# Utilities for Zonation Spatial Conservation Prioritization Software

## Documentation for package ‘zonator’ version 0.5.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

C D F G H J L M N O P R S V W Z

## -- C --

check_names | A function check feature/group names.
check_path | A function to deal with potentially relative paths.
check_zonation | Check if Zonation is installed.
clean_str | Clean leading and trailing whitespaces from a given string. Additionally, all occurrences of multiple whitespaces are replaced with a single whitespace.
comp | Compare matrices in various ways.
copy_zvariant | Copy existing variant as a new 'Zvariant' object.
copy_zvariant-method | Copy existing variant as a new 'Zvariant' object.
correlation | Correlation between two matrices.
cost | Get cost data of a Z* object.
cost-method | Get cost data of a Z* object.
create_spp | Generate spp_file based on a directory of input rasters.
create_zproject | Create a new Zonation project on file system.
cross_jaccard | Calculate Jaccard coefficients bewteen all the RasterLayers within a single RasterStack.
curves | Get curves results data of a Z* object.
curves-method | Get curves results data of a Z* object.

## -- D --

decimalplaces | Find out the number of decimal places in a number.
ds_alpha | Calculate alpha value for distribution smoothing.

## -- F --

featurenames | Feature names of Zonation variant.
featurenames-method | Feature names of Zonation variant.
featurenames<- | Feature names of Zonation variant.
featurenames<--method | Feature names of Zonation variant.
features_info | Get the features info component of Zresults.
features_info-method | Get the features info component of Zresults.
file_path_relative_to | Transform an absolute path to relative path in relation to given location
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.

## -- G --

get_dat_param | Get a specified run setting parameter value
get_dat_param-method | Get a specified run setting parameter value
get_tutorialdir | Get the directory of Zonation tutorial.
get_variant | Get a specified variant in a Zonation project
get_variant-method | Get a specified variant in a Zonation project
groupnames | Get group names for a class 'Zvariant' instance.
groupnames-method | Get group names for a class 'Zvariant' instance.
groupnames<- | Get group names for a class 'Zvariant' instance.
groupnames<--method | Get group names for a class 'Zvariant' instance.
groups | Get group codes of a class 'Zvariant' instance.
groups-method | Get group codes of a class 'Zvariant' instance.
groups<- | Get group codes of a class 'Zvariant' instance.
groups<--method | Get group codes of a class 'Zvariant' instance.

## -- H --

has_results | Check which results a Z* object has.
has_results-method | Check which results a Z* object has.

## -- J --

jaccard | Calculate the Jaccard coefficient.

## -- L --

leaf_tags | 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.
load_zproject | Load a Zonation project.

## -- M --

map_indexes | Map vector to actual column indexes.

## -- N --

names-method | Names of variants in Zproject
nfeatures | Get the number of feature included in a Zonation variant
nfeatures-method | Get the number of feature included in a Zonation variant
nvariants | Get the number of variants included in a Zonation project
nvariants-method | Get the number of variants included in a Zonation project

## -- O --

opendir | Open the directory of a Zproject using the system file browser.
opendir-method | Open the directory of a Zproject using the system file browser.
outdir | Get path to output directory.
outdir-method | Get path to output directory.

## -- P --

parse_bat | Parse the content of a Zonation batch (bat) file and make OS specific adjustments if needed.
performance | Get performance levels.
performance-method | Get performance levels.
plot-method | Plot Zonation performance curves for individual features.
plot-method | Plot Zonation performance curves for groups.
plot_hist | Create a ggplot2 histogram of a 'RasterLayer'.
ppa_lsm | Get ppa.lsm results data of a Z* object.
ppa_lsm-method | Get ppa.lsm results data of a Z* object.
print-method | Print Zvariant information.

## -- R --

rank_raster | Get Zonation result rank raster.
rank_raster-method | Get Zonation result rank raster.
rank_rasters | Get Zonation result rank rasters of a project.
rank_rasters-method | Get Zonation result rank rasters of a project.
read_bat | Read Zonation-specific (MS Windows) batch file.
read_curves | Read in performance curves produced by Zonation.
read_dat | Read a dat file (Windows-style ini-file) for configuration information.
read_features_info | Read a features info file.
read_groups | Read a groups file.
read_grp_curves | Read in performance curves for grouped features produced by Zonation.
read_ppa_lsm | Read Zonation post-processing analysis (ppa) result file.
read_result_rasters | Read Zonation-specific raster result files.
read_spp | Read Zonation variant specific spp-file.
regroup_curves | Re-calculate group curves data.
require_package | Requires a given package and if not present installs and loads it.
results | Getter method for results ('Zresults') in a class 'Zvariant' object.
results-method | Getter method for results ('Zresults') in a class 'Zvariant' object.
run_bat | Try to run a given batch (bat) files.

## -- S --

save_zvariant | 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.
save_zvariant-method | 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.
selection_coverage | Intersection of two coverages.
set_dat_param | Set a specified run setting parameter value
set_dat_param-method | Set a specified run setting parameter value
set_tutorialdir | Set the package options to point to a correct location of the Zonation tutorial
show-method | Print Zvariant information.
sppdata | Simple getter mehtod for spp data in a class 'Zvariant'object.
sppdata-method | Simple getter mehtod for spp data in a class 'Zvariant'object.
sppdata<- | Simple getter mehtod for spp data in a class 'Zvariant'object.
sppdata<--method | Simple getter mehtod for spp data in a class 'Zvariant'object.
sppweights | Get biodiversity feature weights of a Zonation variant
sppweights-method | Get biodiversity feature weights of a Zonation variant
sppweights<- | Get biodiversity feature weights of a Zonation variant
sppweights<--method | Get biodiversity feature weights of a Zonation variant

## -- V --

variants | Get all variants in a Zonation project
variants-method | Get all variants in a Zonation project

## -- W --

write_dat | Write a Zonation run configuration (dat) file.

## -- Z --

ZCurvesDataFrame | The ZCurvesDataFrame class
ZCurvesDataFrame-class | The ZCurvesDataFrame class
ZGroupCurvesDataFrame | The ZGroupCurvesDataFrame class
ZGroupCurvesDataFrame-class | The ZGroupCurvesDataFrame class
zlegend | Get various Zonation legends
zparameters | Get all Zonation run configuration parameters.
Zproject | The Zproject class
Zproject-class | The Zproject class
Zresults | The Zresults class
Zresults-class | The Zresults class
Zvariant | The Zvariant class
Zvariant-class | The Zvariant class