Introduction to the spca package

Package spca

This package contains functions to compute, print and plot Least Squares Sparse Principal Components Analysis (LS-SPCA). Methodological details, references and full presentation can be found in the extended_vignette document.

Installation

You can install the release version from CRAN

install.packages("spca")

or the development version from GitHub

remotes::install_github("merolagio/spca")

Usage

The main function spca() computes the sparse loadings and various statistics, such as the variance explained by each sparse component (sPC). print, summery and plot methods are available. PCA solutions stored as an *spca* object cn be obtained with the function pca().

Utilities available are compare_spca()(to compare two or more spca solutions), *aggregate_by_scale()* (to visualize the contribution by scale) and *new.spca()* (to create anspca` object from a set of loadings).

Example

Load data

The holzinger dataset is the small classic Holzinger-Swineford dataset with 145 cases on 12 variables grouped in 4 scales.

library(spca)
data(holzinger)
dim(holzinger)
#> [1] 145  12
holzinger_scales
#>  [1] SPL SPL SPL VBL VBL VBL SPD SPD SPD MTH MTH MTH
#> Levels: SPL VBL SPD MTH

Preliminary PCA

ho_pca = pca(holzinger, screeplot =  TRUE, qq_plot = TRUE)
summary(ho_pca,cols = 10)
#>          sPC1   sPC2   sPC3   sPC4   sPC5   sPC6   sPC7   sPC8   sPC9  sPC10
#> Vexp    40.2%  13.7%  10.6%   6.4%   5.6%   5.1%   4.3%   3.9%   3.2%   2.6%
#> Cvexp   40.2%  53.9%  64.5%  70.9%  76.5%  81.6%  85.9%  89.8%  93.0%  95.6%
#> Rvexp  100.0% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0%
#> Rcvexp 100.0% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0%
#> Card       12     12     12     12     12     12     12     12     12     12

We settle for 4 components

Compute the sparse loadings

Important parameters in the spca() function are: alpha which controls for the minimum \(R^2\) [default]) or the minimum proportion of cumulative variance explained (VEXP) by the sPCs realtive to that explained by the corresponding PCs; n_comps the number of components to compute; method the LS-SPCA method to use (“u” for uncorrelated, “c” for correlated [default]) and “p” for projection; var_selection (“forward” [default], “stepwise”, or “backward”). See the **spca** help for details on these parameters and more.

The following command computes four sPCs with default settings: alpha = 0.95, var_selection = forward, method = “c” that selects the cSPCA method. Hence, we expect each sPC to yield at least 0.95% cumulative VEXP, allowing some very mild correlation between sPCs.

myspca = spca(holzinger, n_comps = 4)

Inspect spca results

Methods are print, plot (several options available) and summary. By defaut, plot and print show the percentage contributions, that is the loadings scaled to have sum of their absolute values equal to 1.

myspca # print
#> Contributions (%)
#>             sPC1   sPC2   sPC3   sPC4
#> visual     11.9%         13.2% -24.2%
#> cubes                    22.1%  20.8%
#> flags      14.2%         17.0%       
#> paragraph        -22.6% -11.9%       
#> sentence   19.6%        -17.2%       
#> wordm            -21.9%              
#> addition   12.2%  21.2% -18.5%   9.6%
#> counting          20.3%              
#> straight   12.3%  14.0%        -18.6%
#> deduct     13.7%                 9.3%
#> numeric                         17.5%
#> series     16.1%                     
#>            -----  -----  -----  -----
#> Cvexp      38.6%  51.9%  62.3%  68.8%
#> 

summary(myspca, cor_with_pc = TRUE)
#>          sPC1   sPC2   sPC3   sPC4
#> Vexp    38.6%  13.3%  10.4%   6.4%
#> Cvexp   38.6%  51.9%  62.3%  68.8%
#> Rvexp   96.0%  97.3%  98.3% 100.6%
#> Rcvexp  96.0%  96.3%  96.7%  97.0%
#> Card        7      5      6      6
#> r       0.978  0.973  0.979 -0.876

plot(myspca, plot_type = "bar")


#sPCs correlation
round(myspca$spc_cor, 2)
#>       sPC1  sPC2  sPC3  sPC4
#> sPC1  1.00  0.03 -0.01  0.02
#> sPC2  0.03  1.00 -0.01 -0.01
#> sPC3 -0.01 -0.01  1.00 -0.01
#> sPC4  0.02 -0.01 -0.01  1.00

Other plot types are available.

Circular:

plot(myspca, plot_type = "c") # "c" for "circular"

Heatmap:

plot(myspca, plot_type = "h", controls = list(legend_position = "b")) # "h" is enough to call "heatmap" type and "b" to indicate "bottom".

Variable groups

The variables in the holzinger dataset belong to four different scales, recorded in the factor holzinger_scales. These can be differentiated in the barplot

plot(myspca, plot_type = "bars", variable_groups = holzinger_scales, controls = list(legend_position = "right"))


aggregate_by_group(myspca,groups = holzinger_scales)
#> [1] "percentage contributions"
#>      sPC1   sPC2   sPC3  sPC4
#> SPL 26.0%         52.4% -3.5%
#> VBL 19.6% -44.5% -29.1%      
#> SPD 24.6%  55.5% -18.5% -8.9%
#> MTH 29.8%               26.8%

Comparison of two or more spca solutions

Compare the CSPCA solutions with alpha = 0.95 those with alpha = 0.90.

myspca90 = spca(holzinger, n_comps = 4, alpha = 0.9)

compare_spca(obj_list = list(myspca, myspca90), 
             methods_names = c("alpha = 95", "alpha = 90"))

#> [1] "Percentage Contributions"
#>           C1.M1 C1.M2 C2.M1 C2.M2 C3.M1 C3.M2 C4.M1 C4.M2
#> visual     11.9                    13.2  13.3 -24.2      
#> cubes                              22.1  23.4  20.8  21.5
#> flags      14.2  16.6                17  16.2         -10
#> paragraph             -22.6       -11.9               6.2
#> sentence   19.6  23.7       -18.8 -17.2 -27.9            
#> wordm                 -21.9 -20.1                     6.2
#> addition   12.2        21.2  22.7 -18.5 -19.1   9.6  13.6
#> counting               20.3  24.8                        
#> straight   12.3  21.1    14  13.5             -18.6 -19.2
#> deduct     13.7  16.6                           9.3      
#> numeric                                        17.5  12.9
#> series     16.1  21.9                               -10.4
#>  
#> [1] Summary statistics
#>        C1.M1  C1.M2  C2.M1  C2.M2  C3.M1  C3.M2  C4.M1  C4.M2 
#> Vexp    38.6%  37.3%  13.3%  13.2%  10.4%  10.1%   6.4%   6.6%
#> Cvexp   38.6%  37.3%  51.9%  50.5%  62.3%  60.6%  68.8%  67.2%
#> Rvexp   96.0%  92.8%  97.3%  96.6%  98.3%  95.3% 100.6% 102.7%
#> Rcvexp  96.0%  92.8%  96.3%  93.7%  96.7%  94.0%  97.0%  94.8%
#> Card        7      5      5      5      6      5      6      8
#> abs_r    0.98   0.96   0.97   0.96   0.98   0.96   0.88   0.56