Package: psm3mkv 0.3.2

Dominic Muston

psm3mkv: Evaluate Partitioned Survival and State Transition Models

Fits and evaluates three-state partitioned survival analyses (PartSAs) and Markov models (clock forward or clock reset) to progression and overall survival data typically collected in oncology clinical trials. These model structures are typically considered in cost-effectiveness modeling in advanced/metastatic cancer indications. Muston (2024). "Informing structural assumptions for three state oncology cost-effectiveness models through model efficiency and fit". Applied Health Economics and Health Policy.

Authors:Dominic Muston [aut, cre], Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph, fnd]

psm3mkv_0.3.2.tar.gz
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psm3mkv.pdf |psm3mkv.html✨
psm3mkv/json (API)
NEWS

# Install 'psm3mkv' in R:
install.packages('psm3mkv', repos = c('https://merck.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/merck/psm3mkv/issues

On CRAN:

27 exports 9 stars 2.31 score 61 dependencies 1 scripts 204 downloads

Last updated 3 months agofrom:b09105e457. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-winOKSep 12 2024
R-4.5-linuxOKSep 12 2024
R-4.4-winOKSep 12 2024
R-4.4-macOKSep 12 2024
R-4.3-winOKSep 12 2024
R-4.3-macOKSep 12 2024

Exports:calc_allrmdscalc_haz_psmcalc_likescalc_rmdcalc_surv_psmppscheck_consistent_pfscompare_psm_likesconstrain_survprobcreate_dummydatacreate_extrafieldsfind_bestfitfit_ends_mods_parfit_ends_mods_splgraph_psm_hazardsgraph_psm_survsgraph_survsprob_os_psmprob_os_stm_cfprob_os_stm_crprob_pd_psmprob_pd_stm_cfprob_pd_stm_crprob_pf_psmprob_pf_stmprob_pps_cfprob_pps_crvlookup

Dependencies:admiraladmiraldevassertthatbbmlebdsmatrixBHclicolorspacecpp11data.tabledeSolvedplyrfansifarverfastGHQuadflexsurvgenericsggplot2gluegtablehmsisobandlabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmstatemuhazmunsellmvtnormnlmenumDerivpharmaverseadampillarpkgconfigpurrrquadprogR6RColorBrewerRcppRcppArmadillorlangrstpm2scalesSimplicialCubaturestatmodstringistringrsurvivaltibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithr

Example use of psm3mkv

Rendered fromexample.Rmdusingknitr::rmarkdownon Sep 12 2024.

Last update: 2024-06-07
Started: 2023-09-01

Mortality adjustments

Rendered frommortality-adjustments.Rmdusingknitr::rmarkdownon Sep 12 2024.

Last update: 2024-06-07
Started: 2024-04-08

Readme and manuals

Help Manual

Help pageTopics
Calculate restricted mean durations for each health state and all three modelscalc_allrmds
Derive pre and post-progression hazards of death under PSMcalc_haz_psm
Calculate likelihoods for three three-state model structurescalc_likes
Calculate restricted mean durationscalc_rmd
Derive PPS survival function under a PSMcalc_surv_psmpps
Check consistency of PFS definition Check that PFS is defined consistently with TTP and OS in a dataset. This convenience function compares 'pfs.durn' with the lower of 'ttp.durn' and 'os.durn', and checks that the event field 'pfs.flag' is consistent with 'ttp.flag' and 'os.flag' (is 1 when either 'ttp.flag' or 'os.flag' is one).check_consistent_pfs
Compare likelihoods of PSMscompare_psm_likes
Constrain survival probabilities according to hazards in a lifetable Recalculated constrained survival probabilities (by week) as the lower of the original unadjusted survival probability and the survival implied by the given lifetable (assumed indexed as years).constrain_survprob
Create dummy dataset for illustrationcreate_dummydata
Create the additional time-to-event endpoints, adjusting for cutpointcreate_extrafields
Find the "best" survival regression from a list of model fitsfind_bestfit
Fit multiple parametric survival regressions to the multiple required endpointsfit_ends_mods_par
Fit multiple spline regressions to the multiple required endpointsfit_ends_mods_spl
Graph the PSM hazard functionsgraph_psm_hazards
Graph the PSM survival functionsgraph_psm_survs
Graph the observed and fitted state membership probabilitiesgraph_survs
Calculate probability of being alive in a partitioned survival modelprob_os_psm
Calculate probability of being alive under the state transition clock forward modelprob_os_stm_cf
Calculate probability of being alive under the state transition clock reset modelprob_os_stm_cr
Calculate membership probability of progressed disease state in a partitioned survival modelprob_pd_psm
Calculate probability of having progressed disease under the state transition clock forward modelprob_pd_stm_cf
Calculate probability of having progressed disease under the state transition clock reset modelprob_pd_stm_cr
Calculate probability of being progression free in partitioned survival modelprob_pf_psm
Calculate probability of being progression free in either state transition model (clock forward or clock reset)prob_pf_stm
Calculate probability of post progression survival under the state transition clock forward modelprob_pps_cf
Calculate probability of post progression survival under the state transition clock reset modelprob_pps_cr
VLOOKUP functionvlookup