Factor analysis or principal component analysis

This is a wrapper for the psych functions psych::pca() and psych::fa() to produce output that it similar to the output produced by jamovi.

factorAnalysis(
  data,
  nfactors,
  items = names(data),
  rotate = "oblimin",
  covar = FALSE,
  na.rm = TRUE,
  kaiser = 1,
  loadings = TRUE,
  summary = FALSE,
  correlations = FALSE,
  modelFit = FALSE,
  eigenValues = FALSE,
  screePlot = FALSE,
  residuals = FALSE,
  itemLabels = items,
  colorLoadings = FALSE,
  fm = "minres",
  digits = 2,
  headingLevel = 3,
  ...
)

principalComponentAnalysis(
  data,
  items,
  nfactors,
  rotate = "oblimin",
  covar = FALSE,
  na.rm = TRUE,
  kaiser = 1,
  loadings = TRUE,
  summary = FALSE,
  correlations = FALSE,
  eigenValues = FALSE,
  screePlot = FALSE,
  residuals = FALSE,
  itemLabels = items,
  colorLoadings = FALSE,
  digits = 2,
  headingLevel = 3,
  ...
)

rosettaDataReduction_partial(
  x,
  digits = x$input$digits,
  headingLevel = x$input$headingLevel,
  echoPartial = FALSE,
  partialFile = NULL,
  quiet = TRUE,
  ...
)

# S3 method for rosettaDataReduction
knit_print(
  x,
  digits = x$input$digits,
  headingLevel = x$input$headingLevel,
  echoPartial = FALSE,
  partialFile = NULL,
  quiet = TRUE,
  ...
)

# S3 method for rosettaDataReduction
print(
  x,
  digits = x$input$digits,
  headingLevel = x$input$headingLevel,
  forceKnitrOutput = FALSE,
  ...
)

Arguments

data: The data frame that contains the items.
nfactors: The number of factors to extract, or 'eigen' to extract all factors with an eigen value higher than the number specified in kaiser. In the future, parallel can be specified here to extract the number of factors suggested by parallel analysis.
items: The items to analyse; if not specified, all variables in data will be used.
rotate: Which rotation to use; see psych::fa() for all options. The most common options are 'none' to not rotate at all; 'varimax' for an orthogonal rotation (assuming/imposing that the components or factors are not correlated); or 'oblimin' for an oblique rotation (allowing the components/factors to correlate).
covar: Whether to analyse the correlation matrix (FALSE) or the covariance matrix (TRUE).
na.rm: Whether to first remove all cases with missing values.
kaiser: The minimum eigenvalue when applying the Kaiser criterion (see nfactors).
loadings: Whether to display the component or factor loadings.
summary: Whether to display the factor or component summary.
correlations: Whether to display the correlations between factors of components.
modelFit: Whether to display the model fit Only for EFA).
eigenValues: Whether to display the eigen values.
screePlot: Whether to display the scree plot.
residuals: Whether to display the matrix with residuals.
itemLabels: Optionally, labels to use for the items (optionally, named, with the names corresponding to the items; otherwise, the order of the labels has to match the order of the items)
colorLoadings: Whether, when producing an Rmd partial (i.e. when calling the command while knitting) to colour the cells using kableExtra::kable_styling().
fm: The method to use for the factor analysis: 'fm' for Minimum Residuals; 'ml' for Maximum Likelihood; and 'pa' for Principal Factor.
digits: The number of digits to round to.
headingLevel: The number of hashes to print in front of the headings when printing while knitting
...: Any additional arguments are passed to psych::fa(), psych::pca(), to the default print method by the print method, and to rmdpartials::partial() when knitting an RMarkdown partial.
x: The object to print.
echoPartial: Whether to show the executed code in the R Markdown partial (TRUE) or not (FALSE).
partialFile: This can be used to specify a custom partial file. The file will have object x available.
quiet: Passed on to knitr::knit() whether it should b chatty (FALSE) or quiet (TRUE).
forceKnitrOutput: Force knitr output.

Value

An object with the object resulting from the call to the psych functions and some extracted information that will be printed.

Details

The code in these functions uses parts of the code in jamovi, written by Jonathon Love and Ravi Selker.

Examples

### Load example dataset
data("pp15", package="rosetta");

### Get variable names with expected
### effects of a high dose of MDMA
items <-
  grep(
    "highDose_AttBeliefs_",
    names(pp15),
    value=TRUE
  );

