predict.opls() doesn't work when Y is a matrix
3
0
Entering edit mode
scottericr • 0
@scottericr-16195
Last seen 5.8 years ago

I'm not sure if this is a bug, or a limitation of predict(), but when I try to use predict() on an PLS object created by opls() where X and Y are both matrices with multiple columns, it throws an error.

library(ropls)

data(sacurine)
attach(sacurine)

train.X <- dataMatrix[1:130, ]
train.Y <- sampleMetadata[1:130, 1:2]
sacurine.pls <- opls(train.X, as.matrix(train.Y))
#> PLS
#> 130 samples x 109 variables and 2 responses
#> standard scaling of predictors and response(s)
#>       R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort
#> Total    0.203    0.343   0.156  6.19   2   0

test.X <- dataMatrix[131:183, ]
predict(sacurine.pls, test.X)
#> Error in dimnames(predMCNFcVcn) <- list(rownames(newdata), "pred"): length of 'dimnames' [2] not equal to array extent


devtools::session_info()
#> Session info -------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.4.4 (2018-03-15)
#>  system   x86_64, darwin15.6.0        
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  tz       America/New_York            
#>  date     2018-06-20
#> Packages -----------------------------------------------------------------
#>  package      * version date       source                          
#>  backports      1.1.2   2017-12-13 CRAN (R 3.4.3)                  
#>  base         * 3.4.4   2018-03-15 local                           
#>  Biobase        2.36.2  2017-05-04 Bioconductor                    
#>  BiocGenerics   0.22.1  2017-10-07 Bioconductor                    
#>  compiler       3.4.4   2018-03-15 local                           
#>  datasets     * 3.4.4   2018-03-15 local                           
#>  devtools       1.13.5  2018-02-18 CRAN (R 3.4.3)                  
#>  digest         0.6.15  2018-01-28 CRAN (R 3.4.3)                  
#>  evaluate       0.10.1  2017-06-24 CRAN (R 3.4.0)                  
#>  graphics     * 3.4.4   2018-03-15 local                           
#>  grDevices    * 3.4.4   2018-03-15 local                           
#>  htmltools      0.3.6   2017-04-28 cran (@0.3.6)                   
#>  knitr          1.20    2018-02-20 CRAN (R 3.4.3)                  
#>  magrittr       1.5     2014-11-22 CRAN (R 3.4.0)                  
#>  memoise        1.1.0   2017-04-21 CRAN (R 3.4.0)                  
#>  methods      * 3.4.4   2018-03-15 local                           
#>  parallel       3.4.4   2018-03-15 local                           
#>  Rcpp           0.12.17 2018-05-18 CRAN (R 3.4.4)                  
#>  rmarkdown      1.9     2018-03-01 CRAN (R 3.4.3)                  
#>  ropls        * 1.8.0   2017-04-25 Bioconductor                    
#>  rprojroot      1.3-2   2018-01-03 CRAN (R 3.4.3)                  
#>  stats        * 3.4.4   2018-03-15 local                           
#>  stringi        1.2.2   2018-05-02 CRAN (R 3.4.4)                  
#>  stringr        1.3.1   2018-05-10 CRAN (R 3.4.4)                  
#>  tools          3.4.4   2018-03-15 local                           
#>  utils        * 3.4.4   2018-03-15 local                           
#>  withr          2.1.2   2018-06-07 Github (jimhester/withr@dbcd7cd)
#>  yaml           2.1.19  2018-05-01 CRAN (R 3.4.4)
ropls • 980 views
ADD COMMENT
0
Entering edit mode
@etiennethevenot-8285
Last seen 14 months ago
France

Thanks for reporting this bug which has been fixed in the 1.13.2 version of ropls (dev).

Etienne.

ADD COMMENT

Login before adding your answer.

Traffic: 748 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6