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.
ramlegacy
do?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.load_ramlegacy()ram_dir() to view the path of the
location where the downloaded database was cached.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
Please see the ramlegacy vignette for more detailed examples and additional package functionality.
Start by loading the package using library.
library(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")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.
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")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.
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.
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.
