thresh = 1 always retains only 2 components with preProcess(method = "pca")

[paljenczy]

With a high enough (but not 1) threshold argument thresh, PCA retains all principal components as expected:

library(caret)
#> Loading required package: lattice
#> Loading required package: ggplot2
preProcess(mtcars, method = "pca", thresh = 0.999)
#> Created from 32 samples and 11 variables
#>
#> Pre-processing:
#>   - centered (11)
#>   - ignored (0)
#>   - principal component signal extraction (11)
#>   - scaled (11)
#>
#> PCA needed 11 components to capture 99.9 percent of the variance

However, setting thresh = 1 retains only 2 principal components.

library(caret)
#> Loading required package: lattice
#> Loading required package: ggplot2
preProcess(mtcars, method = "pca", thresh = 1)
#> Created from 32 samples and 11 variables
#>
#> Pre-processing:
#>   - centered (11)
#>   - ignored (0)
#>   - principal component signal extraction (11)
#>   - scaled (11)
#>
#> PCA needed 2 components to capture 100 percent of the variance

sessionInfo()

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin16.7.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.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  
[7] base     

other attached packages:
[1] caret_6.0-78    ggplot2_2.2.1   lattice_0.20-35

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.3   purrr_0.2.4        reshape2_1.4.3    
 [4] kernlab_0.9-25     splines_3.4.3      colorspace_1.3-2  
 [7] stats4_3.4.3       yaml_2.1.16        survival_2.41-3   
[10] prodlim_1.6.1      rlang_0.1.6        ModelMetrics_1.1.0
[13] pillar_1.0.1       withr_2.1.1        foreign_0.8-69    
[16] glue_1.2.0         bindrcpp_0.2       foreach_1.4.4     
[19] bindr_0.1          plyr_1.8.4         dimRed_0.1.0      
[22] lava_1.5.1         robustbase_0.92-8  stringr_1.2.0     
[25] timeDate_3042.101  munsell_0.4.3      gtable_0.2.0      
[28] recipes_0.1.1      codetools_0.2-15   psych_1.7.8       
[31] parallel_3.4.3     class_7.3-14       DEoptimR_1.0-8    
[34] broom_0.4.3        Rcpp_0.12.14       scales_0.5.0      
[37] ipred_0.9-6        CVST_0.2-1         mnormt_1.5-5      
[40] stringi_1.1.6      dplyr_0.7.4        RcppRoll_0.2.2    
[43] ddalpha_1.3.1      grid_3.4.3         tools_3.4.3       
[46] magrittr_1.5       lazyeval_0.2.1     tibble_1.4.1      
[49] tidyr_0.7.2        DRR_0.0.2          pkgconfig_2.0.1   
[52] MASS_7.3-48        Matrix_1.2-12      lubridate_1.7.1   
[55] gower_0.1.2        assertthat_0.2.0   iterators_1.0.9   
[58] R6_2.2.2           rpart_4.1-11       sfsmisc_1.1-1     
[61] nnet_7.3-12        nlme_3.1-131       compiler_3.4.3  

[topepo]

Found it. Should be fixed. Thanks