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