[Bug]: Error in mm %*% object$betas : non-conformable arguments with gridSearch and hinge feature even with addSamplesToBg #38
Description
Describe the bug
Dear Friends,
Every time I add hinge feature (alone) to hyper parameters to fine tune a Maxent model with gridSearch, even using addSamplesToBg before, I get Error in mm %*% object$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_5.7-1Additional information
Bactrocera dorsalis Filtered Clean Occ 2024-03-27.xlsx
Occurrences used to model.
Reproducible example
- I have done my best to provide the steps to reproduce the bug