version 24.3.25

DESCRIPTION

@@ -2,7 +2,7 @@ Package: INLAjoint
 Type: Package
 Title: Multivariate Joint Modeling for Longitudinal and Time-to-Event
         Outcomes with 'INLA'
-Version: 24.2.4
+Version: 24.3.25
 Authors@R: c(
     person("Denis", "Rustand", email = "INLAjoint@gmail.com", 
         role = c("cre", "aut"),
@@ -24,18 +24,19 @@ BugReports: https://github.com/DenisRustand/INLAjoint/issues
 Encoding: UTF-8
 LazyData: true
 Depends: R (>= 3.6), utils, stats
-Imports: numDeriv, lme4, ggplot2, methods, Matrix
+Imports: numDeriv, lme4, ggplot2, methods, Matrix, nlme, mvtnorm
 Additional_repositories: https://inla.r-inla-download.org/R/testing
-RoxygenNote: 7.2.3
-Suggests: INLA, knitr, rmarkdown, splines, graphics, grDevices, R.rsp
+RoxygenNote: 7.3.1
+Suggests: INLA, knitr, rmarkdown, splines, graphics, grDevices, R.rsp,
+        survival, JMbayes2, rstanarm, frailtypack, smcure
 BuildVignettes: true
 VignetteBuilder: R.rsp
 Maintainer: Denis Rustand <INLAjoint@gmail.com>
 NeedsCompilation: no
-Packaged: 2024-02-04 08:26:40 UTC; dr
+Packaged: 2024-03-25 08:20:45 UTC; dr
 Author: Denis Rustand [cre, aut] (<https://orcid.org/0000-0001-9708-5220>),
   Elias Teixeira Krainski [aut] (<https://orcid.org/0000-0002-7063-2615>),
   Haavard Rue [aut] (<https://orcid.org/0000-0002-0222-1881>),
   Janet van Niekerk [aut] (<https://orcid.org/0000-0002-4334-2057>)
 Repository: CRAN
-Date/Publication: 2024-02-04 11:30:06 UTC
+Date/Publication: 2024-03-25 19:50:02 UTC

