Comments (6)
simonrolph
commented on May 29, 2024
1
I've added a gist here:
https://gist.github.com/simonrolph/d38d2d5a56a95782786a04f7178bdb34
I have added a CRS (wgs84) to all the layers now (I think) but I still get the error. However if I use xgboost then it works fine.
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simonrolph
commented on May 29, 2024
1
Thanks Martin! Yes I think it was my library being out of date because it works fine now. Assertion messages look useful too
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simonrolph
commented on May 29, 2024
Ok bear with, I also get the error if I add a CRS
> print(mod)
<Biodiversity distribution model>
Background extent:
xmin: -1.5, xmax: 53,
ymin: 0, ymax: 54
projection: +proj=longlat +datum=WGS84 +no_defs
---------
Biodiversity data:
Point - Presence only <173 records>
---------
predictors: env1, env2, env3 (3 predictors)
priors: <Default>
latent: None
log: <Console>
engine: <INLABRU>
>
> plot(mod$biodiversity)
>
>
> fit <- train(mod,
+ runname = "Test INLA run",
+ verbose = T #
+ )
[Estimation] 2023-08-16 10:04:48 | Collecting input parameters.
[Estimation] 2023-08-16 10:04:50 | Adding engine-specific parameters.
Error in if (sf::st_is_longlat(bdry$crs)) { :
missing value where TRUE/FALSE needed
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Martin-Jung
commented on May 29, 2024
Hi, Thanks a lot for reporting!
Happy to update the error message to be more informative, can you paste me the code for the virtualspecies/NLM package so I can recreate the error? (or upload the testing files). Generally the background and the predictors should all be in similar extent and crs, but maybe there is also something that can be improved (e.g. assign the CRS to the background if missing).
M
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simonrolph
commented on May 29, 2024
So the error is occurring here:
Line 197 in e3f658c
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Martin-Jung
commented on May 29, 2024
Hi Simon,
Thanks, I tested your gist script and it works without issues for me (my SessionInfo below). So could you please run ibis_dependencies() just to be sure that you use the latest packages (from what I can eyeball hot candidates are also sp and sf which you might need to update).
I have also added a bunch of more user friendly assertion messages that are now being raised with a provided background in distribution(), which should always have a CRS. Also added specific minimum dependencies to the description.
I pushed a new commit to the dev branch adding this (version 0.0.8, 1da5dc7).
Note: Generally the INLA implementation might need some love soon as it is currently still partly based on a mix of sp/sf and some of the code will deprecate soon'ish.
Session info on my test instance
> sessionInfo()
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8
[3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] sf_1.0-14 assertthat_0.2.1 uuid_1.1-0 terra_1.7-39 xgboost_1.7.5.1
[6] inlabru_2.8.0 INLA_23.04.24 foreach_1.5.2 Matrix_1.6-0 ibis.iSDM_0.0.8
[11] tidyr_1.3.0 dplyr_1.1.2 virtualspecies_1.5.1 raster_3.6-23 sp_2.0-0
[16] NLMR_1.1.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.11 pillar_1.9.0 compiler_4.2.3 iterators_1.0.14 class_7.3-21
[6] tools_4.2.3 jsonlite_1.8.7 lifecycle_1.0.3 tibble_3.2.1 lattice_0.20-45
[11] pkgconfig_2.0.3 rlang_1.1.1 cli_3.6.1 DBI_1.1.3 rstudioapi_0.15.0
[16] xfun_0.39 proto_1.0.0 e1071_1.7-13 knitr_1.43 generics_0.1.3
[21] vctrs_0.6.3 classInt_0.4-9 grid_4.2.3 tidyselect_1.2.0 data.table_1.14.8
[26] glue_1.6.2 R6_2.5.1 fansi_1.0.4 purrr_1.0.1 magrittr_2.0.3
[31] splines_4.2.3 codetools_0.2-19 units_0.8-3 utf8_1.2.3 KernSmooth_2.23-20
[36] proxy_0.4-27
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Related Issues (20)
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