Author: Martijn W Heymans
Date: 2023-06-16

# Pool Model Performance

#### Martijn W Heymans

#### 2023-06-16

# Introduction

The `psfmi` package includes the function `pool_performance`, to pool the performance measures of logistic and Cox regression models. This vignette show you how to use this function.

# Examples

# Performance Logistic regression model

The performance of a logistic regression model across multiply imputed datasets can be obtained as follows.

    perf <- pool_performance(data=lbpmilr, nimp=5, impvar="Impnr",
      formula = Chronic ~ Gender + Pain + Tampascale +
      Smoking + Function + Radiation + Age +
      Duration + BMI,
      cal.plot=TRUE, plot.method="mean",
      groups_cal=10, model_type="binomial")

    perf
    #> $ROC_pooled
    #>                     95% Low C-statistic 95% Up
    #> C-statistic (logit)  0.7878      0.8626 0.9139
    #>
    #> $coef_pooled
    #>  (Intercept)       Gender         Pain   Tampascale      Smoking     Function
    #> -5.951990403 -0.300998171  0.533421791  0.104519460  0.168974909 -0.063384729
    #>    Radiation          Age     Duration          BMI
    #>  0.256421438 -0.014809697 -0.001136425  0.006379084
    #>
    #> $R2_pooled
    #> [1] 0.4882147
    #>
    #> $Brier_Scaled_pooled
    #> [1] 0.3946362
    #>
    #> $nimp
    #> [1] 5
    #>
    #> $HLtest_pooled
    #>       F_value     P(>F) df1      df2
    #> [1,] 1.090127 0.3779371   8 85.96895
    #>
    #> $model_type
    #> [1] "binomial"

# Performance Cox regression model

For a Cox regression model the following code can be used.

    perf <- pool_performance(data=lbpmicox, nimp=5, impvar="Impnr",
      formula = Surv(Time, Status) ~ Duration + Pain + Tampascale +
      factor(Expect_cat) + Function + Radiation + Age ,
      cal.plot=FALSE, model_type="survival")

    perf
    #> $concordance_pooled
    #>                     95% Low C-statistic 95% Up
    #> C-statistic (logit)  0.5733       0.621 0.6664
    #>
    #> $coef_pooled
    #>            Duration                Pain          Tampascale factor(Expect_cat)2
    #>        -0.007680610        -0.085077440        -0.018125989         0.306105694
    #> factor(Expect_cat)3            Function           Radiation                 Age
    #>         0.269403151         0.038106572        -0.037816020        -0.008903958
    #>
    #> $R2_pooled
    #> [1] 0.09049936
    #>
    #> $nimp
    #> [1] 5
    #>
    #> $model_type
    #> [1] "survival"