Powered by prcomp. When creating the nested_data,
the data should be scaled (i.e, trans = scale) if all variables are not
in the same unit.
nested_prcomp(.data, data_column = .data$data, ...)A data frame with a list column of data frames, possibly created using nested_data.
An expression that evalulates to the data object within each row of .data
Passed to prcomp.
.data with additional columns 'model', 'loadings', 'variance' and 'scores'
library(dplyr, warn.conflicts = FALSE)
nested_pca <- alta_lake_geochem %>%
nested_data(
qualifiers = c(depth, zone),
key = param,
value = value,
trans = scale
) %>%
nested_prcomp()
# get variance info
nested_pca %>% unnested_data(variance)
#> # A tibble: 6 × 6
#> component component_text standard_deviation variance variance_propor…¹ varia…²
#> <int> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 1 PC1 2.15 4.61 0.768 0.768
#> 2 2 PC2 0.884 0.781 0.130 0.899
#> 3 3 PC3 0.603 0.364 0.0607 0.959
#> 4 4 PC4 0.381 0.145 0.0242 0.984
#> 5 5 PC5 0.276 0.0761 0.0127 0.996
#> 6 6 PC6 0.151 0.0228 0.00380 1
#> # … with abbreviated variable names ¹variance_proportion,
#> # ²variance_proportion_cumulative
# get loadings info
nested_pca %>% unnested_data(loadings)
#> # A tibble: 6 × 7
#> variable PC1 PC2 PC3 PC4 PC5 PC6
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 C -0.380 -0.540 -0.460 0.162 -0.567 0.0718
#> 2 C/N 0.401 -0.451 0.207 -0.735 -0.223 -0.0408
#> 3 Cu -0.387 -0.340 0.760 0.173 0.0609 0.352
#> 4 Ti 0.439 0.0783 0.356 0.483 -0.565 -0.350
#> 5 d13C 0.458 0.0890 -0.144 0.145 -0.126 0.851
#> 6 d15N -0.377 0.613 0.144 -0.386 -0.539 0.149
# scores, requalified
nested_pca %>% unnested_data(c(qualifiers, scores))
#> # A tibble: 32 × 9
#> depth zone row_number PC1 PC2 PC3 PC4 PC5 PC6
#> <dbl> <chr> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0.25 Zone 3 1 -3.41 1.05 -0.517 -1.14 -0.261 -0.363
#> 2 0.75 Zone 3 2 -3.71 -0.00229 -0.280 -0.954 0.156 0.0447
#> 3 1.25 Zone 3 3 -3.75 -0.980 0.833 0.0304 0.187 0.0475
#> 4 1.75 Zone 3 4 -3.89 -0.925 1.12 0.0765 -0.0739 0.202
#> 5 2.5 Zone 3 5 -3.46 -1.19 0.967 0.270 -0.0480 0.0348
#> 6 3.5 Zone 3 6 -2.88 -0.835 0.394 0.151 0.0405 -0.179
#> 7 4.5 Zone 2 7 -1.49 -0.293 -0.144 0.248 -0.0819 -0.0934
#> 8 5.5 Zone 2 8 -0.223 0.0818 -0.218 0.575 0.342 -0.237
#> 9 6.5 Zone 2 9 -0.331 0.573 -0.181 0.366 0.354 -0.0660
#> 10 7.5 Zone 2 10 -0.638 0.543 -0.904 0.145 0.239 0.150
#> # … with 22 more rows