Package: smcfcs 2.0.2

smcfcs: Multiple Imputation of Covariates by Substantive Model Compatible Fully Conditional Specification

Implements multiple imputation of missing covariates by Substantive Model Compatible Fully Conditional Specification. This is a modification of the popular FCS/chained equations multiple imputation approach, and allows imputation of missing covariate values from models which are compatible with the user specified substantive model.

Authors:Jonathan Bartlett [aut, cre], Ruth Keogh [aut], Edouard F. Bonneville [aut], Lars van der Burg [aut], Claus Thorn Ekstrøm [ctb]

smcfcs_2.0.2.tar.gz
smcfcs_2.0.2.zip(r-4.7)smcfcs_2.0.2.zip(r-4.6)smcfcs_2.0.2.zip(r-4.5)
smcfcs_2.0.2.tgz(r-4.6-any)smcfcs_2.0.2.tgz(r-4.5-any)
smcfcs_2.0.2.tar.gz(r-4.7-any)smcfcs_2.0.2.tar.gz(r-4.6-any)
smcfcs_2.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
smcfcs/json (API)

# Install 'smcfcs' in R:
install.packages('smcfcs', repos = c('https://jwb133.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jwb133/smcfcs/issues

Datasets:
  • ex_cc - Simulated case cohort data
  • ex_coarsening - Simulated example data with a coarsened factor covariate
  • ex_compet - Simulated example data with competing risks outcome and partially observed covariates
  • ex_coxquad - Simulated example data with time to event outcome and quadratic covariate effects
  • ex_dtsam - Simulated discrete time survival data set
  • ex_finegray - Simulated example data with competing risks outcome and partially observed covariates
  • ex_flexsurv - Simulated example data with time-to-event Weibull outcome and two covariates
  • ex_lininter - Simulated example data with continuous outcome and interaction between two partially observed covariates
  • ex_linquad - Simulated example data with continuous outcome and quadratic covariate effects
  • ex_logisticquad - Simulated example data with binary outcome and quadratic covariate effects
  • ex_ncc - Simulated nested case-control data
  • ex_poisson - Simulated example data with count outcome, modelled using Poisson regression

On CRAN:

Conda:

9.00 score 14 stars 1 packages 83 scripts 4.0k downloads 8 mentions 7 exports 15 dependencies

Last updated from:789bbcdeec. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK163
source / vignettesOK207
linux-release-x86_64OK164
macos-release-arm64OK125
macos-oldrel-arm64OK101
windows-develOK114
windows-releaseOK94
windows-oldrelOK128
wasm-releaseOK144

Exports:smcfcssmcfcs.casecohortsmcfcs.dtsamsmcfcs.finegraysmcfcs.flexsurvsmcfcs.nestedccsmcfcs.parallel

Dependencies:abindbackportsbrglm2checkmateenrichwithlatticeMASSMatrixnleqslvnnetnumDerivrlangstatmodsurvivalVGAM

smcfcs
Introduction | Joint model and FCS multiple imputation | Imputation model compatibility | Substantive Model Compatible Fully Conditional Specification multiple imputation | Sampling from the imputation distribution | Statistical properties | When SMC-FCS may be preferable to FCS/MICE | The smcfcs package | Example - linear regression substantive model with quadratic covariate effects | Imputing using auxiliary variables with smcfcs | Rejection sampling warnings | Assessing convergence
Rendered fromsmcfcs-vignette.Rmdusingknitr::rmarkdown

Last update: 2025-03-18
Started: 2015-01-15

smcfcs for coarsened factor covariates
Rendered fromcoarsening.Rmdusingknitr::rmarkdown

Last update: 2025-03-18
Started: 2025-03-13

smcfcs for covariate measurement error correction
Validation data | Replication data | Multiple covariates measured with error
Rendered fromcoverror.Rmdusingknitr::rmarkdown

Last update: 2025-03-13
Started: 2025-03-13

Readme and manuals

Help Manual

Help pageTopics
Simulated case cohort dataex_cc
Simulated example data with a coarsened factor covariateex_coarsening
Simulated example data with competing risks outcome and partially observed covariatesex_compet
Simulated example data with time to event outcome and quadratic covariate effectsex_coxquad
Simulated discrete time survival data setex_dtsam
Simulated example data with competing risks outcome and partially observed covariatesex_finegray
Simulated example data with time-to-event Weibull outcome and two covariatesex_flexsurv
Simulated example data with continuous outcome and interaction between two partially observed covariatesex_lininter
Simulated example data with continuous outcome and quadratic covariate effectsex_linquad
Simulated example data with binary outcome and quadratic covariate effectsex_logisticquad
Simulated nested case-control dataex_ncc
Simulated example data with count outcome, modelled using Poisson regressionex_poisson
Assess convergence of a smcfcs objectplot.smcfcs
Substantive model compatible fully conditional specification imputation of covariates.smcfcs
Substantive model compatible fully conditional specification imputation of covariates for case cohort studiessmcfcs.casecohort
Substantive model compatible fully conditional specification imputation of covariates for discrete time survival analysissmcfcs.dtsam
Substantive model compatible fully conditional specification imputation of covariates for a Fine-Gray modelsmcfcs.finegray
Substantive model compatible fully conditional specification imputation of covariates and event times using flexible parametric survival modelssmcfcs.flexsurv
Substantive model compatible fully conditional specification imputation of covariates for nested case control studiessmcfcs.nestedcc
Parallel substantive model compatible imputationsmcfcs.parallel