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Add citation section to readme #49

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64 changes: 30 additions & 34 deletions README.md
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Expand Up @@ -11,7 +11,7 @@ coverage](https://codecov.io/gh/Merck/psm3mkv/branch/main/graph/badge.svg)](http

The goal of psm3mkv is to evaluate the efficiency and fit of certain
three state model structures to data typical from an oncology clinical
trial, as described in an accompanying article [1]. The package
trial, as described in an accompanying article (Muston 2024). The package
evaluates the following structures:

- Partitioned Survival Model/analysis (PSM),
Expand All @@ -22,7 +22,8 @@ evaluates the following structures:

The state transition models differ from each other in that the
transition from progressive disease to death is a function of time from
baseline in the STM-CF and time from progression in the STM-CR [2, 3].
baseline in the STM-CF and time from progression in the STM-CR
(Jackson 2016; Woods et al. 2020).

The package requires a patient-level dataset of time to progression
(TTP), progression-free survival (PFS) and overall survival (OS).
Expand All @@ -34,7 +35,7 @@ Given this, the package enables:
- One piece parametric (distributions according to flexsurv).

- Royston-Parmar splines (1-3 internal knots, hazard/odds/normal
scales, again as per flexsurv) [4].
scales, again as per flexsurv) (Royston and Parmar 2002).

- Two piece parametric (given a time cutoff).

Expand Down Expand Up @@ -114,49 +115,44 @@ package [documentation website](https://merck.github.io/psm3mkv/).
### Additional dependencies

Running the vignettes requires additional dependencies, which are all
either imported by or suggested by *psm3mkv*. Thus you can ensure they
either imported by or suggested by psm3mkv. Thus you can ensure they
are all installed by specifying `dependencies = TRUE`.

``` r
pak::pak("Merck/psm3mkv@*release", dependencies = TRUE)
```

## Licensing
## Citation

Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its
affiliates. All rights reserved.
If you use this software, please cite it as below.

This file is part of the psm3mkv program.
> Muston, D. 2024. "Informing Structural Assumptions for Three State Oncology
> Cost-Effectiveness Models through Model Efficiency and Fit."
> _Applied Health Economics and Health Policy_. DOI: 10.1007/s40258-024-00884-2

psm3mkv is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your
option) any later version.
A BibTeX entry for LaTeX users is

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
Public License for more details.

You should have received a copy of the GNU General Public License along
with this program. If not, see <http://www.gnu.org/licenses/>.

psm3mkv uses third-party R packages which may be distributed under
different licenses.
```bibtex
@article{muston2024informing,
author = {Dominic Muston},
title = {Informing structural assumptions for three state oncology cost-effectiveness models through model efficiency and fit},
journal = {Applied Health Economics and Health Policy},
year = {2024},
doi = {10.1007/s40258-024-00884-2}
}
```

## References

1. Muston, D. 2024. "Informing Structural Assumptions for Three State Oncology Cost-Effectiveness Models through Model Efficiency and Fit." _Appl Health Econ Health Policy_. DOI: 10.1007/s40258-024-00884-2

2. Jackson, Christopher. 2016. "flexsurv: A Platform for Parametric
Survival Modeling in R." _Journal of Statistical Software_ 70 (8): 1--33.
Jackson, Christopher. 2016. "flexsurv: A Platform for Parametric
Survival Modeling in R." _Journal of Statistical Software_ 70 (8): 1--33.

3. Woods, Beth S, Eleftherios Sideris, Stephen Palmer, Nick Latimer,
and Marta Soares. 2020. "Partitioned Survival and State Transition Models
for Healthcare Decision Making in Oncology: Where Are We Now?"
_Value in Health_ 23 (12): 1613--1621.
Woods, Beth S, Eleftherios Sideris, Stephen Palmer, Nick Latimer,
and Marta Soares. 2020. "Partitioned Survival and State Transition Models
for Healthcare Decision Making in Oncology: Where Are We Now?"
_Value in Health_ 23 (12): 1613--1621.

4. Royston, Patrick, and Mahesh KB Parmar. 2002. "Flexible Parametric
Proportional-Hazards and Proportional-Odds Models for Censored Survival
Data, with Application to Prognostic Modelling and Estimation of
Treatment Effects." _Statistics in Medicine_ 21 (15): 2175--2197.
Royston, Patrick, and Mahesh KB Parmar. 2002. "Flexible Parametric
Proportional-Hazards and Proportional-Odds Models for Censored Survival
Data, with Application to Prognostic Modelling and Estimation of
Treatment Effects." _Statistics in Medicine_ 21 (15): 2175--2197.
101 changes: 50 additions & 51 deletions vignettes/psm3mkv.bib
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Expand Up @@ -4,7 +4,7 @@ @misc{hanpu2021predictive
year = {2021},
month = {July},
howpublished = {\url{https://cran.r-project.org/package=SurvMetrics/vignettes/SurvMetrics-vignette.html}},
note = {Vignette to the {SurvMetrics} R package}
note = {Vignette to the {SurvMetrics} {R} package}
}

