Import, Clean and Update Data from the New Zealand Freshwater Fish Database.

nzffdr

Package overview

The purpose of this package is to allow for direct access to the NZ Freshwater Fish Database (NZFFD) from R and additional functions for cleaning imported data and adding missing data.

For a detailed guide to using the package see the help page.

A preprint describing the package is now available (if you wish to cite the package please use this):

Lee, F., & Young, N. (2021). nzffdr: an R package to import, clean and update data from the New Zealand Freshwater Fish Database. bioRxiv. https://doi.org/10.1101/2021.06.22.449519

Installation

install.packages("nzffdr")

Development version

To install the latest development version install from GitHub.

devtools::install_github("flee598/nzffdr")

Import data from the NZFFD

This function requires an internet connection to query the NZFFD database.

# import all records
library(nzffdr)

dat <- nzffdr_import(download_format = "essential")
head(dat)
#>   nzffdRecordNumber  eventDate eventTime institution       waterBody
#> 1                 1 1979-06-05     10:30        NIWA Limestone Creek
#> 2                 1 1979-06-05     10:30        NIWA Limestone Creek
#> 3                 1 1979-06-05     10:30        NIWA Limestone Creek
#> 4                 1 1979-06-05     10:30        NIWA Limestone Creek
#> 5                 1 1979-06-05     10:30        NIWA Limestone Creek
#> 6                 1 1979-06-05     10:30        NIWA Limestone Creek
#>   waterBodyType site catchmentNumber catchmentName eastingNZTM northingNZTM
#> 1   Not Entered              691.021       Hinds R     1463229      5157184
#> 2   Not Entered              691.021       Hinds R     1463229      5157184
#> 3   Not Entered              691.021       Hinds R     1463229      5157184
#> 4   Not Entered              691.021       Hinds R     1463229      5157184
#> 5   Not Entered              691.021       Hinds R     1463229      5157184
#> 6   Not Entered              691.021       Hinds R     1463229      5157184
#>   minimumElevation distanceOcean                  samplingMethod
#> 1              480            60 Electric fishing - Type unknown
#> 2              480            60 Electric fishing - Type unknown
#> 3              480            60 Electric fishing - Type unknown
#> 4              480            60 Electric fishing - Type unknown
#> 5              480            60 Electric fishing - Type unknown
#> 6              480            60 Electric fishing - Type unknown
#>   samplingProtocol                   taxonName     taxonCommonName totalCount
#> 1          Unknown                    Anguilla    Unidentified eel         NA
#> 2          Unknown           Galaxias vulgaris Canterbury galaxias         NA
#> 3          Unknown      Gobiomorphus breviceps        Upland bully         NA
#> 4          Unknown Scardinius erythrophthalmus                Rudd         NA
#> 5          Unknown       Salvelinus fontinalis          Brook char         NA
#> 6          Unknown           Carassius auratus            Goldfish         NA
#>   present soughtNotDetected minLength maxLength dataVersion
#> 1    true             false        NA        NA          V1
#> 2    true             false        NA        NA          V1
#> 3    true             false        NA        NA          V1
#> 4    true             false        NA        NA          V1
#> 5    true             false        NA        NA          V1
#> 6    true             false        NA        NA          V1

# To import the entire NZFF Database:
# dat <- nzffd_import()