Readme.md
In NINAnor/NIcalc: Functions to Calculate a Nature Index

R-package for calculation of the Nature Index.

Bård Pedersen April 21, 2021

NIcalc

NIcalc contains a set of utility functions tailored for working with the Nature Index for Norway (see https://hdl.handle.net/11250/2739962). Functions in NIcalc may be used to upload new and revised data into the Nature Index database, to harvest and assemble data sets from the database, to use these data sets in calculations of the Nature Index and similar indices, and to summarize and visualize the results.

NIcalc contains documentation and explanations for all functions included. There are three vignettes: NatureIndexCalculation describes the mathematical framework for calculating the Nature Index and the associated terminology, objectsInNIcalc describes the S3 classes defined within NIcalc, while Distributions describes how one may interact with the Nature Index database in scripts when uploading new and revised data.

devtools::install_github("NINAnor/NIcalc", build_vignettes = T)

The functions importDatasetApi(), assembleNiObject(), calculateIndex(), getIndicatorValues(), setIndicatorValues(), and writeIndicatorValues() represent the core of NIcalc.

Updating the Nature Index database with new data

getIndicatorValues(), setIndicatorValues(), and writeIndicatorValues() may be used in scripts for updating the NI database with new or revised measurements. getIndicatorValues() retrieves the current values for a given indicator from the NI database as an S3 object of class indicatorData, setIndicatorValues() updates indicatorData objects with new measurements, and writeIndicatorValues() posts objects with updated values to the Nature Index database.

How to calculate the Nature Index

importDatasetApi() harvests data sets from the database. assembleNiObject() assembles and structures data into a complete and consistent data set for calculating the Nature Index. calculateIndex() calculates the Nature Index and similar indices. It produces an extensive output for each index value to facilitate further analyses of the results.

An example:

# Not run: 
# Import data set
amphibiaImport <- NIcalc::importDatasetApi(username = "...",password = "...",
                        eco = NULL, indic = c("Småsalamander","Buttsnutefrosk",
                                              "Storsalamander"),
                        year = c("2010","2014","2019"))
# Assemble
amphibiaInput <- NIcalc::assembleNiObject(inputData = amphibiaImport,
                        predefNIunits = c(allArea = T, parts = T, counties = F),
                        indexType = "thematic")
# Calculate index for amphibians 
amphibiaIndex <- NIcalc::calculateIndex(x = amphibiaInput, nsim = 1000,
                        fids = FALSE, tgroups = FALSE, keys = "ignore",
                        w = 0, awbs = TRUE, awBSunit = "Ferskvann")

If you have questions regarding NIcalc please contact bard.pedersen@nina.no.

Bug reports can submitted via email to bard.pedersen@nina.no or you can submit an issue here

Please provide a reproducible error so that we can see what went wrong. Reprex is very helpful in this regard.

Please tell us what you expected to achieve and what the error message was.

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