Package: progme 0.1.0

Mukul Bijalwan

progme: Extended Progression Models for Repeated Measures

Extended progression models for repeated measures in progressive disease clinical trials. Provides nonlinear mixed-effects progression models (linear, plateau, Emax, exponential decay), delayed treatment onset estimation by profile likelihood, joint longitudinal-survival models for informative dropout, competing-risks extensions, biomarker-informed adaptive dosing rules, and simulation-based power and sample-size calculation. The progression-model view of treatment effects, in which effects are characterised on the underlying disease trajectory rather than as additive shifts on the outcome scale, follows Raket (2022) <doi:10.1002/sim.9581>. The nonlinear mixed-effects machinery is built on the 'nlme' implementation described by Pinheiro and Bates (2000, ISBN 978-0-387-98957-0), and the joint modelling of longitudinal and time-to-event data follows Rizopoulos (2012, ISBN 978-1-4398-7286-4).

Authors:Mukul Bijalwan [aut, cre], Gunjan Aggrwal [aut], Mukul Jain [aut]

progme_0.1.0.tar.gz
progme_0.1.0.zip(r-4.7-any)progme_0.1.0.zip(r-4.6-any)
progme_0.1.0.tar.gz(r-4.7-any)progme_0.1.0.tar.gz(r-4.6-any)
progme_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
progme/json (API)

# Install 'progme' in R:
install.packages('progme', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mukulbijalwan/progme/issues

Datasets:

On CRAN:

Conda:

3.18 score 31 exports 21 dependencies

Last updated from:75ba93ebdc. Checks:6 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK240
source / vignettesOK336
linux-releaseOK155
windows-develOK135
windows-releaseOK136
wasm-releaseOK315

Exports:biomarker_dosing_rulecheck_convergencedefault_priorsdelayed_effectemax_biomarkerfind_sample_sizefit_pmrmgoodness_of_fitinitialize_subjectsparametric_bootstrappkpd_concentrationplot.pmrm_delayedpmrm_adaptive_trialpmrm_competingpmrm_delayedpmrm_jointpmrm_nlmepopulation_trajectorypower_pmrmpredict.pmrm_nlmeprint.pmrm_delayedscenario_basescenario_optimisticscenario_pessimisticsimulate_biomarkersimulate_joint_trialsimulate_progression_trialsubject_summariessummary.pmrm_delayedto_event_datavpc

Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglatticelifecycleMatrixnlmeR6RColorBrewerrlangS7scalessurvivalvctrsviridisLitewithr

Alzheimer's Trial: Linear Progression with Delayed Treatment Onset

Last update: 2026-10-22
Started: 2026-10-22

Parkinson's Data: Joint Model for Informative Dropout

Last update: 2026-10-22
Started: 2026-10-22

Simulation-Based Sample Size with Delayed Onset

Last update: 2026-10-22
Started: 2026-10-22

Readme and manuals

Help Manual

Help pageTopics
Simulated ADNI-style Alzheimer's trial dataadni_simulated
Biomarker-informed adaptive dosing rulebiomarker_dosing_rule
Convergence checkscheck_convergence check_convergence.default
Default priors for Bayesian progression modelsdefault_priors
Delayed treatment effect functiondelayed_effect
Emax biomarker modelemax_biomarker
Find sample size by simulationfind_sample_size
Unified estimation wrapperfit_pmrm
Goodness-of-fit summarygoodness_of_fit
Initialize subjects for an adaptive trial simulationinitialize_subjects
Parametric bootstrap for confidence intervalsparametric_bootstrap
Simulated Parkinson's trial data with informative dropoutparkinsons_simulated
PK/PD helpers for biomarker dosingpkpd_concentration
Plot a delayed-effect fitplot.pmrm_delayed
Run a biomarker-informed adaptive trial simulationpmrm_adaptive_trial
Fit a competing-risks progression modelpmrm_competing
Fit a progression model with delayed treatment onsetpmrm_delayed
Fit a joint longitudinal-survival modelpmrm_joint
Fit a nonlinear progression mixed-effects modelpmrm_nlme
Population-level trajectory over a time gridpopulation_trajectory
Simulation-based power for progression trialspower_pmrm
Predict from a fitted progression modelpredict.pmrm_nlme
Print method for delayed-effect fitsprint.pmrm_delayed
Scenario builders for trial simulation studiesscenario_base scenario_optimistic scenario_pessimistic
Simulate biomarker measurements under the PK/PD modelsimulate_biomarker
Simulate a trial with informative dropout via a joint model mechanismsimulate_joint_trial
Simulate a progression trialsimulate_progression_trial
Extract subject-level summary (EB intercept and slope)subject_summaries
Summarize a competing-risks fitsummary.pmrm_competing
Summarize a delayed-effect fitsummary.pmrm_delayed
Summarize a joint model fitsummary.pmrm_joint
Reshape long trial data to per-subject event datato_event_data
Visual predictive check (VPC)vpc