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ApexRMS / wisdm

SyncroSim Workbench for Integrated Species Distribution Models
https://apexrms.github.io/wisdm/
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Variable Reduction [BUG] #21

Open lfraser1 opened 2 weeks ago

lfraser1 commented 2 weeks ago

Describe the bug Variable reduction does not run and puts out "Error in round(devExp, 2) : non-numeric argument to mathematical function Execution halted." No variable reduction screen appears. It seems like the issue may be produced by the site data preparation step (see screenshot of datasheet). The site data appears to have multiple values for a variable for an individual site, or values do not match input rasters.

To Reproduce I am sending the library that produced this error to Katie.

Expected behavior I expect site preparation to pull values of each variable at each site. Then I expect the variable reduction screen to pop up showing a matrix of correlations between site variables for my points.

Screenshots image

Relevant log output SyncroSim Version: 3.0.2.0 Operating System: Microsoft Windows NT 6.2.9200.0

Packages: core -> 3.0.2 wisdm -> 2.0.1

Parent Scenario is: [10] Brassica tournifortii - steps 3-6 Result scenario is: [30] Brassica tournifortii - steps 3-6 ([10] @ 04-Oct-2024 9:28 AM)

STARTING SIMULATION: 10/4/2024 : 9:28:52 AM

Conda installation: C:\Users\lfraser\AppData\Local\SyncroSim3\Conda Conda environment: C:\Users\lfraser\AppData\Local\SyncroSim3\Conda\envs\wisdm-1\wisdm-conda-s3

Only one field data observation present per pixel; no aggregation or weighting required.

3 - Site Data Preparation => Total time: 00:02:17

Conda installation: C:\Users\lfraser\AppData\Local\SyncroSim3\Conda Conda environment: C:\Users\lfraser\AppData\Local\SyncroSim3\Conda\envs\wisdm-1\wisdm-conda-s3

4 - Background Data Generation => Total time: 00:00:30

Conda installation: C:\Users\lfraser\AppData\Local\SyncroSim3\Conda Conda environment: C:\Users\lfraser\AppData\Local\SyncroSim3\Conda\envs\wisdm-1\wisdm-conda-s3

5 - Prepare Training/Testing Data => Total time: 00:00:24

Conda installation: C:\Users\lfraser\AppData\Local\SyncroSim3\Conda Conda environment: C:\Users\lfraser\AppData\Local\SyncroSim3\Conda\envs\wisdm-1\wisdm-conda-s3

6 - Variable Reduction => Total time: 00:00:27 [Failure] The external program failed. Program name was: C:\Users\lfraser\AppData\Local\SyncroSim3\Conda\envs\wisdm-1\wisdm-conda-s3\Scripts\Rscript.exe Arguments were: "C:\Users\lfraser\AppData\Local\SyncroSim3\Packages\wisdm\2.0.1\6-variable-reduction.R" Exit code was: 1 More information: Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Saved Error in round(devExp, 2) : non-numeric argument to mathematical function Execution halted

SIMULATION COMPLETE: 10/4/2024 : 9:32:31 AM

Total simulation time: 00:03:39 Software versions:

katieb1 commented 1 day ago

@lfraser1 from the screenshot it looks like there is a single row per site/variable, which I think is what we would expect. One thing that seems weird to me are the extremely large negative numbers for some variables. I think these numbers are probably NO DATA, but are getting interpreted as numeric values by SyncroSim. Unfortunately the library you shared with me is too big for me to download. Is there a smaller library that you can repro the problem? Or can you create the backup without including the external outputs?

katieb1 commented 1 day ago

Looking at the gHM raster in QGIS, I can see that the NO DATA value is indeed this really big negative number. image

When I look at a covariate raster from the WISDM example library, the NO DATA value is -9999. I wonder if WISDM is expecting NO DATA to be -9999 and that's what's causing the issue. image

lfraser1 commented 1 day ago

Yes, let me see if Catherine can help me delete superfluous runs and then repair so there are fewer versions of the rasters. I think I put in the raw rasters in the folder that I shared before, so I'll try to share the backup without the external output.

Linnea Fraser (she/her) SCC - Biological Science Technician

U.S. Geological Survey Fort Collins Science Center 2150 Center Ave Bldg C

From: Katie Birchard @.> Sent: Wednesday, October 23, 2024 10:45 AM To: ApexRMS/wisdm @.> Cc: Fraser, Linnea (Contractor) @.>; Mention @.> Subject: [EXTERNAL] Re: [ApexRMS/wisdm] Variable Reduction [BUG] (Issue #21)

This email has been received from outside of DOI - Use caution before clicking on links, opening attachments, or responding.

@lfraser1https://github.com/lfraser1 from the screenshot it looks like there is a single row per site/variable, which I think is what we would expect. One thing that seems weird to me are the extremely large negative numbers for some variables. I think these numbers are probably NO DATA, but are getting interpreted as numeric values by SyncroSim. Unfortunately the library you shared with me is too big for me to download. Is there a smaller library that you can repro the problem? Or can you create the backup without including the external outputs?

— Reply to this email directly, view it on GitHubhttps://github.com/ApexRMS/wisdm/issues/21#issuecomment-2432832375, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BKW2N2VCNPP7XL4YPBPP7DLZ47HBTAVCNFSM6AAAAABPVBXEWOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZSHAZTEMZXGU. You are receiving this because you were mentioned.Message ID: @.***>

lfraser1 commented 1 day ago

Hmm I can navigate to Library>SyncroSim Core> and then backup, but the options are greyed out. They won't let me unselect Include external files in backup.

Linnea Fraser (she/her) SCC - Biological Science Technician

U.S. Geological Survey Fort Collins Science Center 2150 Center Ave Bldg C

From: Katie Birchard @.> Sent: Wednesday, October 23, 2024 10:45 AM To: ApexRMS/wisdm @.> Cc: Fraser, Linnea (Contractor) @.>; Mention @.> Subject: [EXTERNAL] Re: [ApexRMS/wisdm] Variable Reduction [BUG] (Issue #21)

This email has been received from outside of DOI - Use caution before clicking on links, opening attachments, or responding.

@lfraser1https://github.com/lfraser1 from the screenshot it looks like there is a single row per site/variable, which I think is what we would expect. One thing that seems weird to me are the extremely large negative numbers for some variables. I think these numbers are probably NO DATA, but are getting interpreted as numeric values by SyncroSim. Unfortunately the library you shared with me is too big for me to download. Is there a smaller library that you can repro the problem? Or can you create the backup without including the external outputs?

— Reply to this email directly, view it on GitHubhttps://github.com/ApexRMS/wisdm/issues/21#issuecomment-2432832375, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BKW2N2VCNPP7XL4YPBPP7DLZ47HBTAVCNFSM6AAAAABPVBXEWOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZSHAZTEMZXGU. You are receiving this because you were mentioned.Message ID: @.***>

katieb1 commented 1 day ago

Ok, not sure why the option is greyed out, but I just sent you a new release to test over email that might fix this bug. Basically it allows for NO DATA values in the covariate rasters other than -9999. I think before investing time trying to download and run this library, it's worth you testing the potential fix on your end first. Let me know if this still doesn't fix things!