azmpdata R package

Benoit Casault, Emily Chisholm 15 December, 2020

azmpdata

The R package azmpdata provides a series of data products derived from raw data collected as part of the Atlantic Zone Monitoring Program (AZMP). The data products provided in this package are used to generate the different figures contained in the Research Documents produced annually by Fisheries and Ocean Canada’s Maritimes region. The Research Documents describe the physical, chemical and biological conditions observed in Maritimes region since the inception of the AZMP program (see example documents for the physical conditions and for the optical, chemical and biological conditions).

Package Installation

The azmpdata R package can be installed from GitHub with:

# install.packages("devtools")
devtools::install_github("casaultb/azmpdata")

Datasets

The azmpdata package provides three types of data products: physical, chemical and biological variables, which are summarized below. Each data product is organized into a data table by temporal and regional scale and category.

To access a dataset in data frame format:

library(azmpdata)
#> 
#>  casaultb/azmpdata status:
#>  (Package ver: 0.2019.0.9000) Up to date
#>  (Data ver:2020-11-26) is up to date
data("Derived_Annual_Broadscale")
head(Derived_Annual_Broadscale)
#>   year          area density_gradient_0_50 temperature_at_sea_floor
#> 1 1948 Scotion Shelf              -0.00139                       NA
#> 2 1949 Scotion Shelf              -0.00968                       NA
#> 3 1950 Scotion Shelf              -0.01883                       NA
#> 4 1951 Scotion Shelf              -0.00092                       NA
#> 5 1952 Scotion Shelf               0.00155                       NA
#> 6 1953 Scotion Shelf              -0.00313                       NA
#>   cold_intermediate_layer_volume minimum_temperature_in_cold_intermediate_layer
#> 1                           <NA>                                           <NA>
#> 2                           <NA>                                           <NA>
#> 3                           <NA>                                           <NA>
#> 4                           <NA>                                           <NA>
#> 5                           <NA>                                           <NA>
#> 6                           <NA>                                           <NA>

To access a dataset in csv format:

system.file("extdata/csv", "Derived_Annual_Broadscale.csv", package = "azmpdata")
#> [1] "C:/Users/ChisholmE/Documents/R/R-4.0.2/library/azmpdata/extdata/csv/Derived_Annual_Broadscale.csv"

Variable Organization

Each table contains multiple variables, which fall under the temporal and regional scale in a particular category. The example shown above includes derived variables at an annual scale for broad regions (eg. Scotian Shelf or Gulf of Maine). Variables can be found via the search function variable_lookup(), which allows a user to search by variable name or keyword. For more information see ?variable_lookup. This function searches through variable names and (optionally) help files from each dataset including metadata and variable definitions.

Package Functionality

Although the main goal of azmpdata is to provide easy access to a variety of data products, the package also supports a few basic functions for which examples are shown below.

Searching Data

A custom search function has been developed in order to allow users to find specific data. The function variable_lookup() can be used to search through variable names in all azmpdata dataframes. Using the argument search_help, this function can also search through all the help text for package data. A sample use of this search function may look as below:

res <- variable_lookup(keywords = c('nitrate', 'phosphate'), search_help = TRUE)
#> Joining, by = c("keyword", "variable", "dataframe")

head(res)
#> # A tibble: 6 x 3
#>   keyword variable                  dataframe                   
#>   <chr>   <chr>                     <chr>                       
#> 1 nitrate integrated_nitrate_0_50   Derived_Annual_Sections     
#> 2 nitrate integrated_nitrate_0_50   Derived_Annual_Stations     
#> 3 nitrate integrated_nitrate_0_50   Derived_Occupations_Sections
#> 4 nitrate integrated_nitrate_50_150 Derived_Annual_Sections     
#> 5 nitrate integrated_nitrate_50_150 Derived_Annual_Stations     
#> 6 nitrate integrated_nitrate_50_150 Derived_Occupations_Sections

Dataset Documentation

A detailed description of the whole package is available using the following command:

library(azmpdata)
help("azmpdata")

In addition, each dataset is documented and the following command returns a detailed description about a given dataset:

library(azmpdata)
help("Derived_Annual_Broadscale")

Plotting

Plotting azmpdata is covered in a detailed vignette plotting_azmpdata.

For developers

Data managers and developers may need to update data within the package. For more details on this process, please see the vignette update_azmpdata. The vignette style_guide also provides more details on the formatting of new data.