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Fix technical issues #27

Merged
merged 33 commits into from
Nov 21, 2024
Merged

Fix technical issues #27

merged 33 commits into from
Nov 21, 2024

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wlangera
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@wlangera wlangera mentioned this pull request Nov 12, 2024
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@wlangera
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@LBreugelmans I have merged your code with my fixes. There are no errors anymore, but there are still some issues:

  • I cannot run the README.Rmd. This is because this path does not exist (empty): pa_filepath <- system.file("extdata","protected_areas_NPHogeKempen.shp", package = "pdindicatoR")
  • get_pd() uses mcube object which does not exist. You should only use variables from the function itself.

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@wlangera
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Just to clarify. It is not so urgent that I can run the README.Rmd. It is just that I cannot create the README.md file.
You can knit the README.Rmd file and commit the README.md. This way we do not have to worry at this time about the large files.

The second part about get_pd() using the global variable mcube is most important.

@LBreugelmans
Add 'data' argument
99ed67b 
Optional data argument added and code updated to allow for selection of example dataset

Signed-off-by: LBreugelmans <[email protected]>
@LBreugelmans
Update
c4e13dc 
- pull in pa (Protected Area) shapefile within function
- make sure map is saved correctly when no cutoff is provided

Signed-off-by: LBreugelmans <[email protected]>
@LBreugelmans
Update README.Rmd
bc6604f 
Use function retrieve_example_data() to read in example data files

Signed-off-by: LBreugelmans <[email protected]>
@LBreugelmans
Function get_pd_cube() replaces get_pd()
a0c673a 
- In order to resolve problem with argument mcube, the aggregate_cube() and calculate_faithpd functions are now being called in the function get_pd_cube() which replaces get_pd()
@LBreugelmans
Update documentation
868b3b7
@LBreugelmans
Solve R CMD Check errors & warnings
2602e1d 
Mostly due to incorrect specifications in function examples
@LBreugelmans LBreugelmans merged commit 186f066 into main Nov 21, 2024
5 of 6 checks passed
@LBreugelmans LBreugelmans deleted the fix-technical-issues branch November 21, 2024 15:34
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LBreugelmans commented Nov 22, 2024 •
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@wlangera I have solved the issues you mentioned:

  • the example data shapefile should be available from the mentioned path once the package is installed
  • I have created the overarching function get_pd_cube() to replace get_pd(), which takes mcube as a parameter and calls on the functions aggregate_cube() and calculate_faithpd()

I am running into problems knitting README.Rmd because in the second chunk the package gets loaded from the repo main branch, which currently contains an older version. I need to first merge this branch with main in order to knit the README.Rmd.

Unsure why Mac OS check did not pass.

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@LBreugelmans LBreugelmans LBreugelmans approved these changes

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@wlangera @LBreugelmans