I'm confused now because Running the following code gives me error:
Train1=Train
Train1 <- subset(Train1, select = -c(Item_Fat_Content.LF,Item_Fat_Content.reg))
Train1=as.matrix(Train1)
outEM = PPCAEM(Train1, nComp=2, tol=0.00000000000001, maxit=100)#Probabilistic PCA
Xrecon = outEM$Xrecon
loadingsEM = outEM$loadings
scoresEM = outEM$scores
mean((Xrecon-Train1)^2)
prin_comp <- princomp(Train1, scale. = T,center = TRUE)#scale.=F, meaning that it will adjust if there's multicolinearity. But we have treated multicoll above (FULL RANK dummy)
scores_origpca = prin_comp$scores[,1:2]
loadings_origpca = prin_comp$loadings[,1:2]
Xrecon_origpca = scores_origpca%*%t(loadings_origpca)
outpcam = pca(Train1, nPcs=2, threshold=1e-8, method='ppca', scale='none', center=T)
loadings_pcam = loadings(outpcam)
scores_pcam = scores(outpcam)
This code:
> scores_pcam = scores(outpcam)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘scores’ for signature ‘"psych"’
Note that i have installed psych and pcaMethods from biocLite("pcaMethods").
One of the reasons we always ask people to post the output from sessionInfo() is to ensure that they have all packages loaded that they are trying to use. Simply installing a package doesn't mean you had it loaded, which is one possible problem. Another possible problem is that you might have the wrong version of psych, which sessionInfo() would show as well.
Hi.
Here is sessionInfo() output that was wrote in RStudio:
> sessionInfo()
attached base packages:
[1] grid parallel splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] psych_1.6.12 pracma_1.9.9 replyr_0.2.4 xts_0.9-7 zoo_1.7-14
[6] rsparkling_0.2.0 sparklyr_0.5.3-9002 SparseM_1.76 plyr_1.8.4 glmnet_2.0-5
[11] vtreat_0.5.30 tidyr_0.6.1 dplyr_0.5.0.9000 dummies_1.5.6 sigr_0.1.4
[16] WVPlots_0.2.3 stringr_1.2.0 rpart.plot_2.1.1 h2o_3.11.0.3815 randomForest_4.6-12
[21] doSNOW_1.0.14 snow_0.4-2 testthat_1.0.2 pcaMethods_1.66.0 Biobase_2.34.0
[26] BiocGenerics_0.20.0 Matrix_1.2-7.1 MASS_7.3-45 jsonlite_1.3 rjson_0.2.15
[31] rJava_0.9-8 R2jags_0.5-7 rjags_4-6 coda_0.19-1 reshape2_1.4.2
[36] magrittr_1.5 doParallel_1.0.10 iterators_1.0.8 foreach_1.4.3 caTools_1.17.1
[41] ROCR_1.0-7 gplots_3.0.1 pROC_1.9.1 robustbase_0.92-7 car_2.1-4
[46] DMwR_0.4.1 mice_2.30 data.table_1.10.4 C50_0.1.0-24 adabag_4.1
[51] caret_6.0-73 ggplot2_2.2.1 mlbench_2.1-1 rpart_4.1-10 xgboost_0.6-4
[56] e1071_1.6-8 gbm_2.1.3 lattice_0.20-34 survival_2.39-5 mlr_2.11
[61] ParamHelpers_1.10
loaded via a namespace (and not attached):
[1] minqa_1.2.4 colorspace_1.3-2 class_7.3-14 rprojroot_1.2 base64enc_0.1-3
[6] rstudioapi_0.6 MatrixModels_0.4-1 codetools_0.2-15 mnormt_1.5-5 Formula_1.2-1
[11] nloptr_1.0.4 pbkrtest_0.4-7 shiny_1.0.0 httr_1.2.1 backports_1.0.5
[16] assertthat_0.1 lazyeval_0.2.0 htmltools_0.3.5 quantreg_5.29 tools_3.3.2
[21] partykit_1.1-1 gtable_0.2.0 glue_0.0.0.9000 Rcpp_0.12.10 parallelMap_1.3
[26] gdata_2.17.0 nlme_3.1-128 lme4_1.1-12 mime_0.5 gtools_3.5.0
[31] DEoptimR_1.0-8 scales_0.4.1 BBmisc_1.11 quantmod_0.4-7 gridExtra_2.2.1
[36] stringi_1.1.2 checkmate_1.8.2 TTR_0.23-1 boot_1.3-18 rlang_0.0.0.9001
[41] bitops_1.0-6 wrapr_0.1.1 R6_2.2.0 DBI_0.6 foreign_0.8-67
[46] mgcv_1.8-15 abind_1.4-5 RCurl_1.95-4.8 nnet_7.3-12 tibble_1.2
[51] crayon_1.3.2 KernSmooth_2.23-15 ModelMetrics_1.1.0 digest_0.6.12 xtable_1.8-2
[56] httpuv_1.3.3 stats4_3.3.2 munsell_0.4.3 quadprog_1.5-5 R2WinBUGS_2.1-21
please kindly let me know if anything :)