logRegr {rosetta}

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 class '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 class 'rosettaLogRegr'
print(
  x,
  digits = x$input$digits,
  pvalueDigits = x$input$pvalueDigits,
  headingLevel = x$input$headingLevel,
  forceKnitrOutput = FALSE,
  ...
)

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.

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.

Author(s)

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

Maintainer: Gjalt-Jorn Peters [e-mail]

See Also

regr and fanova for similar functions for linear regression and analysis of variance and stats::glm() for the regular interface for logistic regression.

Examples

### 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
);

## Not run: 
### 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
  )
);

## End(Not run)