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zonator

zonator is a utility R package for dealing with various tasks related to Zonation conservation prioritization software. The package started out as a collection of helper scripts which have now been packaged for anybody interested in using a familiar tool (R) in setting up Zonation runs and managing Zonation results.

Functions and classes found in zonator can be useful for the following stages of running a Zonation analysis.

Setting up a Zonation project and pre-processing files (examples).
Running Zonation.
Post-processing, results analysis and comparison, and plotting (examples).

Installation

Release version

NOTE: As of 2019-03-15 zonator isn't on CRAN. Hopefully it will get back there soon, but in the meantime you can install it directly from Github:

You can install the latest release version from CRAN:

install.packages("remotes")
remotes::install_github("cbig/zonator")

Development version

Alternatively, you can install the latest (potentially unstable) development version from Github.

Make sure you have package remotes installed and loaded in R:

# Open R prompt or RStudio and type the following on the command line
install.packages("remotes")

Then install zonator directly from GitHub by running the following line in R:

remotes::install_github("cbig/zonator", ref = "develop", build_vignettes = TRUE)

Examples

Some examples are provided by the package vignettes. You can view these after installing the package by:

vignette("zonator-project")

and

vignette("zonator-results")

Developers

Joona Lehtomäki joona.lehtomaki@gmail.com
Aija Kukkala aija.kukkala@helsinki.fi

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Version

Install

install.packages('zonator')

Monthly Downloads

29

Version

0.6.0

License

FreeBSD

Maintainer

Joona Lehtomaki

Last Published

May 18th, 2020

Functions in zonator (0.6.0)

Get the features info component of Zresults.

file_path_relative_to

Transform an absolute path to relative path in relation to given location

Copy existing variant as a new Zvariant object.

Correlation between two matrices.

The Zproject class

create_zproject

Create a new Zonation project on file system.

names,Zproject-method

Names of variants in Zproject

A function check feature/group names.

Get the number of feature included in a Zonation variant

Clean leading and trailing whitespaces from a given string. Additionally, all occurrences of multiple whitespaces are replaced with a single whitespace.

Calculate Jaccard coefficients bewteen all the RasterLayers within a single RasterStack.

The Zresults class

Get Zonation result rank raster.

Generate spp_file based on a directory of input rasters.

print,Zvariant-method

Print Zvariant information.

Check zvariant object's attributes for consistency.

get_tutorialdir

Get the directory of Zonation tutorial.

Get cost data of a Z* object.

Get a specified variant in a Zonation project

Get the number of variants included in a Zonation project

Check if Zonation is installed.

Compare matrices in various ways.

file_path_sans_ext

Re-implementation of file_path_sans_ext in tools. This version can handle "." just before the file extenstion, unlike the original implementation.

Get a specified run setting parameter value

Find all the leaf tags in a potentially nested list. The generic form of a list is tag = value; find all the tags in a list.

plot,ZGroupCurvesDataFrame,missing-method

Plot Zonation performance curves for groups.

Open the directory of a Zproject using the system file browser.

Read Zonation post-processing analysis (ppa) result file.

Calculate the Jaccard coefficient.

Saves the current state of an instance of Zvariant-class on the file system. Zvariant object tracks the location of relevant files, but the root path can be changed. If it is not changed, then the current files can be overwritten.

Create ggplot2 object for performance curves.

read_grp_curves

Read in performance curves for grouped features produced by Zonation.

Get performance levels.

Get group codes of a class Zvariant instance.

Load a Zonation project.

Get group names for a class Zvariant instance.

Check which results a Z* object has.

Create a ggplot2 histogram of a RasterLayer.

plot,ZCurvesDataFrame,missing-method

Plot Zonation performance curves for individual features.

Map vector to actual column indexes.

Get Zonation result rank rasters of a project.

initialize,Zproject-method

Create an instance of the Zproject class using new/initialize.

Find out the number of decimal places in a number.

Getter method for results (Zresults) in a class Zvariant object.

Try to run a given batch (bat) files.

Calculate alpha value for distribution smoothing.

selection_coverage

Intersection of two coverages.

Read in performance curves produced by Zonation.

Get ppa.lsm results data of a Z* object.

Read a dat file (Windows-style ini-file) for configuration information.

Get subset of curves/group curves columns.

Get various Zonation legends

Read Zonation-specific (MS Windows) batch file.

Get all Zonation run configuration parameters.

Read a groups file.

read_features_info

Read a features info file.

Feature names of Zonation variant.

Set a specified run setting parameter value

unique_grp_names

Get unique group names.

Get path to output directory.

show,Zvariant-method

Print Zvariant information.

Get curves results data of a Z* object.

Simple getter mehtod for spp data in a class Zvariantobject.

Get biodiversity feature weights of a Zonation variant

Parse the content of a Zonation batch (bat) file and make OS specific adjustments if needed.

read_result_rasters

Read Zonation-specific raster result files.

Read Zonation variant specific spp-file.

Re-calculate group curves data.

require_package

Requires a given package and if not present installs and loads it.

Get all variants in a Zonation project

Write a Zonation run configuration (dat) file.

ZGroupCurvesDataFrame

The ZGroupCurvesDataFrame class

A function to deal with potentially relative paths.

ZCurvesDataFrame

The ZCurvesDataFrame class

The Zvariant class

Check zvariant object's attributes for consistency.