HabitatSampler merge requestshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests2021-07-07T18:18:52+02:00https://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/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/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/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/27update Progressbar2021-08-05T13:10:17+02:00Daniela Rabeupdate ProgressbarDaniela RabeDaniela Rabehttps://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/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/30bug fixes for multiClass2022-01-17T09:57:06+01:00Carsten Neumannbug fixes for multiClassI have solved the two issues in outer_procedure.r multiClass argument should work now. I wonder if this option can be made part of the GUI?I have solved the two issues in outer_procedure.r multiClass argument should work now. I wonder if this option can be made part of the GUI?Carsten NeumannCarsten Neumannhttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/31changed order of lines for avoiding NA in the final map2022-01-17T10:02:16+01:00Johannes Knochchanged order of lines for avoiding NA in the final mapWhen the threshold in the last step was less then the number of habitats it leaded to NA-pixels or "holes" in the final habitat map.
fixes #51When the threshold in the last step was less then the number of habitats it leaded to NA-pixels or "holes" in the final habitat map.
fixes #51Johannes KnochJohannes Knochhttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/32Save samplepoints2022-01-19T10:18:31+01:00Romulo Pereira GoncalvesSave samplepointsDaniela RabeDaniela Rabehttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/33Optimized version.2022-03-24T16:49:23+01:00Romulo Pereira GoncalvesOptimized version.In this version we have improved several things.
1. We are now able to define the number of trees for randomForest.
2. Run in optimized mode
a. Improve the code to only use raster objects in memory. Clean the temporary storage.
b. ...In this version we have improved several things.
1. We are now able to define the number of trees for randomForest.
2. Run in optimized mode
a. Improve the code to only use raster objects in memory. Clean the temporary storage.
b. Use matrices instead of raster when possible.
3. Add a new sample method which only works for the optimized_mode since it runs with matrices. Now we have `random_raster` (equivalent to old `random` which uses `raster::sampleRandom` function), `raster_regular` (equivalent to old `regular` which uses `raster::sampleRegular` function), and `random_matrix` (new one which uses matrices and the stats::sample function over the only existent pixels and not over all as raster::sampleRandom - more info [here](https://github.com/rspatial/raster/issues/245)).
4. Add `last_ref_val`, this is, the default reference value for the last step (default: 1000)
@dara, @jknoch and @carstenn the official reviewer will be Daniela, but it would be great if all of you could review the changes and test it. There is still the documentation to update which I hope to get it done tomorrow based on your feedback. I am aware the review of this branch will take a while because we did quite some changes.
I have tested the optimized version several times and it all seemed running as expected. In case you want to repeat your previous run, just restart R, run again the function with the same seed (now as default we recommend to always set the seed to the current time as integer), the same `init.samples`, `sample_type`, and `models`, and use the same thresholds and you will get exactly the same results (it works for random_raster and random_matrix as well). About the seeds, more info in issue #59 and #58.
Closes issue #54, #53, #55, #56 ,#58, #59, #61Romulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/34Increase the range of colors. Specify the R package name to avoid the use a...2022-03-02T12:12:40+01:00Romulo Pereira GoncalvesIncrease the range of colors. Specify the R package name to avoid the use a...Increase the range of colors. Specify the R package name to avoid the use a function from another packages.Increase the range of colors. Specify the R package name to avoid the use a function from another packages.Romulo 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/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/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/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/40SVM predict omits NaN on the prediction.2022-05-30T22:24:58+02:00Romulo Pereira GoncalvesSVM predict omits NaN on the prediction.Closes issue #64Closes issue #64Unit and Integration testsRomulo Pereira GoncalvesRomulo Pereira Goncalveshttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/42bugfix for #692022-10-17T14:49:33+02:00Johannes Knochbugfix for #69fast fix for issue #69fast fix for issue #69Johannes KnochJohannes Knochhttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/43Unitests2022-10-13T15:32:45+02:00Romulo Pereira GoncalvesUnitestsUnit and Integration testsJohannes KnochJohannes Knochhttps://git.gfz-potsdam.de/habitat-sampler/HabitatSampler/-/merge_requests/44Tag new version2022-10-14T09:40:57+02:00Johannes KnochTag new versionFill HISTORY.rst and increase version in DESCRIPTIONFill HISTORY.rst and increase version in DESCRIPTIONDaniela RabeDaniela Rabe