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RE: Cross Validation error in Biomod2 [ Reply ] By: Maya Guéguen on 2022-03-14 08:19

[forum:49370]

Hi Danyang, A new version of biomod2 (4.0) is available on github. You can install it with the following commands : library(devtools) install_github("biomodhub/biomod2") and check the new documentation here : https://biomodhub.github.io/biomod2/index.html Help messages should also be reported onto the github in order to gather everything in the same place :) https://github.com/biomodhub/biomod2/issues The BIOMOD_CrossValidation has been updated, hopefully you will not get your error message anymore. Maya

RE: Cross Validation error in Biomod2 [ Reply ] By: Danyang Shi on 2022-03-14 06:27	[forum:49369]
Hi Jean, I encountered the exact same issue. I wonder have you found out a solution for this error? Thanks. Danyang

Cross Validation error in Biomod2 [ Reply ] By: Jean Purdon on 2017-09-14 06:50

[forum:45328]

HI All I have been getting this error when trying to cross validate my model lowered k for by group: NA because the number of observations was 0 Error in if (i < 1) { : missing value where TRUE/FALSE needed 3. singlefold(length(i), kk) 2. dismo::kfold(data@data.species, by = data@data.species, k = k) 1. BIOMOD_cv(myBiomodData, k = 5, rep = 2, do.full.models = F) I followed this function from another thread https://r-forge.r-project.org/forum/attachment.php?attachid=313&group_id=302&forum_id=995 but it is still not working. My code is myRespName <- 'BWwinterAllModelsNO maxent' # the presence/absences data for our species myResp <- read.csv("/Users/Jean/Desktop/PhD/Ensemble modeling/Whales/BW/winter/myRespBWwinter.csv") climate <- stack(c( list.files('/Users/Jean/Desktop/PhD/Whales env/NoDisttoshoreWinter/', full.names=TRUE ) )) myRespXY <- read.csv("/Users/Jean/Desktop/PhD/Ensemble modeling/Whales/BW/winter/myRespXYBWwinter.csv") ``` ```{r} # 1. Formatting Data myBiomodData <- BIOMOD_FormatingData(resp.var = myResp, expl.var = climate, resp.xy = myRespXY, resp.name = myRespName, PA.nb.rep = 5, PA.nb.absences = 100, PA.strategy = 'random', PA.dist.min = 0, PA.dist.max = NULL, PA.sre.quant = NULL, PA.table = NULL, na.rm = TRUE) And my output is -=-=-=-=-=-=-=-= BWwinterAllModelsNO maxent Data Formating -=-=-=-=-=-=-=-= Response variable name was converted into BWwinterAllModelsNO.maxent ! No data has been set aside for modeling evaluation > Pseudo Absences Selection checkings... > random pseudo absences selection ! Some NAs have been automaticly removed from your data -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Done -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -=-=-=-=-=-=-=-=-=-=-=-= 'BIOMOD.formated.data.PA' -=-=-=-=-=-=-=-=-=-=-=-= sp.name = BWwinterAllModelsNO.maxent 103 presences, 0 true absences and 886557 undifined points in dataset 4 explanatory variables bathy chaWinter slope sstwinter Min. :-6935 Min. : 0.0588 Min. : 0.00 Min. :13.00 1st Qu.:-4814 1st Qu.: 0.1029 1st Qu.: 5.00 1st Qu.:17.96 Median :-4212 Median : 0.1748 Median : 10.00 Median :20.24 Mean :-3854 Mean : 0.3103 Mean : 16.34 Mean :20.58 3rd Qu.:-3227 3rd Qu.: 0.2434 3rd Qu.: 20.00 3rd Qu.:23.47 Max. : -1 Max. :19.7048 Max. :489.00 Max. :27.31 5 Pseudo Absences dataset available ( PA1 PA2 PA3 PA4 PA5 ) with 100 absences in each (true abs + pseudo abs) Any help would be much appreciated. Kind regards.