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ConsBiol-unibern / SDMtune

Performs Variables selection and model tuning for Species Distribution Models (SDMs). It provides also several utilities to display results.
https://consbiol-unibern.github.io/SDMtune/
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[Bug]: Error in mm %*% object$betas : non-conformable arguments with gridSearch and hinge feature even with addSamplesToBg #38

Open geamaro opened 6 months ago

geamaro commented 6 months ago

Describe the bug

Dear Friends,

Every time I add hinge feature (alone) to hyper parameters to fine tune a Maxent model with gridSearch, even using addSamplesToBg before, I get Error in mm %*% object$betas : non-conformable arguments message after RM > 4.

I have the same problema with different occurrence data sets from different species, all using 19 Worldclim 2.1 bioclimatic variables together. The intent is to run a complete model for tuning and then reduce variables.

Steps to reproduce the bug

library(SDMtune)

presence.points.coord <- presence.points.model[c("x", "y")]
background.points.coord <- background.points.model[c("x", "y")]

data.model.SWD <- prepareSWD(
  species = my.species, 
  p = presence.points.coord, 
  a = background.points.coord,
  env = predictors.model,
)

data.model.SWD <- addSamplesToBg(data.model.SWD, all = TRUE)
folds <- randomFolds(
  data.model.SWD,
  k = 4,
  only_presence = FALSE,
  seed = 1968
)

maxent.model.base <- train(
  method = "Maxnet", 
  data = data.model.SWD, 
  folds = folds
)

tune.grid <- list(
  reg = seq(1, 5, 0.5),
  fc = c("l", "q", "h", "lq", "qh", "lqh", "lqph")
)

maxent.model.tune <- gridSearch(
  maxent.model.base,
  hypers = tune.grid,
  metric = "tss",
  # test = val.data.SWD
)

Session information

> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.7.10

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Boa_Vista
tzcode source: internal

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

other attached packages:
 [1] MASS_7.3-60.0.1          grinnell_0.0.22          rnaturalearthhires_1.0.0
 [4] flexsdm_1.3.4            htmlwidgets_1.6.4        datazoom.amazonia_1.1.0 
 [7] bdc_1.1.4                SDMtune_1.3.1            raster_3.6-26           
[10] sp_2.1-3                 flextable_0.9.5          gtsummary_1.7.2         
[13] officer_0.6.5            tidyr_1.3.1              data.table_1.15.2       
[16] kableExtra_1.4.0         formattable_0.2.1        gt_0.10.1               
[19] ggpubr_0.6.0             countrycode_1.6.0        geobr_1.8.2             
[22] scales_1.3.0             viridis_0.6.5            viridisLite_0.4.2       
[25] ENMeval_2.0.4            magrittr_2.0.3           pROC_1.18.5             
[28] usdm_2.1-7               RColorBrewer_1.1-3       corrplot_0.92           
[31] dplyr_1.1.4              geodata_0.5-9            terra_1.7-71            
[34] CoordinateCleaner_3.0.1  maps_3.4.2               tmap_3.3-4              
[37] sf_1.0-16                ggplot2_3.5.0            pacman_0.5.1            

