modelReport can't find ROC curve file and fails

[consbiol-unibern]

modelReport can't find ROC curve file and fails

[sgvignali]

Hi, thank you for reporting the issue.
Can you provide a script to reproduce the error?

[DevinALyons]

It happens after I try to get a model report for any model, with any set of options I choose (and I've tried a bunch of combinations). This includes using the data and the example from your package, so I'm not sure recreating your own code here will be helpful. It seems like this must be some kind of package compatibility problem. I guess it should be said I don't always get the "n addition: Warning message: In matrix(as.numeric(d)) : NAs introduced by coercion" but the "File ./plots/ROC_curve.png not found in resource path Error: pandoc document conversion failed with error 99" happens for any and all uses of the modelReport function.

[sgvignali]

Ok, I'll have a look at it in the following days.
Could you please post the output of sessionInfo()?

[DevinALyons]

Here it is:

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252

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

other attached packages:
[1] oceanmap_0.1.1 extrafont_0.17 mapdata_2.3.0 OceanView_1.0.6 plot3Drgl_1.0.2 rgl_0.108.3 plot3D_1.4
[8] crsuggest_0.3.1 viridis_0.6.2 viridisLite_0.4.0 cowplot_1.1.1 ggplot2_3.3.5 maps_3.4.0 knitr_1.37
[15] kableExtra_1.3.4 enmSdm_0.5.1.7 dismo_1.3-5 SDMtune_1.1.5 tidync_0.2.4 raster_3.5-15 sp_1.4-6
[22] RNetCDF_2.5-2 ncdf4_1.19 lattice_0.20-41 RColorBrewer_1.1-2 chron_2.3-56

loaded via a namespace (and not attached):
[1] SparseM_1.81 ModelMetrics_1.2.2.2 earth_5.3.1 tidyr_1.2.0 nabor_0.5.0 multcomp_1.4-18
[7] data.table_1.14.2 rpart_4.1-15 doParallel_1.0.17 generics_0.1.2 leaflet_2.0.4.1 terra_1.5-17
[13] TH.data_1.1-0 polspline_1.1.19 proxy_0.4-26 future_1.23.0 ecodist_2.0.7 adehabitatMA_0.3.14
[19] webshot_0.5.2 xml2_1.3.3 lubridate_1.8.0 adehabitatLT_0.3.25 assertthat_0.2.1 gower_1.0.0
[25] xfun_0.29 hms_1.1.1 jquerylib_0.1.4 rJava_1.0-6 satellite_1.0.4 adehabitatHR_0.4.19
[31] evaluate_0.14 fansi_1.0.2 progress_1.2.2 DBI_1.1.2 htmlwidgets_1.5.4 reshape_0.8.8
[37] mapview_2.10.0 stats4_4.0.3 purrr_0.3.4 ellipsis_0.3.2 crosstalk_1.2.0 ks_1.13.3
[43] dplyr_1.0.8 backports_1.4.1 permute_0.9-7 deldir_1.0-6 vctrs_0.3.8 quantreg_5.88
[49] abind_1.4-5 caret_6.0-90 withr_2.4.3 checkmate_2.0.0 rgdal_1.5-28 vegan_2.5-7
[55] prettyunits_1.1.1 mclust_5.4.9 svglite_2.1.0 cluster_2.1.0 pacman_0.5.1 ape_5.6-1
[61] dotCall64_1.0-1 crayon_1.4.2 glmnet_4.1-3 recipes_0.1.17 pkgconfig_2.0.3 labeling_0.4.2
[67] units_0.8-0 nlme_3.1-149 nnet_7.3-14 rlang_1.0.1 globals_0.14.0 lifecycle_1.0.1
[73] MatrixModels_0.5-0 sandwich_3.0-1 extrafontdb_1.0 PresenceAbsence_1.1.9 biomod2_3.5.1 tcltk_4.0.3
[79] randomForest_4.6-14 matrixStats_0.61.0 Matrix_1.2-18 boot_1.3-25 zoo_1.8-9 base64enc_0.1-3
[85] png_0.1-7 rasterVis_0.51.2 KernSmooth_2.23-17 spam_2.8-0 pROC_1.18.0 shape_1.4.6
[91] classInt_0.4-3 stringr_1.4.0 maxnet_0.1.4 ncmeta_0.3.0 maptools_1.1-2 parallelly_1.30.0
[97] jpeg_0.1-9 scales_1.1.1 magrittr_2.0.2 plyr_1.8.6 hexbin_1.28.2 compiler_4.0.3
[103] plotROC_2.2.1 plotrix_3.8-2 cli_3.1.1 ade4_1.7-18 blockCV_2.1.4 ENMeval_0.3.1
[109] listenv_0.8.0 htmlTable_2.4.0 Formula_1.2-4 MASS_7.3-53 mgcv_1.8-38 tidyselect_1.1.1
[115] stringi_1.7.6 forcats_0.5.1 highr_0.9 yaml_2.2.2 latticeExtra_0.6-29 grid_4.0.3
[121] sass_0.4.0 tools_4.0.3 future.apply_1.8.1 CircStats_0.2-6 parallel_4.0.3 rstudioapi_0.13
[127] foreach_1.5.2 foreign_0.8-80 snowfall_1.84-6.1 gridExtra_2.3 prodlim_2019.11.13 farver_2.1.0
[133] digest_0.6.29 rgeos_0.5-9 pracma_2.3.6 ecospat_3.2.1 lava_1.6.10 TeachingDemos_2.12
[139] Rcpp_1.0.8 httr_1.4.2 mda_0.5-2 sf_1.0-6 colorspace_2.0-2 rvest_1.0.2
[145] splines_4.0.3 fields_13.3 systemfonts_1.0.3 jsonlite_1.7.3 leafem_0.1.6 timeDate_3043.102
[151] poibin_1.5 plotmo_3.6.1 ipred_0.9-12 R6_2.5.1 Hmisc_4.6-0 pillar_1.7.0
[157] htmltools_0.5.2 glue_1.6.1 fastmap_1.1.0 class_7.3-17 codetools_0.2-16 mvtnorm_1.1-3
[163] utf8_1.2.2 bslib_0.3.1 tibble_3.1.6 gbm_2.1.8 gtools_3.9.2 misc3d_0.9-1
[169] Rttf2pt1_1.3.10 survival_3.2-7 rmarkdown_2.11 munsell_0.5.0 e1071_1.7-9 iterators_1.0.14
[175] reshape2_1.4.4 gtable_0.3.0 rms_6.2-0