### Do a factor analysis
rosetta::factorAnalysis(
  data = pp15,
  items = items,
  nfactors = "eigen",
  scree = TRUE
);
#> 
#> Exploratory Factor Analysis (EFA)
#> 
#>   Extraction method: Minimum Residuals
#>   Rotation :         Oblimin rotation
#>   Sample size :      212
#> 
#> Factor loadings
#> 
#>                                         Factor 1 Factor 2 Uniqueness
#> highDose_AttBeliefs_long                    0.24     0.37       0.82
#> highDose_AttBeliefs_intensity               0.16     0.73       0.45
#> highDose_AttBeliefs_intoxicated             0.02     0.69       0.52
#> highDose_AttBeliefs_energy                  0.45     0.11       0.79
#> highDose_AttBeliefs_euphoria                0.73     0.23       0.44
#> highDose_AttBeliefs_insight                 0.69    -0.14       0.50
#> highDose_AttBeliefs_connection              0.77     0.12       0.40
#> highDose_AttBeliefs_contact                 0.77     0.09       0.40
#> highDose_AttBeliefs_sex                     0.41    -0.16       0.80
#> highDose_AttBeliefs_coping                  0.18     0.47       0.75
#> highDose_AttBeliefs_isolated               -0.52     0.14       0.71
#> highDose_AttBeliefs_boundaries              0.31    -0.09       0.89
#> highDose_AttBeliefs_music                   0.56     0.36       0.58
#> highDose_AttBeliefs_hallucinate            -0.24     0.47       0.72
#> highDose_AttBeliefs_timeAwareness           0.01     0.54       0.71
#> highDose_AttBeliefs_memory                  0.40    -0.40       0.66
#> highDose_AttBeliefs_health                  0.34    -0.51       0.60
#> highDose_AttBeliefs_better                  0.71    -0.05       0.49
#> highDose_AttBeliefs_physicalSideEffects    -0.46     0.38       0.63
#> highDose_AttBeliefs_psychicSideEffects     -0.53     0.30       0.61
#> highDose_AttBeliefs_regret                 -0.55     0.31       0.58
#> <table style='border:0px solid black !important; font-family: "Arial Narrow", "Source Sans Pro", sans-serif; margin-left: auto; margin-right: auto;' class="table table-condensed">
#>  <thead>
#>   <tr>
#>    <th style="text-align:left;">   </th>
#>    <th style="text-align:right;"> Factor 1 </th>
#>    <th style="text-align:right;"> Factor 2 </th>
#>    <th style="text-align:right;"> Uniqueness </th>
#>   </tr>
#>  </thead>
#> <tbody>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_long </td>
#>    <td style="text-align:right;"> 0.24 </td>
#>    <td style="text-align:right;"> 0.37 </td>
#>    <td style="text-align:right;"> 0.82 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_intensity </td>
#>    <td style="text-align:right;"> 0.16 </td>
#>    <td style="text-align:right;"> 0.73 </td>
#>    <td style="text-align:right;"> 0.45 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_intoxicated </td>
#>    <td style="text-align:right;"> 0.02 </td>
#>    <td style="text-align:right;"> 0.69 </td>
#>    <td style="text-align:right;"> 0.52 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_energy </td>
#>    <td style="text-align:right;"> 0.45 </td>
#>    <td style="text-align:right;"> 0.11 </td>
#>    <td style="text-align:right;"> 0.79 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_euphoria </td>
#>    <td style="text-align:right;"> 0.73 </td>
#>    <td style="text-align:right;"> 0.23 </td>
#>    <td style="text-align:right;"> 0.44 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_insight </td>
#>    <td style="text-align:right;"> 0.69 </td>
#>    <td style="text-align:right;"> -0.14 </td>
#>    <td style="text-align:right;"> 0.50 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_connection </td>
#>    <td style="text-align:right;"> 0.77 </td>
#>    <td style="text-align:right;"> 0.12 </td>
#>    <td style="text-align:right;"> 0.40 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_contact </td>
#>    <td style="text-align:right;"> 0.77 </td>
#>    <td style="text-align:right;"> 0.09 </td>
#>    <td style="text-align:right;"> 0.40 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_sex </td>
#>    <td style="text-align:right;"> 0.41 </td>
#>    <td style="text-align:right;"> -0.16 </td>
#>    <td style="text-align:right;"> 0.80 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_coping </td>
#>    <td style="text-align:right;"> 0.18 </td>
#>    <td style="text-align:right;"> 0.47 </td>
#>    <td style="text-align:right;"> 0.75 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_isolated </td>
#>    <td style="text-align:right;"> -0.52 </td>
#>    <td style="text-align:right;"> 0.14 </td>
#>    <td style="text-align:right;"> 0.71 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_boundaries </td>
#>    <td style="text-align:right;"> 0.31 </td>
#>    <td style="text-align:right;"> -0.09 </td>
#>    <td style="text-align:right;"> 0.89 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_music </td>
#>    <td style="text-align:right;"> 0.56 </td>
#>    <td style="text-align:right;"> 0.36 </td>
#>    <td style="text-align:right;"> 0.58 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_hallucinate </td>
#>    <td style="text-align:right;"> -0.24 </td>
#>    <td style="text-align:right;"> 0.47 </td>
#>    <td style="text-align:right;"> 0.72 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_timeAwareness </td>
#>    <td style="text-align:right;"> 0.01 </td>
#>    <td style="text-align:right;"> 0.54 </td>
#>    <td style="text-align:right;"> 0.71 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_memory </td>
#>    <td style="text-align:right;"> 0.40 </td>
#>    <td style="text-align:right;"> -0.40 </td>
#>    <td style="text-align:right;"> 0.66 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_health </td>
#>    <td style="text-align:right;"> 0.34 </td>
#>    <td style="text-align:right;"> -0.51 </td>
#>    <td style="text-align:right;"> 0.60 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_better </td>
#>    <td style="text-align:right;"> 0.71 </td>
#>    <td style="text-align:right;"> -0.05 </td>
#>    <td style="text-align:right;"> 0.49 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_physicalSideEffects </td>
#>    <td style="text-align:right;"> -0.46 </td>
#>    <td style="text-align:right;"> 0.38 </td>
#>    <td style="text-align:right;"> 0.63 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_psychicSideEffects </td>
#>    <td style="text-align:right;"> -0.53 </td>
#>    <td style="text-align:right;"> 0.30 </td>
#>    <td style="text-align:right;"> 0.61 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> highDose_AttBeliefs_regret </td>
#>    <td style="text-align:right;"> -0.55 </td>
#>    <td style="text-align:right;"> 0.31 </td>
#>    <td style="text-align:right;"> 0.58 </td>
#>   </tr>
#> </tbody>
#> </table>


if (FALSE) {
  ### To get more output, show the
  ### output as Rmd Partial in the viewer,
  ### and color/size the factor loadings
  rosetta::rosettaDataReduction_partial(
    rosetta::factorAnalysis(
      data = pp15,
      items = items,
      nfactors = "eigen",
      summary = TRUE,
      correlations = TRUE,
      colorLoadings = TRUE
    )
  );
}