loaded via a namespace (and not attached):
  [1] splines_4.3.3           later_1.3.2             rnaturalearth_1.0.1    
  [4] fields_15.2             tibble_3.2.1            cellranger_1.1.0       
  [7] XML_3.99-0.16.1         lifecycle_1.0.4         rstatix_0.7.2          
 [10] rprojroot_2.0.4         doParallel_1.0.17       processx_3.8.4         
 [13] lattice_0.22-6          crosstalk_1.2.1         exactextractr_0.10.0   
 [16] backports_1.4.1         rmarkdown_2.26          remotes_2.5.0          
 [19] httpuv_1.6.15           spam_2.10-0             zip_2.3.1              
 [22] askpass_1.2.0           pkgbuild_1.4.4          DBI_1.2.2              
 [25] abind_1.4-5             purrr_1.0.2             nnet_7.3-19            
 [28] openxlsx2_1.5           gdtools_0.3.7           gbm_2.1.9              
 [31] crul_1.4.0              ellipse_0.5.0           units_0.8-5            
 [34] svglite_2.1.3           codetools_0.2-19        dismo_1.3-14           
 [37] RApiSerialize_0.1.2     DT_0.32                 xml2_1.3.6             
 [40] shape_1.4.6.1           tidyselect_1.2.1        farver_2.1.1           
 [43] httpcode_0.3.0          base64enc_0.1-3         broom.helpers_1.14.0   
 [46] jsonlite_1.8.8          rgnparser_0.3.0         e1071_1.7-14           
 [49] survival_3.5-8          iterators_1.0.14        systemfonts_1.0.6      
 [52] foreach_1.5.2           tools_4.3.3             ragg_1.3.0             
 [55] Rcpp_1.0.12             glue_1.7.0              contentid_0.0.18       
 [58] gridExtra_2.3           here_1.0.1              xfun_0.43              
 [61] mgcv_1.9-1              withr_3.0.0             fastmap_1.1.1          
 [64] fansi_1.0.6             openssl_2.1.1           callr_3.7.6            
 [67] digest_0.6.35           R6_2.5.1                mime_0.12              
 [70] wk_0.9.1                textshaping_0.3.7       colorspace_2.1-0       
 [73] maxnet_0.1.4            dichromat_2.0-0.1       utf8_1.2.4             
 [76] generics_0.1.3          fontLiberation_0.1.0    class_7.3-22           
 [79] httr_1.4.7              tmaptools_3.1-1         whisker_0.4.1          
 [82] pkgconfig_2.0.3         gtable_0.3.4            sys_3.4.2              
 [85] htmltools_0.5.8         fontBitstreamVera_0.1.1 carData_3.0-5          
 [88] dotCall64_1.1-1         spThin_0.2.0            png_0.1-8              
 [91] knitr_1.45              rstudioapi_0.16.0       tzdb_0.4.0             
 [94] geosphere_1.5-18        rgbif_3.7.9             uuid_1.2-0             
 [97] nlme_3.1-164            curl_5.2.1              cachem_1.0.8           
[100] proxy_0.4-27            stringr_1.5.1           KernSmooth_2.23-22     
[103] parallel_4.3.3          desc_1.4.3              s2_1.1.6               
[106] leafsync_0.1.0          pillar_1.9.0            grid_4.3.3             
[109] vctrs_0.6.5             promises_1.2.1          randomForest_4.7-1.1   
[112] stringfish_0.16.0       car_3.1-2               dbplyr_2.5.0           
[115] xtable_1.8-4            evaluate_0.23           oai_0.4.0              
[118] readr_2.1.5             cli_3.6.2               compiler_4.3.3         
[121] rlang_1.1.3             crayon_1.5.2            ggsignif_0.6.4         
[124] labeling_0.4.3          classInt_0.4-10         ps_1.7.6               
[127] plyr_1.8.9              fs_1.6.3                stringi_1.8.3          
[130] stars_0.6-4             taxadb_0.2.1            munsell_0.5.0          
[133] lazyeval_0.2.2          leaflet_2.2.2           glmnet_4.1-8           
[136] fontquiver_0.2.1        Matrix_1.6-5            hms_1.1.3              
[139] patchwork_1.2.0         leafem_0.2.3            gfonts_0.2.0           
[142] shiny_1.8.1             qs_0.26.1               kernlab_0.9-32         
[145] memoise_2.0.1           broom_1.0.5             RcppParallel_5.1.7     
[148] lwgeom_0.2-14           readxl_1.4.3            ape_5.7-1

Additional information

Bactrocera dorsalis Filtered Clean Occ 2024-03-27.xlsx

Occurrences used to model.

Reproducible example

bappa10085 commented 5 months ago

I am also facing the same issue. Any solution?