psfmi

The psfmi package

With this package you can pool logistic or Cox regression models, or perform backward variable selection in multiply imputed datasets. The models may include continuous, dichotomous, categorical (> 2 categories) and spline predictors. Also interaction terms between these type of predictor variables are possible. It is also possible to force (spline)
predictors or interaction terms in the model during predictor selection. This is the first package that contains these possibilities.

The basic pooling method is Rubin’s Rules (RR). For categorical and spline predictors the following pooling methods are available to derive overall p-values: the pooling covariance matrix or D1 method, the pooling of Chi-square values or D2 method, the Meng and Rubin likelihood ratio statistics or D3 method and a method that is called Median P Rule (MPR) that pools the median of the p-values.

A function called psfmi_lr is available for logistic regression models and a function that is called psfmi_coxr, for right censored Cox regression models.

With respect to introducing interaction terms in the model, only two-way interactions are allowed. If interaction terms are included and backward selection is applied, interaction terms are dropped from the model following the hierarchy principle. This means that interactions are considered during backward selection when both main effects are in the model.

A function that is called miperform_lr evaluates the apparent performance of logistic regression prediction models in multiple imputed datasets. The performanance measures that are reported are the pooled ROC/AUC, (Nagerkerke) R-squared and the Hosmer and Lemeshow test. Also calibration curves can be generated, overlayed curves that pool all calibration curves that are estimated in each imputed dataset, or individual curves as a result of calibrating the model in each imputed dataset separately. The pooled linear predictor is also returned.

A function with the name mivalext_lr can be used to externally validate prediction models in multiple imputed datasets. The following information of the externally validated model is provided: pooled ROC/AUC, (Nagelkerke) R-Square value, Hosmer and Lemeshow Test, pooled coefficients when the model is freely estimated in imputed datasets and the pooled linear predictor (LP), with information about miscalibration in intercept and slope.

The package needs R 3.4.0 or higher. You can use the functions, after you have installed the package from CRAN or the Github website (development version). For Github you first have to install and activate the devtools package. Use the following code to install and activate the package from Github:

install.packages(“devtools”)

library(devtools)

devtools::install_github(“mwheymans/psfmi”)

library(psfmi)