set_tutorialdir() has been removed as it is not used anywhere within the package and the usefulness is limited.testthat was happily passing the tests, but checks failed. This has now been fixed.zonator does not behave well with staged install because of some of the hardcoded paths in the package. Disabling staged install is a stopgap measure and ideally the path definition should be handled more gracefully.testthat 2.0.check_zonation() was failing on Solaris. This patch-release tries to fix that issue by using Sys.which() as suggested by BDR, but it cannot be tested before submitting to CRAN.zdat. This is not true.zdat package needed for development and building the vignettes is now installed from Github using drat. Accordingly, various checks are done to condition some code to run only if zdat is installed.zonator website now generated using pkgdowncost() can be used to extract cost data from results. Implemented for Zresults and Zvariant.file_path_relative_to() can be used to dynamically construct relative paths for spp data.copy_zvariant() can be used to create a copy of an existing variant with a new name.zonator and placed to a separate data package zdat. This package is required for developing zonator.XXX.features_info.txt is now parsed into Zresults objects. This way, e.g. species distribution sum information becomes readilly available.zonator in dir inst/extdata/tutorial have been truncated to avoid unportable long paths strings.sppweights()<-.plot_curves() dynamically between ColorBrewer’s Set1 and Set2. Where the former has better colors, the latter has more.create_spp() accepts new argument recursive = TRUE which will look for rasters in target directory recursively.spp_file_dir for create_spp() accepsts multiple directories (in vector) instead of just one.decimalplaces() can figure out how many decimal places a number has.save_zvariant() now dynamically decides how to format weight and alpha column values based on max(decimalplaces(x)) in the vector.create_zproject() now actually checkst if template dat-file exists.spp_file_pattern in create_spp(). Previous version did find .tif and .img file, but also some directories.groupnames()<-. This doesn’t make much sense, so now there can be extra groups in the value being assigned as long as as all group codes are found in the keys.regroup_curves() always return a ZGroupCurvesDataFrame object.leaf_tags() is a new utility function that can get leaf (outermost) tags and their values in a nested list (used for dat-parsing).get_dat_param() can be used to get values of a (valid) Zonation run configuration parameter (i.e. the content of a dat-file) from a Zvariant object.set_dat_param() can be used to set values of a (valid) Zonation run configuration parameter (i.e. the content of a dat-file) for a Zvariant object.zparameters() is used to fetch all accepted Zonation run configuration parameters (i.e. parameters in the dat file). Can return just the parameter names or a list of [[parameter_name]][[section]]".show() for Zvariant now prints run configuration parameters as well.set_dat_param() can be used to set run configuration parameters (i.e. dat file parameters). Only valid parameters are accepted.get_dat_param() can be used to get run configuration parameters (i.e. dat file parameters).sppdata()<- allows spp data to be modified. This is mostly needed in creating/cpoying variants as editing spp data in place is not probably a good idea.save_zvarint() saves the current state of a Zvariant object on the file system. Saving can overwrite exisiting configuration files or create new.create_zproject() now stops if spp_template_dir doesn’t exist.tools::file_path_sans_ext() that can handle periods (“.”) just before file extension.Zvariant object when no groups were used initially failed before (see issue #45.), fixed now.read_ini() renamed to read_dat().create_zproject() no longer uses “do_” prefix when generating bat files.plyr from the dependencies.ggplot2 >= 2.0.0. This way aes_() can be used and CHECK doesn’t complain about “undefined global variables” anymore.create_zproject() functionality has been split into two. create_zproject() now handles the creation of a completely new Zonation project (also on the file system) whereas load_zproject() can be used to load existing Zonation projects. This change creates a cleaner and more intuitice API. NOTE The API for create_zproject() has changed, so check your code.zonator classes.dir.exists() replaced with file.exists() in spp-creation.plot_curves() accepts new argument fix.y which can be used to fix the y-axis to [0, 1]. Useful e.g. plotting runs with condition layers.modified slot of a zresults object is now parsed from the run info file. Not ideal, but couldn’t figure out a way how to do this reliably on Linux.print() and show() methods are now implemented for objects of class Zvariant. Makes printing basic data a bit easier.RdYlBu added. This ColorBrewer’s 7-level RdYlBu palette.create_spp() can be used to create spp files based on a directory of input raster files.create_zproject() now works by giving it a directory containing input rasters based on which the spp files are created.read_ini().BrBG added. This a slight variation from ColorBrewer’s 7-level BrBG scheme with the lowest value replaced with grey.Fix imports in roxygen2 docs
Generic group names assigned at initiation. If Zvariant object has groups enabled, assign generic group names “group1”, “group2” to groups automatically.
