mmrm
The mmrm package implements mixed models for repeated measures (MMRM)
in R based on Template Model Builder (TMB).
Installation
GitHub
You can install the current development version from GitHub with:
if (!require("remotes")) {
install.packages("remotes")
}
remotes::install_github("openpharma/mmrm")Getting Started
You can get started by trying out the example:
library(mmrm)
fit <- mmrm(
formula = FEV1 ~ RACE + SEX + ARMCD * AVISIT + us(AVISIT | USUBJID),
data = fev_data
)This specifies an MMRM with the given covariates and an unstructured
covariance matrix for the timepoints (also called visits in the clinical
trial context, here given by AVISIT) within the subjects (here
USUBJID). While by default this uses restricted maximum likelihood
(REML), it is also possible to use ML, see ?mmrm.
You can look at the results high-level:
fit
#> mmrm fit
#>
#> Formula: FEV1 ~ RACE + SEX + ARMCD * AVISIT + us(AVISIT | USUBJID)
#> Data: fev_data (used 537 observations from 197 subjects with maximum 4
#> timepoints)
#> Covariance: unstructured (10 variance parameters)
#> Method: REML
#> Deviance: 3386.45
#>
#> Coefficients:
#> (Intercept) RACEBlack or African American
#> 30.77747548 1.53049977
#> RACEWhite SEXFemale
#> 5.64356535 0.32606192
#> ARMCDTRT AVISITVIS2
#> 3.77423004 4.83958845
#> AVISITVIS3 AVISITVIS4
#> 10.34211288 15.05389826
#> ARMCDTRT:AVISITVIS2 ARMCDTRT:AVISITVIS3
#> -0.04192625 -0.69368537
#> ARMCDTRT:AVISITVIS4
#> 0.62422703
#>
#> Model Inference Optimization:
#> Converged with code 0 and message: convergence: rel_reduction_of_f <= factr*epsmchThe summary() method then provides the coefficients table with
Satterthwaite degrees of freedom as well as the covariance matrix
estimate:
summary(fit)
#> mmrm fit
#>
#> Formula: FEV1 ~ RACE + SEX + ARMCD * AVISIT + us(AVISIT | USUBJID)
#> Data: fev_data (used 537 observations from 197 subjects with maximum 4
#> timepoints)
#> Covariance: unstructured (10 variance parameters)
#>
#> Model selection criteria:
#> AIC BIC logLik deviance
#> 3406.4 3439.3 -1693.2 3386.4
#>
#> Coefficients:
#> Estimate Std. Error df t value Pr(>|t|)
#> (Intercept) 30.77748 0.88656 218.80000 34.715 < 2e-16
#> RACEBlack or African American 1.53050 0.62448 168.67000 2.451 0.015272
#> RACEWhite 5.64357 0.66561 157.14000 8.479 1.56e-14
#> SEXFemale 0.32606 0.53195 166.13000 0.613 0.540744
#> ARMCDTRT 3.77423 1.07415 145.55000 3.514 0.000589
#> AVISITVIS2 4.83959 0.80172 143.88000 6.037 1.27e-08
#> AVISITVIS3 10.34211 0.82269 155.56000 12.571 < 2e-16
#> AVISITVIS4 15.05390 1.31281 138.47000 11.467 < 2e-16
#> ARMCDTRT:AVISITVIS2 -0.04193 1.12932 138.56000 -0.037 0.970439
#> ARMCDTRT:AVISITVIS3 -0.69369 1.18765 158.17000 -0.584 0.559996
#> ARMCDTRT:AVISITVIS4 0.62423 1.85085 129.72000 0.337 0.736463
#>
#> (Intercept) ***
#> RACEBlack or African American *
#> RACEWhite ***
#> SEXFemale
#> ARMCDTRT ***
#> AVISITVIS2 ***
#> AVISITVIS3 ***
#> AVISITVIS4 ***
#> ARMCDTRT:AVISITVIS2
#> ARMCDTRT:AVISITVIS3
#> ARMCDTRT:AVISITVIS4
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#>
#> Covariance estimate:
#> VIS1 VIS2 VIS3 VIS4
#> VIS1 40.5537 14.3960 4.9747 13.3867
#> VIS2 14.3960 26.5715 2.7855 7.4745
#> VIS3 4.9747 2.7855 14.8979 0.9082
#> VIS4 13.3867 7.4745 0.9082 95.5568Details
For the available covariance structures, look at the covariance vignette:
vignette("covariance")In order to understand how mmrm is fitting the models, you can read
the details at:
vignette("algorithm")