@article{jackson2016flexsurv,
Expand All @@ -17,12 +17,12 @@ @article{jackson2016flexsurv
pages = {1--33}
}

@unpublished{muston2024informing,
author = {Dominic Muston},
title = {Informing structural assumptions for three state oncology cost-effectiveness models through model efficiency and fit},
@article{muston2024informing,
author = {Dominic Muston},
title = {Informing structural assumptions for three state oncology cost-effectiveness models through model efficiency and fit},
journal = {Applied Health Economics and Health Policy},
note = {In press},
year = {2024}
year = {2024},
doi = {10.1007/s40258-024-00884-2}
}

@article{naimark2013half,
Expand Down Expand Up @@ -51,7 +51,7 @@ @techreport{nice2022
@article{royston2002flexible,
title = {Flexible parametric proportional-hazards and proportional-odds models for censored survival data, with application to prognostic modelling and estimation of treatment effects},
author = {Royston, Patrick and Parmar, Mahesh KB},
journal = {Statistics in medicine},
journal = {Statistics in Medicine},
volume = {21},
number = {15},
pages = {2175--2197},
Expand All @@ -78,53 +78,52 @@ @article{woods2020partitioned
year = {2020}
}

@Manual{pack_dplyr,
title = {dplyr: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller and Davis Vaughan},
year = {2023},
note = {R package version 1.1.4},
url = {https://CRAN.R-project.org/package=dplyr},
}
@manual{pack_dplyr,
title = {{dplyr}: A Grammar of Data Manipulation},
author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller and Davis Vaughan},
year = {2023},
note = {R package version 1.1.4},
url = {https://CRAN.R-project.org/package=dplyr}
}

@TechReport{pack_HMDHFDplus,
author = {Tim Riffe},
title = {Reading Human Fertility Database and Human Mortality Database data into R},
institution = {MPIDR},
year = {2015},
url = {https://dx.doi.org/10.4054/MPIDR-TR-2015-004},
number = {TR-2015-004},
doi = {10.4054/MPIDR-TR-2015-004},
}
@techreport{pack_HMDHFDplus,
author = {Tim Riffe},
title = {Reading Human Fertility Database and Human Mortality Database data into {R}},
institution = {MPIDR},
year = {2015},
url = {https://dx.doi.org/10.4054/MPIDR-TR-2015-004},
number = {TR-2015-004},
doi = {10.4054/MPIDR-TR-2015-004}
}

@Manual{pack_tibble,
title = {tibble: Simple Data Frames},
author = {Kirill Müller and Hadley Wickham},
year = {2023},
note = {R package version 3.2.1},
url = {https://CRAN.R-project.org/package=tibble},
}
@manual{pack_tibble,
title = {{tibble}: Simple Data Frames},
author = {Kirill Müller and Hadley Wickham},
year = {2023},
note = {R package version 3.2.1},
url = {https://CRAN.R-project.org/package=tibble}
}

@Manual{pack_boot,
title = {boot: Bootstrap R (S-Plus) Functions},
author = {{Angelo Canty} and {B. D. Ripley}},
year = {2024},
note = {R package version 1.3-29},
}
@manual{pack_boot,
title = {boot: Bootstrap {R} ({S-Plus}) Functions},
author = {{Angelo Canty} and {B. D. Ripley}},
year = {2024},
note = {{R} package version 1.3-29}
}

@Manual{pack_ggsci,
title = {ggsci: Scientific Journal and Sci-Fi Themed Color Palettes for
'ggplot2'},
author = {Nan Xiao},
year = {2024},
note = {R package version 3.0.3},
url = {https://CRAN.R-project.org/package=ggsci},
}
@manual{pack_ggsci,
title = {{ggsci}: Scientific Journal and Sci-Fi Themed Color Palettes for '{ggplot2}'},
author = {Nan Xiao},
year = {2024},
note = {R package version 3.0.3},
url = {https://CRAN.R-project.org/package=ggsci}
}


@Manual{pack_purrr,
title = {purrr: Functional Programming Tools},
author = {Hadley Wickham and Lionel Henry},
year = {2023},
note = {R package version 1.0.2},
url = {https://CRAN.R-project.org/package=purrr},
}
@manual{pack_purrr,
title = {{purrr}: Functional Programming Tools},
author = {Hadley Wickham and Lionel Henry},
year = {2023},
note = {R package version 1.0.2},
url = {https://CRAN.R-project.org/package=purrr}
}
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