Trouble using a protected areas shapefile

amcilwee commented 4 years ago

Hi, I'd like to run IUCN.eval on fauna and flora species in New South Wales (Australia). I want to create maps and look at the status of species post the 2019-2020 bushfire season, so I am substituting a RFS fire extent map for National Park boundaries. The problem I have, is that no matter what shapefile I include - I get an error "Error in { : task 1 failed - "need finite 'ylim' values" when creating png maps, and "Error in { : task 1 failed - "figure margins too large" when creating pdf maps.

This only seems to happen when the script hits a species that has records inside the fire-affected area.

I have attached a test file (frog records) and associated shapefiles. The settings I've applied are:

Results <- IUCN.eval(MyData, country_map = NSW_NPWS_Branch, Cell_size_AOO = 2, Cell_size_locations = 10, SubPop=TRUE, Resol_sub_pop = 5, method_locations = "fixed_grid", Rel_cell_size = 0.05, DrawMap = TRUE, add.legend = TRUE, file_name = NULL, export_shp = TRUE, write_shp = TRUE, write_results=TRUE, map_pdf = TRUE, draw.poly.EOO=TRUE, exclude.area = TRUE, method_protected_area = "other", protec.areas=NSW_RFS_FireExtent, ID_shape_PA = "FID_RFSfir", buff_width = 0.1, alpha=0.9, buff.alpha=0.1, method.range="alpha.hull", nbe.rep.rast.AOO=0, showWarnings=TRUE, write_file_option="csv", parallel=TRUE, NbeCores=12)

NSW_ConR_Test.zip

Cheers, Allen

PS. Is there a way I can change "number of protected areas" on the maps to "number of records in burnt area". In updated versions, it would also be great if a shapefile of the point locations of each species could be automatically generated (in the folder shapesIUCN), along with the EEO and subpop polys.

gdauby commented 4 years ago

Hi I am on the field with limited email access until 26th March. I try to look at this asap, perhaps before that date. Best regards Gilles

Le lun. 9 mars 2020 à 05:11, amcilwee notifications@github.com a écrit :

Hi, I'd like to run IUCN.eval on fauna and flora species in New South Wales (Australia). I want to create maps and look at the status of species post the 2019-2020 bushfire season, so I am substituting a RFS fire extent map for National Park boundaries. The problem I have, is that no matter what shapefile I include - I get an error "Error in { : task 1 failed - "need finite 'ylim' values" when creating png maps, and "Error in { : task 1 failed - "figure margins too large" when creating pdf maps.

This only seems to happen when I the script hits a species that has records inside the fire-affected area.

I have attached a test file (frog records) and associated shapefiles. The settings I've applied are:

Results <- IUCN.eval(MyData, country_map = NSW_NPWS_Branch, Cell_size_AOO = 2, Cell_size_locations = 10, SubPop=TRUE, Resol_sub_pop = 5, method_locations = "fixed_grid", Rel_cell_size = 0.05, DrawMap = TRUE, add.legend = TRUE, file_name = NULL, export_shp = TRUE, write_shp = TRUE, write_results=TRUE, map_pdf = TRUE, draw.poly.EOO=TRUE, exclude.area = TRUE, method_protected_area = "other", protec.areas=NSW_RFS_FireExtent, ID_shape_PA = "FID_RFSfir", buff_width = 0.1, alpha=0.9, buff.alpha=0.1, method.range="alpha.hull", nbe.rep.rast.AOO=0, showWarnings=TRUE, write_file_option="csv", parallel=TRUE, NbeCores=12)

NSW_ConR_Test.zip https://github.com/gdauby/ConR/files/4304736/NSW_ConR_Test.zip

Cheers, Allen

PS. Is there a way I can change "number of protected areas" on the maps to "number of records in burnt area"

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amcilwee commented 4 years ago

Thanks Gilles. Anytime you get the chance would be great. It’s a fantastic package you’ve developed.

