Method interfaces
All unsupervised methods supplied by this package share a common interface which expects a list of blocks as the first input. Methods that are imported from other packages are wrapped in a function that gives the mentioned interface. Results from the imported method are stored in a separate slot in the output in case specialised plot or summary functions are available or direct inspection is needed. If default parameters are used, a single list of blocks with suitably linked matrices (shared objects or variables) will result in a basic analysis (see first code block below). In addition, all methods have parameters that control their behaviour, e.g., number of components, convergence criteria etc.
Common output elements across methods
Output from all methods include slots called loadings, scores, blockLoadings and blockScores, or a suitable subset of these. An info slot describes which types of (block) loadings/scores are in the output. There may be various extra elements in addition to the common elements, e.g. coefficients, weights etc.
# SCA used with shared variable mode data returns block loadings and common scores:
names(pot.sca)
#> [1] "blockLoadings" "scores" "samplelinked" "info"
#> [5] "explvar" "call" "data"
summary(pot.sca)
#> Simultaneous Component Analysis
#> ===============================
#>
#> $scores: Common scores (26x2)
#> $blockLoadings: Block loadings:
#> - Chemical (14x2), Compression (12x2), Sensory (9x2)
# MFA stores individual PCA scores and loadings as block elements:
names(pot.mfa)
#> [1] "scores" "loadings" "blockScores" "blockLoadings"
#> [5] "info" "MFA" "call" "explvar"
#> [9] "data"
summary(pot.mfa)
#> Multiple Factor Analysis
#> ========================
#>
#> $scores: Global scores (26x5)
#> $loadings: Global loadings (35x5)
#> $blockScores: Individual PCA scores:
#> - Chemical (26x5), Compression (26x5), Sensory (26x5)
#> $blockLoadings: Individual PCA loadings:
#> - Chemical (14x5), Compression (12x5), Sensory (9x5)Scores and loadings
Functions for accessing scores and loadings are based on functions from the pls package, but extended with a block parameter to allow extraction of common/global scores/loadings and their block counterparts. The default block is 0, corresponding to the common/global block. Block scores/loadings can be accessed by number or name.
# Block loadings for Sensory block with variable labels in scatter format
loadingplot(pot.sca, block = "Sensory", labels = "names")
Plot from imported package
Some methods in the package are wrappers for imported methods from other packages. Using the stored object from an imported method (see $statis code below), one can exploit methods from the original package to expand on the methods available in this package. An example is the summary plot for the statis method in the package ade4.
