tamatoamlr

tamatoamlr and Tamatoa, the package's accompanying Shiny app, are for analyzing and visualizing data collected by the U.S. AMLR Program's Pinniped Research Group.

Installation

You can install the development version of tamatoamlr from GitHub with the following. Using the pak package may work around some GitHub/certificate issues on NOAA machines.

# install.packages("devtools")
devtools::install_github("us-amlr/tamatoamlr")

### OR ###
# install.packages("pak")
pak::pkg_install("us-amlr/tamatoamlr")

Tamatoa: Shiny app

To run Tamatoa, the tamatoamlr Shiny app, locally, you must have R and RStudio installed. From within RStudio, install tamatoamlr as described above, and then run the following code in your RStudio console to launch the Shiny app:

tamatoamlr::tamatoa()

By default, Tamatoa attempts to connect to the database on the SWFSC server. For it to connect, you must be logged into VPN on whatever computer you are using to run the app. You can also choose to connect to a local copy of the database, if appropriate.

Shiny app overview and guiding principles, for developers:

• mod_database_server, from amlrDatabases, returns the connection to the user-specified database via a pool object that is used by the rest of the tamatoamlr Shiny App modules. Users may use the filedsn argument to 'pre-define' a database connection. If the filedsn argument is provided, then Tamatoa will open with this as the selected database connection

• mod_season_info_server returns the season information data used by the rest of the modules

• The 'Database and season info' tab relies on mod_database and mod_season_info. The rest of the tabs all have a dedicated module that takes at least the pool object from mod_database, and generally the season.df data frame output from mod_season_info_server, as inputs. These modules pass both a table and a plot to mod_output_server from amlrDatabases, which displays the table and plot along with associated visualization and download options. These modules generally depend on views created in the database.

Disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.