Package: smcfcs 1.8.0

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], Claus Thorn Ekstrøm [ctb]

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smcfcs.pdf |smcfcs.html✨
smcfcs/json (API)

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

Peer review:

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

Datasets:
  • ex_cc - Simulated case cohort data
  • 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_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:

6 exports 11 stars 2.85 score 13 dependencies 1 dependents 8 mentions 55 scripts 1.8k downloads

Last updated 4 months agofrom:61901f867d. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 02 2024
R-4.5-winNOTESep 02 2024
R-4.5-linuxNOTESep 02 2024
R-4.4-winNOTESep 02 2024
R-4.4-macNOTESep 02 2024
R-4.3-winNOTESep 02 2024
R-4.3-macNOTESep 02 2024

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

Dependencies:abindbackportsbrglm2checkmateenrichwithlatticeMASSMatrixnnetnumDerivrlangsurvivalVGAM

smcfcs

Jonathan Bartlett

Rendered fromsmcfcs-vignette.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2024-06-04
Started: 2015-01-15

smcfcs for covariate measurement error correction

Jonathan Bartlett

Rendered fromsmcfcs_coverror-vignette.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2024-06-04
Started: 2019-03-22

Readme and manuals

Help Manual

Help pageTopics
Simulated case cohort dataex_cc
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 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 for nested case control studiessmcfcs.nestedcc
Parallel substantive model compatible imputationsmcfcs.parallel