MD5

@@ -1,43 +1,64 @@
-f8fa5557b7a30a4bb0fba0a559164e6b *DESCRIPTION
-691b869d4d9adbeab8b5e25d5bbd453e *NAMESPACE
-93dcba9c920f6dfc023cc5955918995d *R/INLAjoint.R
-21e027bad13804187d99ae14932c9a58 *R/INLAjoint.object.R
-df7ecef15ec0a4d439faada441e0d656 *R/Long.R
+0024819970717a87a54bbde4901d0df0 *DESCRIPTION
+e6e192cee4dfdd3237057f92d37ac457 *NAMESPACE
+e87abe7bb9bead6bd6ffa0ab4df6e1b6 *R/INLAjoint.R
+af5a94fc4b44e69bd727821d67043423 *R/INLAjoint.object.R
 af146bd1fe869d7e1688305932f51855 *R/LongMS.R
-ffc4d6b39d824c8bd06a6bf2b1370160 *R/Surv.R
+3226228f418cfebdae2238906c4e3e3b *R/Longsim.R
 a1cd2c8308deb214a786964d1f277b86 *R/SurvMS.R
-5f63e7220da5837112b8d5065598e558 *R/joint.R
+d96fbdec2d94ea44108a8ae3769e2bbf *R/Survsim.R
+fb92a29f90cea91c1bf62961a6372a4b *R/coef.INLAjoint.R
+7808a64e4737202f120d8fe78c4a733e *R/family.INLAjoint.R
+b530b2f48c61324037b8193fdd45a627 *R/fitted.INLAjoint.R
+81441f864e8b83894b5eeb3a6656df44 *R/fixef.INLAjoint.R
+a59472d3821558332b9ce788c411ab4b *R/formula.INLAjoint.R
+3299d29ed77eb9cd20c822bf2b272e77 *R/joint.R
 ef5f512cb9d831bd3202b080ade79fdb *R/joint.rerun.R
-923637a7d129c28892a1a379ebaab570 *R/plot.INLAjoint.R
-3d42997b7e9f31f362a4f7c7c75b48a0 *R/predict.INLAjoint.R
-6a74f214c8c6c5f34b2451b9a6dd758a *R/print.INLAjoint.R
+19248cb0be4ced08f207f6cf1dbea1f6 *R/logLik.INLAjoint.R
+f80616ba9238b3ecc5f89b85038d4fe0 *R/nobs.INLAjoint.R
+1c7a1c17a3cae7c609ecc1df37943b5e *R/plot.INLAjoint.R
+b28c62e7a1e97b8c384da582cbc5329d *R/predict.INLAjoint.R
+bfdc0ac0d1c9e45959c752e3c598205c *R/print.INLAjoint.R
+7e9e5299096a276cd2451ac3ac632abf *R/print.plot.INLAjoint.R
 27da5bd1c6b5ea73181f752f2447a1fb *R/print.summary.INLAjoint.R
-bc018df9c34a92d1da31400a891b2ddf *R/priors.used.R
-0032549b4e0daa4f52b867875cdfbab1 *R/setupFonctions.R
-8797279037cd8f4e670b25807c90df52 *R/summary.INLAjoint.R
+a77d47d03d397b7ecfb9ec4ba892bd0b *R/ranef.INLAjoint.R
+d19dff023c5991fa7b9b7ca8812e20f1 *R/setupFonctions.R
+b7f75540ce9ed7643098a946a34b914a *R/summary.INLAjoint.R
 1a26dbd399d695c749b83355f75f74da *R/zzz.R
-6e3e5a2bbbf227d9fb3ea1f78a7ed5cf *README.md
-6f16682a7369682d5b76e03957a713f9 *build/vignette.rds
-6af0c18c4fba79580c32357fba3349e3 *data/Long.RData
+0d392216e2a12fe512b450d87cb03395 *README.md
+1f840d027d39dcaad94c12b7d37f1e39 *build/vignette.rds
 43765ba9ca3e5cb9f339b81c3277e720 *data/LongMS.RData
-27f1fbc94a5c0a77eca3db79a42fb70d *data/Surv.RData
+1defc23b0ba5826b1e2354ef53392733 *data/Longsim.RData
 e1f25fe275136fa60827f03ccb3b8cf8 *data/SurvMS.RData
+5f2cb91231bd7c719a351a9135194260 *data/Survsim.RData
 3a5b15390022c51e1e2f932fb0953d4c *inst/CITATION
-a1522831209570de2724d5b5219d8bc6 *inst/doc/INLAjoint.pdf
+3fecba890bbdaf695a813cb17e5a2c8a *inst/doc/INLAjoint.pdf
 dcdacf5c9841484e6defa5380b731e81 *inst/doc/INLAjoint.pdf.asis
-d57fb6ec5d6bacf287aad11fb8e1f28e *man/INLAjoint.Rd
-0408f6752e4b3c9d47d206e46470896e *man/INLAjoint.object.Rd
-9febe1e66f54b24ae4bd8cefc8aafb92 *man/Long.Rd
+ce410e59c252cf9bdca61e8591bed93a *man/INLAjoint.Rd
+3449d51e7a9ffd6d21cb932927e048a9 *man/INLAjoint.ginv.Rd
+f81c2a22cdbae70506d02f55c9e1af7d *man/INLAjoint.object.Rd
+447027c837f9705ccdc4ab1bd914d070 *man/INLAjoint.rw.Rd
+50a748b007bb4b5e0adbaa930c525f15 *man/INLAjoint.rw2.Rd
+9c5bd37d67fbe1a5e738352760520bee *man/INLAjoint.scopy.define.Rd
 c5d52e9c31477cfc93eca23b6a7f0215 *man/LongMS.Rd
-3a65f53aaee7e1ff5c825ae7188d9b97 *man/Surv.Rd
+e49bfa62a801a33409931cdf633b5a03 *man/Longsim.Rd
 c42360f8c8c5a61d7a18e45311b5eb6f *man/SurvMS.Rd
-86c4c74aa5be69fc5eff697164aac5b3 *man/joint.Rd
+5c137bc76d8a6b417aa9f44b0c7671be *man/Survsim.Rd
+ded14fc63c06e786a9d0dedb8ed77826 *man/coef.INLAjoint.Rd
+516032e488ed7eef61195eb21d85bb88 *man/family.INLAjoint.Rd
+bfdd10ca4312f15ad559bc82d84374fb *man/fitted.INLAjoint.Rd
+64dd898299e66683e80bbc8ab76417d6 *man/fixef.INLAjoint.Rd
+2e3bb2bdd9e5e58024faefe6a9368fc7 *man/formula.INLAjoint.Rd
+876714bec890e201a18fd67f77cdd90f *man/joint.Rd
 d77f56002f98cab9179f1502d1fa66fd *man/joint.rerun.Rd
+cabf34db3c560016f3d3d431b6adf6c4 *man/logLik.INLAjoint.Rd
+0a153d08ce7c7ef69c8b67e9a1168418 *man/nobs.INLAjoint.Rd
 f9d30faf45dd1976215cc84487c03d46 *man/plot.INLAjoint.Rd
-cd990675ed41473066f5d899f4b2a996 *man/priors.used.Rd
+a7482c94c853f2fcc7a7665f826898b1 *man/predict.INLAjoint.Rd
+fba00c06d66840f2884f412681bd2c5e *man/print.plot.INLAjoint.Rd
+2770352767ad4cd1c49354cab1cfe6de *man/ranef.INLAjoint.Rd
 1b28e67718b7bdf174eb1e568e53b3cc *man/setup_FE_model.Rd
 46e86834ea16b38cc86757095f77565a *man/setup_RE_model.Rd
 89171c3aa65a6f5d1d417fa7b755f62f *man/setup_S_model.Rd
 fcf10d59f5c52f516888994a1917fc09 *man/setup_Y_model.Rd
-d70db68fb30c3d9048c8472a64a4aa95 *vignettes/INLAjoint.Rmd
+434f33703577de5562646c5765b2fb3c *vignettes/INLAjoint.Rmd
 dcdacf5c9841484e6defa5380b731e81 *vignettes/INLAjoint.pdf.asis

