HabitatSampler merge requestshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests2022-01-17T09:38:45+01:00https://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/28To be able to handle NAs we need to add the parameter: na.action = na.omit,...2021-09-23T15:30:45+02:00Romulo Pereira GoncalvesTo be able to handle NAs we need to add the parameter: na.action = na.omit,...To be able to handle NAs we need to add the parameter: na.action = na.omit, this is, omit pixels with NA value.To be able to handle NAs we need to add the parameter: na.action = na.omit, this is, omit pixels with NA value.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/26Carsten optimization2022-03-28T13:14:31+02:00Daniela RabeCarsten optimizationMerge optimization branch to masterMerge optimization branch to masterPerformanceDaniela RabeDaniela Rabehttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/25Offer the options to overwrite files. In case the file exists and the user di...2021-07-16T15:32:19+02:00Romulo Pereira GoncalvesOffer the options to overwrite files. In case the file exists and the user did...Offer the options to overwrite files. In case the file exists and the user did not choose the option to overwrite, raise an error.Offer the options to overwrite files. In case the file exists and the user did not choose the option to overwrite, raise an error.PerformanceRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/24When results is NULL, we should create an empty SpatialPolygonsDataframe. To...2021-07-09T16:23:31+02:00Romulo Pereira GoncalvesWhen results is NULL, we should create an empty SpatialPolygonsDataframe. To...When results is NULL, we should create an empty SpatialPolygonsDataframe. To save empty SpatialTemporalDataframes we need to use sf, since it supports the empty Geometries.When results is NULL, we should create an empty SpatialPolygonsDataframe. To save empty SpatialTemporalDataframes we need to use sf, since it supports the empty Geometries.PerformanceRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/22Check if either kml or kmz files exist.2021-07-07T18:18:52+02:00Romulo Pereira GoncalvesCheck if either kml or kmz files exist.Unit and Integration testsRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://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/20We are saving run1 object and not run.2021-07-07T15:02:28+02:00Romulo Pereira GoncalvesWe are saving run1 object and not run.Unit and Integration testsRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/19renamed the function and output names and put in missing packages for functio...2021-07-02T16:37:56+02:00Johannes Knochrenamed the function and output names and put in missing packages for functions usedUnit and Integration testsJohannes KnochJohannes Knochhttps://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/17the functions from save_files.r are now used in outer_procedure.r2021-06-22T09:52:09+02:00Johannes Knochthe functions from save_files.r are now used in outer_procedure.rJohannes KnochJohannes Knochhttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/16fixes issue#272021-06-14T08:54:57+02:00Johannes Knochfixes issue#27**1.**
To achive the goal to fix #27 it was necessary to change the code in line 512 of `outer_procedure.r` as follows
`raster::KML(kml, paste(outPath, paste("step_", ni, sep = ""), sep = ""), overwrite = overwrite, zip = FALSE)`
to...**1.**
To achive the goal to fix #27 it was necessary to change the code in line 512 of `outer_procedure.r` as follows
`raster::KML(kml, paste(outPath, paste("step_", ni, sep = ""), sep = ""), overwrite = overwrite, zip = FALSE)`
to no longer generate `kmz` files, but the "unzipped" version consisting of a `kml` and a `png`.
After this change it is now possible to check for the `png` files in `plot_results.r`.
I didnt found a good solution to unzip or "look into" the `kmz` files to check for `png` or `kml` files. So now the `plot_results()` can be used with the demo and new produced data. That's why I used this adjustment.
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**2.**
`outer_procedure.r` and `plot_results.r` now only check for `tif` files which begin with "step_".Johannes KnochJohannes Knochhttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/15changes in the documentation due to new probability map threshold and legend2021-06-09T12:22:16+02:00Johannes Knochchanges in the documentation due to new probability map threshold and legendchanges in the documentation due to new probability map threshold and legend; new screenshot (/images/inter_map_ex_new.png) with probabilty map changes; changed the links to the pictures under 3.2 and 4.1.1 in the README.md because of a ...changes in the documentation due to new probability map threshold and legend; new screenshot (/images/inter_map_ex_new.png) with probabilty map changes; changed the links to the pictures under 3.2 and 4.1.1 in the README.md because of a new directory (/figure-markdown_github instead of /figure-gfm)DocumentationJohannes 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/13Allow inline plotting and plotting on the the browser.2021-06-08T12:51:32+02:00Romulo Pereira GoncalvesAllow inline plotting and plotting on the the browser.Allow inline plotting and plotting on the the browser. For Jupyter notebooks we recommend inline plotting.Allow inline plotting and plotting on the the browser. For Jupyter notebooks we recommend inline plotting.DocumentationRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/12Revert code optimization which was leading to incorrect results.2021-06-08T07:40:56+02:00Romulo Pereira GoncalvesRevert code optimization which was leading to incorrect results.PerformanceRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/11Fixes for #20 and improvements like suggested in #222021-06-08T14:12:24+02:00Johannes KnochFixes for #20 and improvements like suggested in #22fixes #20 and implements the suggestions of #22
The legend isn't perfect yet, but usable.fixes #20 and implements the suggestions of #22
The legend isn't perfect yet, but usable.Johannes KnochJohannes Knochhttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/10Documentation branch2021-06-08T11:22:32+02:00Romulo Pereira GoncalvesDocumentation branchIt re-organizes the repository for a better user experience and automatic generation of documentation. While improving the documentation, we also add some auxiliary functions to improve the load of time-series data and reference data.
W...It re-organizes the repository for a better user experience and automatic generation of documentation. While improving the documentation, we also add some auxiliary functions to improve the load of time-series data and reference data.
We have now automatic Web-Page generation for the repository thanks to Continuous integration. It opens doors to start implementation of unit tests.
@alibeam I added Carsten as review, but it would be awesome to get also get your review.
@carstenn this is a long merge request. All the activity related with this work is listed below.DocumentationRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/9Improve the main README and re-structure the repository.2021-06-01T16:21:33+02:00Romulo Pereira GoncalvesImprove the main README and re-structure the repository.DocumentationRomulo Pereira GoncalvesRomulo Pereira Goncalves