cbig/zonator

Utility tools for for anybody interested in using a familiar tool (R) in setting up Zonation runs and managing Zonation results.

zonator's Issues

Boxplot representation levels for a particular landscape protection fraction

Refactor performance curves plotting code

Both plot_curves and plot_grp_curves should have only 1 plotting function. Preprocessing the data (read in and parse) should be done separately (still within 1 function?).

Function for extracting the performance levels for all features for a given fraction of the landscape

performance(x, top.fraction)

x = Zvariant object
top.fraction = Top fraction (in percentage!) of the landscape for which the performance level is returned. E.g. top.fraction=15 would equal to rank >= 0.85. Can be a single value or a vector of values.

value = A data frame with given percentages as columns and feature as rows.

Get rid of the named.raster

regular rasters are just fine

featurenames can't handle backwards slash in paths

E.g. raster path in spp file

C:Data\foo\bar\some_spam.img

becomes name foo bar some_spam

Implement save_zvariant()

Method should save all the associated (Zonation input) files on the file system.

Group curves plot x-axis range wrong

Group names don't get assigned to sppdata

Include option for truly invert x-axis in curves plotting

There is already a invert.x option plot() for ZCurvesDataframe and ZGroupCurvesDataframe, but this only affects the labels on the x-axis. Would be useful if the plotting order could be changed.

Make performance curve plotting more intelligent

If there are many features / groups to plot in performance curves, the graphical resolution of the plot may not be good. Plot generic should inspect how many lines need to be plotted and adjust the linetype/color mappings accordingly.

Implement run-method for class Zvariant

Simply do:

run_bat([email protected])

No tests for parsing an ini-file

Implement rename() for Zvariant

get_variant() should check the index provided

get_variant(x, index) where x is a Zproject object and index is either a character or numeric index (name or a position of a variant). index should be checked for validity.

Refactor dependencies

So far more-or-less necessary packages are all in depends in DESCRIPTION file. See if some of these could be moved to imports or suggests.

bat-files include trailing whitespaces

bat-files created by create_zproject() include trailing whitespaces, remove these.

Feature names not assigned correctly

Feturenames are only assigned if set explicitly. They should be set even is using the default ones.

dir.exists is part of devtools, not base R!

Implement logging when reading in Zproject

When Zproject is being created based on existing project, a lot of files are being read in. Implement debug logging to track which files are read in in case something goes wrong.

Fix check_zonation(exe)

Does not find zig(3or4).exe in windows, even if the path variable is correct.

Write dat (ini) files

Simple functionality for writing dat (ini) files needed.

Recursive search for bat files - could this be done?

It would be good to have this option, as e.g. the project maker makes projects so that the bat file is written under the variant folder.

cross_jaccard() should accept a vector of threshold values

Generate spp files automatically

Provide examples with the documentation

This would probably call for example data. Could the tutorial be used?

Installation instructions a bit unclear

... at least for dummies :)

User defined paths to create_zproject

Create_zproject would benefit from a feature where user could define different paths to be used in .bat files. Now root.path is used automatically which is awkward if one wants to use relative paths.

Make package pass R CMD CHECK without NOTEs

performance should return ave_pr as well

performance only returns pr_lost and feature levels or group means. Overall average would be useful too.

Internal representation of groups and spp features should be merged

Now groups data and spp data are stored separately, these should be merged internally

check_path() doesn't work correctly on Windows

Implement getting and setting of run configuration (dat) parameters

Create functions get_dat_param() and set_dat_param() methods for class Zvariant. These work with @dat.data slot.

Group assignment not working

At least when groups have not been used initially.

Document all the files properly

create.spp.file adds extra white space after every line

Change Depend to imports

Transfer most of the old Depends packages to @import or @importFrom.

Implement create_zvariant()

This is a simpler version of create_zproject() which creates just a single variant.

Move functionality form create_zproject() to load_zproject()

create_zproject() tries to do too much now: it can create a new Zonation project as well load existing. Create a new function load_zproject() for cleaner and more intuitive API.

Extract names for spp features from the feature file path

Subsetting groups in curves()

Using argument cols while groups=TRUE in curves() does not work. Either warn user about this or implement correct group subsetting.

Fix curve plotting for groups

Feature names get lost

Feature names works ok for variants but get lost when analyzing results (e.g. the plots use only f1, f2, f3, etc. and featurenames(results) return this:
[1] "f1" "f2" "f3" "f4"

jaccard() should accept any ranges [0, 1], not only top fractions

Fix the function naming convention

Use underscore "_" instead of dot or camelCase notation.

Results don't work if groups are not used

My simple Z run didn't have groups, and thus 'results' considered my results to be empty, although they were not.

Group naming does not work if group IDs change

Group IDs vector can be changed:

groups(variant) <- something

but trying to add new names mapping does not work as the number of categories is still being checked against the original groups-file.

Get rid of futile.logger

Normal conditional message statements should be enough.

Implement spp feature naming

Similar to groupnames<- / groupnames

Implement str -function for Zvariant class

parse_bat should return a data.frame

Right now parse_bat() will return a command string, returning a data.frame with the command elements would be more versatile