[JepsonNomad]

Checking in with the same problem. I got the same error after modelReport() returns the message "Writing model settings..." though perhaps notable without the matrix warning reported above. I would add that modelReport() does successfully generate folder/plots/ROC_curve.png; it fails somewhere aftwerwards. My sessionInfo() is as follows:

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] kableExtra_1.3.4 dismo_1.3-5      forcats_0.5.1    stringr_1.4.0    dplyr_1.0.7     
 [6] purrr_0.3.4      readr_2.0.2      tidyr_1.1.4      tibble_3.1.6     ggplot2_3.3.5   
[11] tidyverse_1.3.1  zeallot_0.1.0    ENMeval_2.0.3    magrittr_2.0.1   SDMtune_1.1.5   
[16] sf_1.0-3         raster_3.5-2     sp_1.4-5        

loaded via a namespace (and not attached):
 [1] fs_1.5.0                 lubridate_1.8.0          webshot_0.5.2           
 [4] RColorBrewer_1.1-2       progress_1.2.2           httr_1.4.2              
 [7] bslib_0.3.1              tools_4.1.2              backports_1.3.0         
[10] utf8_1.2.2               rgdal_1.5-27             R6_2.5.1                
[13] plotROC_2.2.1            KernSmooth_2.23-20       DBI_1.1.1               
[16] colorspace_2.0-2         withr_2.4.2              tidyselect_1.1.1        
[19] prettyunits_1.1.1        compiler_4.1.2           cli_3.1.0               
[22] rvest_1.0.2              xml2_1.3.2               sass_0.4.0              
[25] labeling_0.4.2           scales_1.1.1             classInt_0.4-3          
[28] hexbin_1.28.2            proxy_0.4-26             systemfonts_1.0.4       
[31] digest_0.6.28            svglite_2.1.0            rmarkdown_2.11          
[34] htmltools_0.5.2          jpeg_0.1-9               pkgconfig_2.0.3         
[37] highr_0.9                fastmap_1.1.0            dbplyr_2.1.1            
[40] rlang_0.4.12             readxl_1.3.1             rstudioapi_0.13         
[43] jquerylib_0.1.4          farver_2.1.0             generics_0.1.1          
[46] zoo_1.8-9                jsonlite_1.7.2           rangeModelMetadata_0.1.4
[49] Rcpp_1.0.7               munsell_0.5.0            fansi_0.5.0             
[52] lifecycle_1.0.1          terra_1.5-21             yaml_2.2.1              
[55] stringi_1.7.5            whisker_0.4              plyr_1.8.6              
[58] grid_4.1.2               parallel_4.1.2           crayon_1.4.2            
[61] rasterVis_0.51.2         lattice_0.20-45          haven_2.4.3             
[64] cowplot_1.1.1            hms_1.1.1                kuenm_1.1.7             
[67] knitr_1.36               pillar_1.6.4             reshape2_1.4.4          
[70] codetools_0.2-18         reprex_2.0.1             glue_1.6.0              
[73] evaluate_0.14            BRRR_1.2                 latticeExtra_0.6-29     
[76] modelr_0.1.8             vctrs_0.3.8              png_0.1-7               
[79] tzdb_0.2.0               foreach_1.5.1            cellranger_1.1.0        
[82] gtable_0.3.0             assertthat_0.2.1         xfun_0.27               
[85] broom_0.7.10             e1071_1.7-9              class_7.3-19            
[88] viridisLite_0.4.0        audio_0.1-8              rJava_1.0-6             
[91] iterators_1.0.13         units_0.7-2              ellipsis_0.3.2 

Perhaps it is related to line 46 on template.Rmd? I wonder if there is a way to convert that ./plots/ROC_curve.png to an absolute path? It seems to me like everything the modelReport() function is supposed to automatically save (train and test.csv, map.tif, model.Rds, and then jackknifing results, marginal and univariate response curves, and ROC_curve.png) is created except for the rendered html.

[JepsonNomad]

I was able to solve this by changing every element <- assignment in the modelReport.Rmd document to a manual conversion to the full path, for example:

element <- paste0("<p><a href=\"",plot_folder,"/ROC_curve.png\"><img src=\"",plot_folder,"/ROC_curve.png\" style=\"width: 70%; display: block; margin-left: auto; margin-right: auto;\"></a></p>")

This was required on lines 46, 74, 119, 151, 152, and 154.

The funny thing is you have the code written to do this on line 93 when var also has to be incorporated.

I also had to remove the css: report.css formatting on line 6 to get it to work.

[sgvignali]

This is solved now in the development version.

@JepsonNomad relative paths were recognised before. This is why I used them for some of the images to shorten the code.
Obviously, pandoc or knitr need a full path now.

Thank you @DevinALyons for reporting the issue