Generic group ID larger than 10 would not get mapped right because of a sloppy gsub-replacement. Regex fixed and groupnames()<- should work correctly when one has more than 10 groups.
get_variant() for Zproject objects now checks the input index properly (issue34)
Trying to get rank rasters from a set of variants with no rank rasters available caused and error, now produces warnings and returns a NA.
ds_alpha() that can be used to calculate alpha value for distribution smoothing.weights to sppweights so that it doesn’t overwrite base generic.Assigning group names now works correctly with generic default values and whenever groups (ids) are changed. (issue29)
Generic group naming now works, i.e. if group ids are changed group names get a generic value “group1”, “group2” etc. (issue22)
Assigning group ids with groups()<- now recalculates group specific stats (min, mean, max, weighted mean) for defined groups. In other words, it is now possible to define groups other than those defined in Zonation groups file and have the group curves data calculated for the new groups.
cross_jaccard() now returns a dataframe with correct RasterLayer names colnames and rownames.
cross_jaccard() now accpets a numeric vector of threshold values for comparison.
jaccard() now has additional parameters for controlling the thresholds for rasters x and y being compared. Arguments xmin, xmax, ymin, and ymax can be used to control which ranges of the raster values are compared.
New methods for class Zproject:
rank_rasters() accepts a new argument variants which can be either a character of numeric vector of variant names / IDs defining which rank rasters are included in the RasterStack that is returned. Default is to return all.New methods for class Zvariant:
weights() returns a numeric vector of weights assigned to a variant.Creating new Zproject object based on an existing Zonation project involves reading in a lot of files and it can be useful to know the sequence of reading in case something goes wront. create_zproject() now accepts a new argument debug=TRUE which enables logging of file reading sequence. (issue28)
New methods for class Zvariant:
groups()<-nfeatures() returns the number of features in a variantcheck_zonation() fixed on Windows (ZCurvesDataFrame:
featurenames()check_path() works on Windows (Results vignette has bee updated.
Post-processign (PPA) LSM results are now handled by Zresults. Results, if present, are read in from the output folder. More specifically:
Zresults now defines a new slot ppa.lsm tha holds the content of PPA LSM resultszlegend() can be used to fetch Zonation rank raster map legend schemes. So far only one scheme (“spectral”) is implemented.
New methods for class Zproject:
rank_rasters(): returns a RasterStack of all priority rank rasters of all variants within a projectNew methods for class Zvariant:
curves()New methods for class Zvariant and Zresults:
rank_raster(): returns RasterLayer of priority rank raster of a given variant or its resultsZproject:
variants(): returns a list containing all the variants within a projectZvariant and Zresults:
outdir(): returns the path to location of output dirctoryMaintance update, R CMD check and TravisCI test passes after few minor fixes.
Zcurves has been refactored to 2 classes: ZCurvesDataFrame and ZGroupCurvesDataFrame. Change was introduced mostly to handle performance curves plotting more sensibly.Generic groupnames() now returns a character vector instead of a named character vector (with names being the original group numbers)
plot() now works for ZCurvesDataFrame and ZGroupCurvesDataFrame objecs.
New methods for class Zresults:
groupnames()bat-files are read recursively when creating a project (issue20)
check_paths() now deals with relative path components
has_results() now returns a list of logicals instead of a single logical
New methods for class Zresults:
has_results(): returns a list of TRUE/FALSE depending on whether the particular results items (curves, grp.curves, rank, wrscr, prop) are available or notNew classes Zresults and Zcurves. See docs for methods and structure.
New methods for class Zvariant:
groupnames()<-: assign human readable group namesgroupnames(): get assigned unique groupnames and codeshas_results(): returns TRUE/FALSE depending on whether the variant has results or notresults(): returns a Zresults object specific to a Zvariant objectZvariant:
featurenames()<-: assign human readable feature namesfeaturenames(): get assigned unique featurenamessppdata(): return the whole spp data frame of a variantZvariant. Groups are read in from the actual Zonation input file and can be used (eventually) in many operations.Zvariant:
groups(): returns a numeric vector containing group codes for featuresgroupnames()<-: assign human readable group names to groupsgroupnames(): get assigned unique groupnames with associated group codesread_groups(): read in Zonation groups fileZpoject:
names(): returns a character vector of the names of variants in a projectZvariant:
has_results(): boolean indicating whether the variant already has associated resultsread.spp(): read in spp files