logRegr: Userfriendly wrapper to do logistic regression in R

Description

This function is meant as a userfriendly wrapper to approximate the way logistic regression is done in SPSS.

Usage

logRegr(
  formula,
  data = NULL,
  conf.level = 0.95,
  digits = 2,
  predictGroupValue = NULL,
  comparisonGroupValue = NULL,
  pvalueDigits = 3,
  crossTabs = TRUE,
  oddsRatios = TRUE,
  plot = FALSE,
  collinearity = FALSE,
  env = parent.frame(),
  predictionColor = rosetta::opts$get("viridis3")[3],
  predictionAlpha = 0.5,
  predictionSize = 2,
  dataColor = rosetta::opts$get("viridis3")[1],
  dataAlpha = 0.33,
  dataSize = 2,
  observedMeansColor = rosetta::opts$get("viridis3")[2],
  binObservedMeans = 7,
  observedMeansSize = 2,
  observedMeansWidth = NULL,
  observedMeansAlpha = 0.5,
  theme = ggplot2::theme_bw(),
  headingLevel = 3
)
rosettaLogRegr_partial(
  x,
  digits = x$input$digits,
  pvalueDigits = x$input$pvalueDigits,
  headingLevel = x$input$headingLevel,
  echoPartial = FALSE,
  partialFile = NULL,
  quiet = TRUE,
  ...
)
# S3 method for rosettaLogRegr
knit_print(
  x,
  digits = x$input$digits,
  headingLevel = x$input$headingLevel,
  pvalueDigits = x$input$pvalueDigits,
  echoPartial = FALSE,
  partialFile = NULL,
  quiet = TRUE,
  ...
)
# S3 method for rosettaLogRegr
print(
  x,
  digits = x$input$digits,
  pvalueDigits = x$input$pvalueDigits,
  headingLevel = x$input$headingLevel,
  forceKnitrOutput = FALSE,
  ...
)

Value

Mainly, this function prints its results, but it also returns them in an object containing three lists:

input: The arguments specified when calling the function
intermediate: Intermediat objects and values
output: The results, such as the plot, the cross tables, and the coefficients.

Arguments

formula: The formula, specified in the same way as for stats::glm() (which is used for the actual analysis).
data: Optionally, a dataset containing the variables in the formula (if not specified, the variables must exist in the environment specified in env.
conf.level: The confidence level for the confidence intervals.
digits: The number of digits used when printing the results.
predictGroupValue, comparisonGroupValue: Can optionally be used to set the value to predict and the value to compare with.
pvalueDigits: The number of digits used when printing the p-values.
crossTabs: Whether to show cross tabulations of the correct predictions for the null model and the tested model, as well as the percentage of correct predictions.
oddsRatios: Whether to also present the regression coefficients as odds ratios (i.e. simply after a call to base::exp()).
plot: Whether to display the plot.
collinearity: Whether to show collinearity diagnostics.
env: If no dataframe is specified in data, use this argument to specify the environment holding the variables in the formula.
predictionColor, dataColor, observedMeansColor: The color of, respectively, the line and confidence interval showing the prediction; the points representing the observed data points; and the means based on the observed data.
predictionAlpha, dataAlpha, observedMeansAlpha: The alpha of, respectively, the confidence interval of the prediction; the points representing the observed data points; and the means based on the observed data (set to 0 to hide an element).
predictionSize, dataSize, observedMeansSize: The size of, respectively, the line of the prediction; the points representing the observed data points; and the means based on the observed data (set to 0 to hide an element).
binObservedMeans: Whether to bin the observed means; either FALSE or a single numeric value specifying the number of bins.
observedMeansWidth: The width of the lines of the observed means. If not specified (i.e. NULL), this is computed automatically and set to the length of the shortest interval between two successive points in the predictor data series (found using ufs::findShortestInterval().
theme: The theme used to display the plot.
headingLevel: The number of hashes to print in front of the headings
x: The object to print (i.e. as produced by rosetta::logRegr).
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).
...: Any additional arguments are passed to the default print method by the print method, and to rmdpartials::partial() when knitting an RMarkdown partial.
forceKnitrOutput: Force knitr output.

Author

Ron Pat-El & Gjalt-Jorn Peters (both while at the Open University of the Netherlands)

Maintainer: Gjalt-Jorn Peters gjalt-jorn@userfriendlyscience.com

Examples

Run this code


### Simplest way to call logRegr
rosetta::logRegr(data=mtcars, formula = vs ~ mpg);

### Also ordering a plot
rosetta::logRegr(
  data=mtcars,
  formula = vs ~ mpg,
  plot=TRUE
);

### Only use five bins
rosetta::logRegr(
  data=mtcars,
  formula = vs ~ mpg,
  plot=TRUE,
  binObservedMeans=5
);

if (FALSE) {
### Mimic output that would be obtained
### when calling from an R Markdown file
rosetta::rosettaLogRegr_partial(
  rosetta::logRegr(
    data=mtcars,
    formula = vs ~ mpg,
    plot=TRUE
  )
);
}