Cheers Allen

From: gdauby notifications@github.com Sent: Monday, 9 March 2020 4:25 PM To: gdauby/ConR ConR@noreply.github.com Cc: Allen McIlwee Allen.McIlwee@environment.nsw.gov.au; Author author@noreply.github.com Subject: Re: [gdauby/ConR] Trouble using a protected areas shapefile (#6)

Hi I am on the field with limited email access until 26th March. I try to look at this asap, perhaps before that date. Best regards Gilles

Le lun. 9 mars 2020 à 05:11, amcilwee notifications@github.com<mailto:notifications@github.com> a écrit :

Hi, I'd like to run IUCN.eval on fauna and flora species in New South Wales (Australia). I want to create maps and look at the status of species post the 2019-2020 bushfire season, so I am substituting a RFS fire extent map for National Park boundaries. The problem I have, is that no matter what shapefile I include - I get an error "Error in { : task 1 failed - "need finite 'ylim' values" when creating png maps, and "Error in { : task 1 failed - "figure margins too large" when creating pdf maps.

This only seems to happen when I the script hits a species that has records inside the fire-affected area.

I have attached a test file (frog records) and associated shapefiles. The settings I've applied are:

Results <- IUCN.eval(MyData, country_map = NSW_NPWS_Branch, Cell_size_AOO = 2, Cell_size_locations = 10, SubPop=TRUE, Resol_sub_pop = 5, method_locations = "fixed_grid", Rel_cell_size = 0.05, DrawMap = TRUE, add.legend = TRUE, file_name = NULL, export_shp = TRUE, write_shp = TRUE, write_results=TRUE, map_pdf = TRUE, draw.poly.EOO=TRUE, exclude.area = TRUE, method_protected_area = "other", protec.areas=NSW_RFS_FireExtent, ID_shape_PA = "FID_RFSfir", buff_width = 0.1, alpha=0.9, buff.alpha=0.1, method.range="alpha.hull", nbe.rep.rast.AOO=0, showWarnings=TRUE, write_file_option="csv", parallel=TRUE, NbeCores=12)

NSW_ConR_Test.zip https://github.com/gdauby/ConR/files/4304736/NSW_ConR_Test.zip

Cheers, Allen

PS. Is there a way I can change "number of protected areas" on the maps to "number of records in burnt area"

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amcilwee commented 4 years ago

Hi Gilles, just wondering if you had a chance to look at the test files and resolve the error issue? This would greatly assist me. cheers Allen.

gdauby commented 4 years ago

Hi could you install the development version and test it? devtools::install_github("gdauby/ConR") Tks I do not recommand you to use map_pdf = TRUE for such a large dataset.

gdauby commented 4 years ago

Try:

Results <- IUCN.eval(MyData,
country_map = NSW_NPWS_Branch,
Cell_size_AOO = 2,
Cell_size_locations = 10,
SubPop=TRUE,
Resol_sub_pop = 5,
method_locations = "fixed_grid",
Rel_cell_size = 0.05,
DrawMap = TRUE,
add.legend = TRUE,
file_name = NULL,
export_shp = TRUE,
write_shp = TRUE,
write_results=TRUE,
map_pdf = FALSE,
draw.poly.EOO=TRUE,
exclude.area = TRUE,
method_protected_area = "other",
protec.areas=NSW_RFS_FireExtent,
ID_shape_PA = "FID_RFSfir",
buff_width = 0.1,
alpha=0.9,
buff.alpha=0.1,
method.range="alpha.hull",
nbe.rep.rast.AOO=0,
showWarnings=TRUE,
write_file_option="csv",
parallel=TRUE,
NbeCores=4)

gdauby commented 4 years ago

The new version now on CRAN should be fine.

amcilwee commented 4 years ago

Thanks so much for this, will be looking at it today.

From: gdauby notifications@github.com Sent: Tuesday, 19 May 2020 1:24 AM To: gdauby/ConR ConR@noreply.github.com Cc: Allen McIlwee Allen.McIlwee@environment.nsw.gov.au; Author author@noreply.github.com Subject: Re: [gdauby/ConR] Trouble using a protected areas shapefile (#6)

The new version now on CRAN should be fine.

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gdauby / ConR

Trouble using a protected areas shapefile #6

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