install the development version from Github with:

install.packages("devtools")
library(devtools)
install_github("ropensci/ramlegacy")

To ensure that the vignette is installed along with the package make sure to remove --no-build-vignettes from the build_opts in install_github

Usage

Please see the ramlegacy vignette for more detailed examples and additional package functionality.

Start by loading the package using library.

download_ramlegacy

download_ramlegacy() downloads the specified version of RAM Legacy Stock Assessment Excel Database and then saves it as an RDS object in user’s application data directory as detected by the rappdirs package. This location is also where load_ramlegacy() by default will look for the downloaded database.

# downloads version 4.44
download_ramlegacy(version = "4.44")

If version is not specified then download_ramlegacy defaults to downloading current latest version (4.44) :

# downloads current latest version 4.44
download_ramlegacy()

The latest versions of the RAM Legacy Database are archived in Zenodo but the older versions (v4.3, v3.0, v2.5, v2.0, v1.0) are not. To ensure access to these older versions of the database download_ramlegacy supports downloading them from this Github repository:

# downloads older version 4.3
download_ramlegacy(version = "4.3")

load_ramlegacy

After the specified version of the database has been downloaded and cached on your local machine through download_ramlegacy you can call load_ramlegacy to obtain a list of specific tables/all the tables from that version of the database. If version is not specified but tables is then load_ramlegacy defaults to returning a list containing the specified dataframes from the latest version (currently 4.44). If both version and tables are not specified then load_ramlegacy defaults to returning a list containing all the dataframes in the latest version (currently 4.44)

# get a list containing area and bioparams tables from
# version 4.3 of the database
load_ramlegacy(version = "4.3", tables = c("area", "bioparams"))

# get a list containing area and bioparams tables from version 4.44
# of the database
load_ramlegacy(version = "4.44", tables = c("area", "bioparams"))

# if tables is specified but version is not then the function defaults
# to returning a list containing the specified tables from the current
# latest version 4.44
load_ramlegacy(tables = c("area", "bioparams"))

# since both tables and version are not specified the function returns
# a list containing all the tables from the current latest version 4.44
load_ramlegacy()

To learn more about the different tables present in the database, what the various acronyms mean and the different stock summaries accompanying the databases please see this page.

ram_dir

To view the exact path where a certain version of the database was downloaded and cached by download_ramlegacy you can run ram_dir(vers = 'version'), specifying the version number inside the function call:

# download version 4.44
download_ramlegacy(version = "4.44")

# view the location where version 4.44 of the database was
# downloaded and cached
ram_dir(vers = "4.44")

Similar Projects

  1. ramlegacy Sean Anderson has a namesake package that appears to be a stalled project on Github (last updated 9 months ago). However, unlike this package which supports downloading and reading in the Excel version of the database, Sean Anderson’s project downloads the Microsoft Access version and converts it to a local sqlite3 database.

  2. RAMlegacyr RAMlegacyr is an older package last updated in 2015. Similar to Sean Anderson’s project, the package seems to be an R interface for the Microsoft Access version of the RAM Legacy Stock Assessment Database and provides a set of functions using RPostgreSQL to connect to the database.

Citation

Current and older versions of the RAM Legacy Database are archived in Zenodo, each version with its own unique DOI. The suggested format for citing data is:

RAM Legacy Stock Assessment Database. 2018. Version 4.44-assessment-only. Released 2018-12-22. Accessed [Date accessed YYYY-MM-DD]. Retrieved from DOI:10.5281/zenodo.2542919.

The primary publication describing the RAM Legacy Stock Assessment Database, and suggested citation for general use is:

Ricard, D., Minto, C., Jensen, O.P. and Baum, J.K. (2012) Evaluating the knowledge base and status of commercially exploited marine species with the RAM Legacy Stock Assessment Database. Fish and Fisheries 13 (4) 380-398. DOI: 10.1111/j.1467-2979.2011.00435.x

Several publications have relied on the RAM Legacy Stock Assessment Database.