Utilities for Zonation Spatial Conservation Prioritization Software


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Documentation for package ‘zonator’ version 0.6.0

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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
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