NAMESPACE

@@ -1,23 +1,37 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(coef,INLAjoint)
+S3method(family,INLAjoint)
+S3method(fitted,INLAjoint)
+S3method(fixef,INLAjoint)
+S3method(formula,INLAjoint)
+S3method(logLik,INLAjoint)
+S3method(nobs,INLAjoint)
 S3method(plot,INLAjoint)
 S3method(predict,INLAjoint)
 S3method(print,INLAjoint)
+S3method(print,plot.INLAjoint)
 S3method(print,summary.INLAjoint)
+S3method(ranef,INLAjoint)
 S3method(summary,INLAjoint)
+export(INLAjoint)
 export(joint)
 export(joint.rerun)
-export(priors.used)
 export(setup_S_model)
 import(ggplot2)
 import(stats)
 import(utils)
 importFrom(Matrix,Diagonal)
 importFrom(Matrix,bdiag)
+importFrom(grDevices,dev.flush)
+importFrom(grDevices,dev.interactive)
 importFrom(grDevices,dev.new)
+importFrom(grDevices,devAskNewPage)
 importFrom(lme4,findbars)
 importFrom(lme4,nobars)
 importFrom(lme4,subbars)
 importFrom(methods,new)
+importFrom(nlme,fixef)
+importFrom(nlme,ranef)
 importFrom(numDeriv,grad)
 importFrom(splines,ns)

