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View Code? Open in Web Editor NEW🌍 Alien species risk modelling and mapping
License: MIT License
🌍 Alien species risk modelling and mapping
License: MIT License
Frederique can you provide 2 species that meet the following prerequisites ?:
Shouldn't the content of PRA_processingSteps.txt be moved to the README.md?
As @amyjsdavis noticed, it's time to move some functions she uses in her modelling to trias
package.
This means:
First thing to do, @amyjsdavis, is list them before deciding which ones are worth to be moved and which ones are just very small help functions which can be left in the Rmd.
I can provide assistance on all these steps.
A question: where is the pra_mammals.csv
file you are using in https://github.com/trias-project/risk-modelling-and-mapping/blob/master/src/global_download.Rmd#L43
It seems you are working on a local directory, ././modelling
which is not synced to this repository. This should be avoided as it makes working with GitHub way less powerful than it could be. And the files in this repo become easily outdated.
Please, contact me or @peterdesmet if you have problems performing the "git jump" :jump
Notice that if you are not confident to share some files as they are not ready for being shared, you can list them in the .gitignore and they will not be pushed to remote (= this repo).
@amyjsdavis @DiederikStrubbe as discussed during the core group meeting, here are some ideas for visualisation of the usual model output (on top of projections for current climate and rcp scenarios 2.6 and 4.5) that could serve the risk assessment of alien species in Belgium, based on Beckmann et al. 2019 Projection of climatic suitability for Pycnonotus cafer establishment. Unpublished. (SDMs prepared for the EC PRA project, based on the method of Chapman et al. 2019.
but then with these regions:
For the EU PRA's, projections were classified into suitable and unsuitable regions using the ‘minROCdist’ method, which minimizes the distance between the ROC plot and the upper left corner of the plot (point (0,1)). No idea how that works though, perhaps there are other methods.
Further ideas:
a limiting factor map following [Elith et al. (2010)](Elith J, Kearney M, Phillips S (2010) The art of modelling range-shifting species. Methods in Ecology and Evolution, 1, 330-342). Such map shows the most strongly limiting factor for establishment estimated by the model. I think this one is less 'important' for PRA-ing but it is informative.
tabular summaries of variable importance, an example:
@amyjsdavis will add Geotiffs of risk maps to GitHub for website testing
This is the file naming protocol I am proposing for the different types of maps for Belgium that will be output by the risk modelling and mapping code:
be_[GBIF_taxonKey][climate scenario][map type].tif (note that "be" indicates " Belgium" and the file format is always a GeoTiff)
Brackets indicate values to be assigned as follows:
[GBIF_taxonKey]== GBIF taxon id corresponding to the modelled species and used in data download and occurrence data cube.
[climate scenario]== can be 1 of 4 values as shown below:
allowed climate scenario values | definition |
---|---|
hist | model based on historical climate data |
rcp26 | model based on climate forecasts under RCP 2.6 for 2040-2070 |
rcp45 | model based on climate forecasts under RCP 4.5 for 2040-2071 |
rcp85 | model based on climate forecasts under RCP 8.5 for 2040-2072 |
[map type]== can be 1 of 3 values (including null) as shown below:
allowed values for map types | definition |
---|---|
null | risk map |
diff | map of difference in risk between the RCP climate scenario risk maps and the risk map based on historical climate |
conf | map of confidence of predicted risk for each risk map |
be_3190653_hist.tif
be_3190653_rcp26.tif
be_3190653_rcp45.tif
be_3190653_rcp85.tif
be_3190653_rcp26_diff.tif
be_3190653_rcp45_diff.tif
be_3190653_rcp85_diff.tif
be_3190653_hist_conf.tif
be_3190653_rcp26_conf.tif
be_3190653_rcp45_conf.tif
be_3190653_rcp85_conf.tif
To improve repeatability the paths should be changed from absolute to relative.
Please, consider to use here
package which is very useful as it allows finding paths from project root directory even if files are in src or if Rmd's are knitted.
Example of absolute path: https://github.com/trias-project/risk-modelling-and-mapping/blob/master/src/trias_sdm.Rmd#L47
To be rewritten as:
global <- read.csv(file = here("data", "external", "PRA", "PRA_mammals", "gbif_speciesFiles", gbif_filename))
I can assist if needed.
Is there a reason of using sp
as you are using sf
as well.
Based on idea of @peterdesmet while discussing on this topic with @amyjsdavis and I.
All figures should be organized as follows:
data/processed/taxonKey/figure_name.extension
where
taxonKey
is the taxon key as mentioned in GBIF and data cubefigure_name
should include the type of model consistentlyAny further suggestion, question or thoughts are welcome.
I don't think that describing the file naming of the output maps in a README pdf stored in the output directory is the best idea. I think this information suits perfectly the repo's README.
@peterdesmet, @amyjsdavis, what do you think about it?
@SoVDH and @timadriaens : Here are a complete sets of PDFs for Symphyotrichum lanceolatum (GBIF taxon key:9202318) with a consistent set of file names. In my notes, I have written that you wanted to keep these simple. The scale is different for the difference maps as otherwise they would be hard to read. For the difference maps, a positive number represents increased risk, a negative number represents decreased risk.
9202318_rcp45_conf.pdf
9202318_rcp45_diff.pdfThe
9202318_rcp85.pdf
9202318_rcp85_conf.pdf
[Uploading 9202318_hist.pdf…]
9202318_hist_conf.pdf
9202318_rcp_85_diff.pdf
9202318_rcp26.pdf
9202318_rcp26_conf.pdf
9202318_rcp26_diff.pdf
This is just a note. @timadriaens: could you please modify title and body of this issue based on what you jsut showed during the workflow meeting of today Oct 13? Please provide examples that @amyjsdavis can work on. I can assist her if needed.
Solve all small issues to make Rmd a nice html. This issue can be followed by many small issues/questions.
Again, I can provide some help on this process.
This issue comes from @amyjsdavis 's reply, #1 (comment).
Indeed, big files cannot be set in GitHub.
You can always ask @peterdesmet or me for advices.
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