HabitatSampler merge requestshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests2024-01-08T15:24:30+01:00https://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/50Clean and improve code2024-01-08T15:24:30+01:00Romulo Pereira GoncalvesClean and improve codeUpgrade code to stop using rgeos, sp, and rgdalRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/45Issue#682022-10-14T16:36:30+02:00Romulo Pereira GoncalvesIssue#68Closes issues #68Closes issues #68Romulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/39Remove version restriction2022-05-12T14:24:50+02:00Romulo Pereira GoncalvesRemove version restrictionUnit and Integration testsRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/38Issue#392022-05-02T11:23:43+02:00Romulo Pereira GoncalvesIssue#39Closes issue #39Closes issue #39Unit and Integration testsRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/37Improvements misac2022-03-29T10:37:10+02:00Romulo Pereira GoncalvesImprovements misacImprove documentationRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/36Improve documentation2022-05-06T15:18:15+02:00Romulo Pereira GoncalvesImprove documentationCloses issues #21, #35, #60, #62Closes issues #21, #35, #60, #62Improve documentationRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/29Predict using the raster in memory.2022-01-17T09:38:45+01:00Romulo Pereira GoncalvesPredict using the raster in memory.PerformanceRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/27update Progressbar2021-08-05T13:10:17+02:00Daniela Rabeupdate ProgressbarDaniela RabeDaniela Rabehttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/21Save sample points2021-07-09T08:23:01+02:00Romulo Pereira GoncalvesSave sample pointsPerformanceRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/18Save samplepoints2021-06-25T15:33:49+02:00Johannes KnochSave samplepointswriteOutSamples.r now writes out a set of samples (SpatialPointsDataFrame) into an ESRI shapefile or a GeoJSON file for a selected habitat type. Each point represents a valid sample location that identifies the selected habitat type.
de...writeOutSamples.r now writes out a set of samples (SpatialPointsDataFrame) into an ESRI shapefile or a GeoJSON file for a selected habitat type. Each point represents a valid sample location that identifies the selected habitat type.
default output format is shape; use output_format = 'geojson' for geojson output
Documentation is adjusted and write_Out_Samples.Rd is commited.GeneralizationJohannes KnochJohannes Knochhttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/14Issue#32021-06-09T14:53:39+02:00Romulo Pereira GoncalvesIssue#3DocumentationRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/4Add the number of nb_models value to the legend. Fix the order of the prints...2021-05-04T09:50:09+02:00Romulo Pereira GoncalvesAdd the number of nb_models value to the legend. Fix the order of the prints...Add the number of nb_models value to the legend. Fix the order of the prints (we need to flush otherwise the outputs will get out of order). Simplify the output.Add the number of nb_models value to the legend. Fix the order of the prints (we need to flush otherwise the outputs will get out of order). Simplify the output.User InterfaceRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/3Tests2021-02-19T15:12:20+01:00Romulo Pereira GoncalvesTestsAdd a docker runner for tests.
The same docker runner will then be used to create a web-page.Add a docker runner for tests.
The same docker runner will then be used to create a web-page.https://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/2Docker2021-02-04T09:53:50+01:00Romulo Pereira GoncalvesDockerWith this merge requests we are now able to create a docker image for HabitatSampler.
In the `docker` directory there is a script to build the image and another one to start a docker container. The script to start a docker container all...With this merge requests we are now able to create a docker image for HabitatSampler.
In the `docker` directory there is a script to build the image and another one to start a docker container. The script to start a docker container allows the user to launch either a bash console to start an R instance or a jupyter-lab to run notebooks.
To be able to run HabitatSampler with less resources as possible we now delete the main objects after their last utilization and call R garbage collector `gc(full = TRUE)`. Furthermore, extra arguments were added to the function `multi_Class_Sampling`:
* save_runs : an Habitat object and extra info (to restart a run) is saved (default TRUE)
* max_num_cores : maximum number of cores for parallelism (default 5)
Since we can't launch a web-browser from a docker container, the user can now decide if the images should be either plot via a browser or plotted inline in a notebook. In both cases the interactive plot is saved as a html file in disk.
* plot_on_browser : plot on the browser or inline in a notebook (default TRUE)
All documentation was improved according to the above changes.Unit and Integration testsRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/1Performance2021-01-26T18:00:53+01:00Romulo Pereira GoncalvesPerformanceIn this merge request we mostly improved performace:
- we have add the `parallel_mode`. With this mode set to `TRUE` some loops are executed using `mcapply`, i.e., instead of single thread it exploits all available cores in the computer....In this merge request we mostly improved performace:
- we have add the `parallel_mode`. With this mode set to `TRUE` some loops are executed using `mcapply`, i.e., instead of single thread it exploits all available cores in the computer.
- remove redundant searches using the function `which`
- replace some `which` calls for `vapply` calls to have vectorized processing.
We also fixed some bugs:
- The last threshold was not saved properly
We also improved the documentation by adding missing files.PerformanceRomulo Pereira GoncalvesRomulo Pereira Goncalves