R/INLAjoint.R

@@ -11,9 +11,10 @@
 #'
 #' Contact: \email{INLAjoint@gmail.com}
 #'
-#' @docType package
 #' @name INLAjoint
+#' @export
+
 INLAjoint <- function() {
   message("Welcome to the INLAjoint package!")
-  #utils::browseVignettes("INLAjoint")
+  utils::vignette("INLAjoint")
 }

R/INLAjoint.object.R

@@ -19,7 +19,7 @@
 #'   \item{\code{mlik}}{log marginal-likelihood.}
 #'   \item{\code{cpo}}{Conditional Predictive Ordinate.}
 #'   \item{\code{gcpo}}{Group-Conditional Predictive Ordinate.}
-#'   \item{\code{po}}{.}
+#'   \item{\code{po}}{Predictive ordinate.}
 #'   \item{\code{waic}}{Widely applicable Bayesian information criterion}
 #'   \item{\code{model.random}}{a vector with the name of the random parameters of
 #'   the model, possibly including the following components: \describe{
@@ -59,7 +59,37 @@
 #'   \item{\code{all.hyper}}{.}
 #'   \item{\code{.args}}{.}
 #'   \item{\code{call}}{INLA call.}
+#'   \item{\code{selection}}{information about parameters for sampling with inla.rjmarginal.}
+#'   \item{\code{cureVar}}{informations about cure fraction submodel for mixture cure survival models.}
+#'   \item{\code{variant}}{information about variant for Weibull baseline hazards.}
+#'   \item{\code{SurvInfo}}{some information about survival submodels (names of event
+#'   indicator and event time variables as well as baseline hazard).}
 #'   \item{\code{famLongi}}{list of distributions for the longitudinal markers.}
+#'   \item{\code{corLong}}{boolean indicating if random effects are correlated accross markers.}
+#'   \item{\code{control.link}}{informations about link function (1=default).}
+#'   \item{\code{longOutcome}}{name of longitudinal outcomes.}
+#'   \item{\code{survOutcome}}{name of survival outcomes.}
+#'   \item{\code{assoc}}{vector with names of all association parameters (longi-surv).}
+#'   \item{\code{id}}{name of the id variable.}
+#'   \item{\code{timeVar}}{name of time variable.}
+#'   \item{\code{range}}{information about range of X-axis values for non-linear associations.}
 #'   \item{\code{REstruc}}{names of the grouped random effects for the longitudinal markers.}
+#'   \item{\code{mat_k}}{contains the list of random effects covariance matrices when they are
+#'   fixed as they are not part of the estimated parameters (used for displaying them in summary).}
+#'   \item{\code{fixRE}}{list of the size of number of groups of random effects, each element is a
+#'   boolean indicating if the random effects of the group is fixed (TRUE) or estimated (FALSE).}
+#'   \item{\code{lonFacChar}}{list of factors and character covariates included in the longitudinal
+#'   submodels to keep track of modalities (used internally when doing predictions to reconstruct
+#'   categorical covariates).}
+#'   \item{\code{survFacChar}}{same as lonFacChar but for survival submodels.}
+#'   \item{\code{corRE}}{list indicating if groups of random effects are correlated within
+#'   longitudinal submodels.}
+#'   \item{\code{basRisk}}{list of the baseline risk used for each survival submodel.}
+#'   \item{\code{priors_used}}{informations about priors used in the model, internally used
+#'   to display priors in plots (with argument priors=TRUE in the call of the plot function).
+#'   Note that priors can also be displayed with the function priors.used() applied to an
+#'   INLAjoint object.}
+#'   \item{\code{dataLong}}{name of the longitudinal dataset.}
+#'   \item{\code{dataSurv}}{name of the survival dataset.}
 #'   }
 "INLAjoint.object" <- NULL

