osmose-model / osmose Goto Github PK

I am working on the replacement of RNetCDF functions by ncdf4 functions

new plot methods need to be created for the yieldByFishery class.

Stacked bars per species (color are by fishery) is a first suggestion. Plot types can be recycled from other classes.

Hi Nicolas,
Recently, I attempted to employ the "Background Species" function. The model did not run with the errors:
Exception in thread "main" java.lang.NullPointerException
at fr.ird.osmose.background.BackgroundMapSet.checkMapIndexation(BackgroundMapSet.java:296)
at fr.ird.osmose.background.BackgroundMapSet.loadMaps(BackgroundMapSet.java:118)
at fr.ird.osmose.background.BackgroundSpecies.(BackgroundSpecies.java:85)
at fr.ird.osmose.Configuration.init(Configuration.java:410)
at fr.ird.osmose.Osmose.runConfiguration(Osmose.java:327)
at fr.ird.osmose.Osmose.run(Osmose.java:269)
at fr.ird.osmose.Osmose.main(Osmose.java:490)
I guess the model failed to read the movement map for the background species (BK0). Would you please help me check the problem? The version is 4.1.0.
Thank you in advance. I am looking forward to your letter.
Best,
Lei

PS: I fail to upload the zip file of model configuration as the zip file is not inclued in the list of upload file type. I sent the file to your e-mail ([email protected]).

Check all functions

Given the changes on handling arguments by command line (absolute vs. relative paths), the output and clean arguments in run_osmose are not consistent anymore. Need to be fixed so arguments are consistent among versions.

replace with isTRUE(.) or !isTRUE(.)

Thanks for your great work!
when I run the code below, I can not find osmose_calib_demo function.
the version of osmose package in my computer is 3.3.4.

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    
system code page: 65001

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] calibrar_0.2.0 ncdf4_1.17     osmose_3.3.4  

loaded via a namespace (and not attached):
 [1] magrittr_2.0.1    knitr_1.33        maps_3.3.0        splines_4.0.3    
 [5] lattice_0.20-44   R6_2.5.0          rlang_0.4.11      foreach_1.5.1    
 [9] fastmap_1.1.0     stringr_1.4.0     fields_11.6       tools_4.0.3      
[13] dotCall64_1.0-1   grid_4.0.3        data.table_1.14.0 spam_2.6-0       
[17] nlme_3.1-152      mgcv_1.8-35       xfun_0.22         cli_2.5.0        
[21] iterators_1.0.13  htmltools_0.5.1.1 ellipsis_0.3.1    yaml_2.2.1       
[25] digest_0.6.27     Matrix_1.3-2      codetools_0.2-18  fs_1.5.0         
[29] rlist_0.4.6.1     memoise_2.0.0     cachem_1.0.4      evaluate_0.14    
[33] rmarkdown_2.7     stringi_1.5.3     compiler_4.0.3