Wrapper for the prc function to allow for formula input.
Arguments
- formula
Model formula accepting a single response (block) and predictors. If no predictor is called 'time', time is assumed to be the second predictor.
- data
The data set to analyse.
- ...
Additional arguments to
prc.
See also
Main methods: asca, apca, limmpca, msca, pcanova, prc and permanova.
Workhorse function underpinning most methods: asca_fit.
Extraction of results and plotting: asca_results, asca_plots, pcanova_results and pcanova_plots
Examples
data(caldana)
(pr <- prc(compounds ~ light * time, caldana))
#> Call: prc(formula = compounds ~ light * time, data = caldana)
#>
#> -- Model Summary --
#>
#> Inertia Proportion Rank
#> Total 11.47745 1.00000
#> Conditional 1.11209 0.09689 6
#> Constrained 2.51542 0.21916 18
#> Unconstrained 7.84993 0.68394 67
#>
#> Inertia is variance
#>
#> -- Eigenvalues --
#>
#> Eigenvalues for constrained axes:
#> RDA1 RDA2 RDA3 RDA4 RDA5 RDA6 RDA7 RDA8 RDA9 RDA10 RDA11
#> 0.9779 0.4049 0.3239 0.1755 0.1540 0.1247 0.0699 0.0607 0.0498 0.0336 0.0311
#> RDA12 RDA13 RDA14 RDA15 RDA16 RDA17 RDA18
#> 0.0273 0.0245 0.0187 0.0168 0.0094 0.0066 0.0061
#>
#> Eigenvalues for unconstrained axes:
#> PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8
#> 1.8824 1.4836 0.7107 0.4964 0.3533 0.3435 0.3159 0.2450
#> (Showing 8 of 67 unconstrained eigenvalues)
#>
summary(pr)
#>
#> Call:
#> prc(formula = compounds ~ light * time, data = caldana)
#> Species scores:
#> Alanine Valine
#> 0.900828 0.175768
#> Leucine Isoleucine
#> -0.657559 -0.264687
#> Proline Serine
#> 1.141926 -0.051640
#> Threonine beta-alanine
#> 0.075174 -0.726471
#> Hydroxyproline GABA
#> -0.007045 -1.087892
#> Aspartate Asparagine
#> -0.696076 -0.338664
#> Methionine O-acetyl-serine
#> 0.863337 0.205739
#> Glutamate Phenylalanine
#> -0.337782 1.245032
#> Ornithine Glutamine
#> 0.041141 1.302687
#> Lysine Tyrosine
#> -1.175389 -0.606966
#> Threonic-acid Citrulline-Arginine
#> -0.323093 0.526770
#> Pyruvic-acid Citric-acid
#> 0.473488 -0.414141
#> Succinic-acid Fumaric-acid
#> -0.690860 0.005060
#> Malic-acid Lactic-acid
#> 0.006521 -0.497413
#> Glycolic-acid Benzoic-acid
#> 1.624649 -0.141741
#> Maleic-acid Nicotinic-acid
#> 0.767982 -0.060987
#> Itaconic-acid Citramalate
#> -0.169012 0.050705
#> 4-hydroxy-benzoic-acid Dehydroascorbic-acid-dimer
#> -0.191369 0.062572
#> Gluconic-acid Dehydroascorbic-acid
#> -0.159411 -0.108530
#> Ascorbic-acid 4-Hydroxycinnamic-acid
#> -0.232603 -0.133527
#> Similar-to-Adenine Shikimate
#> 0.010357 0.878436
#> Erythritol Arabinose
#> -0.068112 -0.110114
#> Arabitol Fucose
#> -0.337455 -0.051972
#> Fructose Mannitol
#> 3.606930 0.215745
#> Galactose Glucose
#> 0.097331 2.777645
#> Sucrose Maltose
#> 0.615215 -0.263945
#> Trehalose Galactinol
#> -0.195746 0.211351
#> myo-inositol Uracil
#> -0.070161 -1.067653
#> Putrescine Ethanolamine
#> -0.210320 -0.546516
#> Glycerol Indole-3-acetonitrile
#> -0.146868 0.185760
#> Sinapic-acid Palmitic-acid
#> 0.131682 -0.267378
#> Octadecanoic-acid Docosanoic-acid
#> -0.361142 -0.299480
#> Tetracosanoic-acid Hexacosanoic-acid
#> 0.060571 0.188997
#> Octacosanoic-acid
#> 0.167153
#>
#> Coefficients for treatment + time:treatment interaction
#> which are contrasts to treatment Dark
#> rows are treatment, columns are time
#> 0 5 10 20 40 80 160
#> Low Light 1.601e-15 -0.003685 -0.05458 -0.121789 -0.006526 0.1098 0.1833
#> Light 3.011e-15 -0.038250 0.10345 -0.084547 0.098440 0.2416 0.3368
#> High Light 1.620e-15 -0.010944 -0.01016 0.009301 0.312173 0.6746 0.7716