R/Long.R → R/Longsim.R

@@ -1,8 +1,8 @@
 #' Simulated multivariate longitudinal dataset
 #'
-#'  A simulated dataset used to illustrate some models (e.g., example of joint() function in the documentation). The corresponding survival dataset is named 'Surv'.
+#'  A simulated dataset used to illustrate some models (e.g., example of joint() function in the documentation). The corresponding survival dataset is named 'Survsim'.
 #'
-#' @format ## `Long`
+#' @format ## `Longsim`
 #' A data frame with 96 rows and 7 columns:
 #' \describe{
 #'   \item{Id}{Individual id}
@@ -12,4 +12,4 @@
 #'   \item{Y1, Y2, Y3}{Gaussian Longitudinal outcomes}
 #'   ...
 #' }
-"Long"
+"Longsim"

R/Surv.R → R/Survsim.R

@@ -1,8 +1,8 @@
 #' Simulated competing risks survival dataset
 #'
-#'  A simulated dataset used to illustrate some models (e.g., example of joint() function in the documentation). The corresponding longitudinal dataset is named 'Long'.
+#'  A simulated dataset used to illustrate some models (e.g., example of joint() function in the documentation). The corresponding longitudinal dataset is named 'Longsim'.
 #'
-#' @format ## `Surv`
+#' @format ## `Survsim`
 #' A data frame with 15 rows and 5 columns:
 #' \describe{
 #'   \item{Id}{Individual id}
@@ -12,4 +12,4 @@
 #'   \item{Event1, Event2, Event3}{Event indicator for the 3 competing risks (individual is censored when the 3 events are 0)}
 #'   ...
 #' }
-"Surv"
+"Survsim"

R/coef.INLAjoint.R

@@ -0,0 +1,24 @@
+#' Extracts model coefficients from a given model fitted with INLAjoint
+#'
+#' @description This function extracts model coefficients from INLAjoint objects.
+#'
+#' @param object an object that contains a model fitted with INLAjoint.
+#' @param ... Extra arguments.
+#'
+#' @export
+
+coef.INLAjoint <- function(object, ...){
+  arguments <- list(...)
+  FEF <- object$summary.fixed
+  HYP <- object$summary.hyperpar
+  OUtc <- list("Fixed_effects" = FEF, "Hyperparameters" = HYP)
+  return(OUtc)
+}
+
+
+
+
+
+
+
+

R/family.INLAjoint.R

@@ -0,0 +1,31 @@
+#' Extracts family from a given model fitted with INLAjoint
+#'
+#' @description This function extracts family from INLAjoint objects.
+#'
+#' @param object an object that contains a model fitted with INLAjoint.
+#' @param ... Extra arguments.
+#'
+#' @export
+
+family.INLAjoint <- function(object, ...){
+  arguments <- list(...)
+  if(!is.null(object$formLong)){
+    Long <- object$famLongi
+  }else{
+    Long <- NULL
+  }
+  if(!is.null(object$formSurv)){
+    Surv <- unlist(object$basRisk)
+  }else{
+    Surv <- NULL
+  }
+  return(list("Longitudinal" = Long, "Survival" = Surv))
+}
+
+
+
+
+
+
+
+

R/fitted.INLAjoint.R

@@ -0,0 +1,25 @@
+#' Extracts fitted values from a given model fitted with INLAjoint
+#'
+#' @description This function extracts fitted values from INLAjoint objects.
+#' Values are associated to a name to keep track of the outcome related to each fitted value.
+#'
+#' @param object an object that contains a model fitted with INLAjoint.
+#' @param ... Extra arguments.
+#'
+#' @export
+
+fitted.INLAjoint <- function(object, ...){
+  arguments <- list(...)
+  PRED <- object$summary.fitted.values$mean
+    OUtc <- as.data.frame(object$.args$data$Yjoint)
+    names(PRED) <- sapply(1:length(PRED), function(x) colnames(OUtc)[which(!is.na(OUtc[x,]))])
+    return(PRED)
+}
+
+
+
+
+
+
+
+