Package: psc 2.1.0

psc: Personalised Synthetic Controls

Allows the comparison of data cohorts (DC) against a Counter Factual Model (CFM) and measures the difference in terms of an efficacy parameter. Allows the application of Personalised Synthetic Controls.

Authors:Richard Jackson [cre, aut, cph]

psc_2.1.0.tar.gz
psc_2.1.0.zip(r-4.7-any)psc_2.1.0.zip(r-4.6-any)psc_2.1.0.zip(r-4.5-any)
psc_2.1.0.tgz(r-4.6-any)psc_2.1.0.tgz(r-4.5-any)
psc_2.1.0.tar.gz(r-4.7-any)psc_2.1.0.tar.gz(r-4.6-any)
psc_2.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
psc/json (API)

# Install 'psc' in R:

install.packages('psc', repos = c('https://richjjackson.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/richjjackson/psc/issues

Pkgdown/docs site:https://richjjackson.github.io

Datasets:

e4_data - Example Dataset of patients treated with GemCap in the ESPAC-4 trial
gemCFM - Model for a survival outcome based on Gemcitbine patients from ESPAC-3

On CRAN:

5.50 score 2 stars 1 packages 21 scripts 306 downloads 11 exports 140 dependencies

Last updated from:ecc2c87092. Checks:4 ERROR, 5 OK. Indexed: yes.

Target	Result	Time
linux-devel	ERROR	238
source / vignettes	OK	248
linux-release	ERROR	238
macos-release	ERROR	126
macos-oldrel	ERROR	134
windows-devel	OK	167
windows-release	OK	170
windows-oldrel	OK	158
wasm-release	OK	141

Exports:init plotCFM postSummary pscCFM pscComb pscData pscEst pscEst_run pscEst_start pscEst_update pscfit

Dependencies:abind assertthat backports base64enc bbmle bdsmatrix bigD bitops boot broom bslib cachem car carData cards cardx checkmate cli colorspace commonmark corrplot cowplot cpp11 curl data.table Deriv deSolve digest distributional doBy dplyr enrichwith evaluate exactRankTests farver fastGHQuad fastmap flexsurv fontawesome forecast Formula fracdiff fs generics ggplot2 ggpubr ggrepel ggsci ggsignif ggtext glue gridExtra gridtext gt gtable gtsummary highr htmltools htmlwidgets isoband jpeg jquerylib jsonlite juicyjuice knitr labeling lattice lifecycle litedown lme4 lmtest lsoda magrittr markdown MASS Matrix MatrixModels matrixStats maxstat memoise mgcv mime minqa modelr mstate muhaz mvtnorm nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig png polynom posterior purrr quadprog quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reactable reactR reformulas rlang rmarkdown rstatix rstpm2 S7 sass scales SparseM statmod stringi stringr survival survminer tensorA tibble tidyr tidyselect timeDate tinytex urca utf8 V8 vctrs viridisLite withr xfun xml2 yaml zoo

psc-vignette

Rendered frompsc.Rmdusingknitr::rmarkdown

Last update: 2026-01-12
Started: 2025-07-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
acc	acc
Example model for a survival outcome	bin.mod
Counter Factual Model - summary	boot_lp
Counter Factual Model - summary	boot_sest
Summarising data within a Counter Factual Model (CFM)	cfmDataSumm
Visualising data within a CFM	cfmDataVis
Visualising Categorical Data	cfmDataVis_fac
Visualising Numerical Data	cfmDataVis_num
Counter Factual Model - summary	cfmSumm.flexsurvreg
Counter Factual Model - summary	cfmSumm.glm
Returns the coefficient estimate of a psc object.	coef.psc
Example model for a survival outcome	cont.mod
Example model for a survival outcome	count.mod
Example Dataset of patients with aHCC receiving Lenvetanib	data
Example Dataset of patients treated with GemCap in the ESPAC-4 trial	e4_data
Visualising Categorical Data	facVisComp
Model for a survival outcome based on Gemcitbine patients from ESPAC-3	gemCFM
Function for estimating initial parameter values	init
Likelihood function for a psc model of class 'flexsurvreg'	lik.flexsurvreg
Likelihood function for a psc model of class 'glm'	lik.glm
A generic function for extracting model information	modelExtract
A generic function for extracting model information	modelExtract.flexsurvreg
A generic function for extracting model information	modelExtract.glm
A generic function for extracting model information	modelExtract.lmerMod
modp	modp
Visualising Numerical Data	numVisComp
Function for Plotting PSC objects	plot.psc
Function for Plotting PSC objects	plot.psc.binary
Function for Plotting PSC objects	plot.psc.cont
Function for Plotting PSC objects #' A function which illsutrates the predicted response under the counter factual model and the observed response under the experimental treatment(s).	plot.psc.count
Function for Plotting PSC objects	plot.psc.flexsurvreg
Function for Plotting PSC objects	plotCFM
Posterior Summary	postSummary
Personalised Synthetic Controls - print	print.psc
quiet_gglist	print.quiet_gglist
quiet_gtsumm	print.quiet_gtsumm
quiet_gtsumm	print.quiet_list
Fitted 'psc' object	psc.object
Creating a CFM model which can be shared	pscCFM
PSC Estiamtion combination	pscComb
A function which structures the Data Cohort in a format for model estimation	pscData
A function that add a likelihood for estimation to the pscObject	pscData_addLik
A function that includes a treatment indicator when multiple treatment comparisons are required	pscData_addtrt
A function which performs error checks between the DC and CFM	pscData_error
A function to ensure that data from the cfm and data cohort are compatible	pscData_match
A function which removes missing data from the DC	pscData_miss
A function which structures the Data Cohort in a format for model estimation	pscData_structure
Function for performing Bayesian MCMC estimation procedures in 'pscfit'	pscEst
Running the Bayesian MCMC routine A procedure which runs the MCMC estimation routine	pscEst_run
Starting conditions for Bayesian MCMC estimation procedures in 'pscfit' A procedure which runs the sampling process for MCMC estimation	pscEst_samp
Starting conditions for Bayesian MCMC estimation procedures in 'pscfit' A procedure which sets the starting conditions for MCMC estimation	pscEst_start
Updating the posterior distribution as part of the MCMC estimation process A procedure which performs a single update of the posterior distribution	pscEst_update
Personalised Synthetic Controls model fit	pscfit
Counter Factual Model - summary	spline_surv_est
Personalised Synthetic Controls - summary	summary.psc
Example model for a survival outcome	surv.mod
Visualising Comparisons between a CFM and a DC	visComp