[Bug]: repeated absence data

[mguerreiro24]

Describe the bug

When I open my dataset (from command trainValTest) I notice that the absence data is repeated in both the test and train sets

Steps to reproduce the bug

library(SDMtune)
species <- 'PheronemaCarpenteri'
presence_locations <- read.csv(paste(species,'/EnvironmentalData.csv',sep=''))
current <- sqrt(presence_locations$horizontalXCurrents^2+presence_locations$horizontalYCurrents^2)
presence_locations <- cbind(presence_locations,current)
presence_locations <- subset(presence_locations,current<1)
presence_locations <- presence_locations[,c(1:7,9,10,13)]#selecting variables
variables <- variable.names(presence_locations)[3:10]
  
background <- read.csv('backgroundEnvironment.csv')
background <- na.omit(background)
current <- sqrt(background$horizontalXCurrents^2+background$horizontalYCurrents^2)
background <- cbind(background,current)
background <- subset(background,current<1)
background <- background[,c(1:7,9,10,13)]#selecting variables

proportion <- dim(presence_locations)[1]*10

#for testing reasons this two variables are being set here. Normally they would be the output of a nested loop (I am doing a small sample SDM, so I am using 2 variables at a time; In this case, I only have 3 points!)
i=1
ii=2
run=1

#this section is normally within a for loop
background <- background[sample(nrow(background),proportion),]
  data_species <- rbind(presence_locations,background)
  df_coords<-data_species[,1:2]#coordinates: presence & absence
  df_data<-data_species[,c(i+2,ii+2)]#environmental data: presence & absence
  pa<- c(rep(1,dim(presence_locations)[1]),rep(0,dim(background)[1]))#vectors of 1 and 0: presence & absence
  data <- SWD(species = species,
              coords = df_coords,
              data = df_data,
              pa = pa)
  # Split presence locations in training (75%) and testing (25%) datasets
  datasets <- trainValTest(data, test = 0.25, only_presence = TRUE, seed = run)
  train <- datasets[[1]]
  test <- datasets[[2]]

Session information

R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default
  LAPACK version 3.12.1

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
locale:
[1] LC_COLLATE=Portuguese_Portugal.utf8  LC_CTYPE=Portuguese_Portugal.utf8   
[3] LC_MONETARY=Portuguese_Portugal.utf8 LC_NUMERIC=C                        
[5] LC_TIME=Portuguese_Portugal.utf8    

time zone: Europe/Berlin
tzcode source: internal

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

other attached packages:
[1] SDMtune_1.3.3

loaded via a namespace (and not attached):
 [1] terra_1.8-70       vctrs_0.6.5        cli_3.6.5          rlang_1.1.6       
 [5] generics_0.1.4     S7_0.2.0           glue_1.8.0         sp_2.2-0          
 [9] scales_1.4.0       grid_4.5.1         tibble_3.3.0       lifecycle_1.0.4   
[13] compiler_4.5.1     dplyr_1.1.4        codetools_0.2-20   RColorBrewer_1.1-3
[17] Rcpp_1.1.0         pkgconfig_2.0.3    rstudioapi_0.17.1  farver_2.1.2      
[21] lattice_0.22-7     R6_2.6.1           tidyselect_1.2.1   pillar_1.11.1     
[25] magrittr_2.0.4     tools_4.5.1        gtable_0.3.6       dismo_1.3-16      
[29] raster_3.6-32      ggplot2_4.0.0

Additional information

No response

Reproducible example

• I have done my best to provide the steps to reproduce the bug