{ "_id": "6a154175acfb0bcc41d55e1a", "Package": "saemix", "Title": "Stochastic Approximation Expectation Maximization (SAEM)\nAlgorithm", "Version": "3.5", "Authors@R": "c(\nperson(\"Emmanuelle\", \"Comets\", role = c(\"aut\", \"cre\"),\nemail = \"emmanuelle.comets@inserm.fr\"),\nperson(\"Audrey\", \"Lavenu\", role = \"aut\"),\nperson(\"Marc\", \"Lavielle\", role = \"aut\"),\nperson(\"Belhal\", \"Karimi\", role = \"aut\"),\nperson(\"Maud\", \"Delattre\", role = \"ctb\"),\nperson(\"Alexandra\", \"Lavalley-Morelle\", role = \"ctb\"),\nperson(\"Marilou\", \"Chanel\", role = \"ctb\"),\nperson(\"Johannes\", \"Ranke\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-4371-6538\")),\nperson(\"Sofia\", \"Kaisaridi\", role = \"ctb\"),\nperson(\"Lucie\", \"Fayette\", role = \"ctb\"))", "Description": "The 'saemix' package implements the Stochastic\nApproximation EM algorithm for parameter estimation in\n(non)linear mixed effects models. It (i) computes the maximum\nlikelihood estimator of the population parameters, without any\napproximation of the model (linearisation, quadrature\napproximation,...), using the Stochastic Approximation\nExpectation Maximization (SAEM) algorithm, (ii) provides\nstandard errors for the maximum likelihood estimator (iii)\nestimates the conditional modes, the conditional means and the\nconditional standard deviations of the individual parameters,\nusing the Hastings-Metropolis algorithm (see Comets et al.\n(2017) ). Many applications of SAEM\nin agronomy, animal breeding and PKPD analysis have been\npublished by members of the Monolix group. The full PDF\ndocumentation for the package including references about the\nalgorithm and examples can be downloaded on the github of the\nIAME research institute for 'saemix':\n.", "License": "GPL (>= 2)", "LazyLoad": "yes", "LazyData": "yes", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Collate": "'aaa_generics.R' 'SaemixData.R' 'SaemixData-methods.R'\n'SaemixData-methods_covariates.R' 'SaemixModel.R' 'SaemixRes.R'\n'SaemixObject.R' 'backward.R' 'compute_LL.R' 'forward.R'\n'func_FIM.R' 'func_aux.R' 'func_bootstrap.R' 'func_compare.R'\n'func_discreteVPC.R' 'func_distcond.R' 'func_estimParam.R'\n'func_exploreData.R' 'func_npde.R' 'func_plots.R'\n'func_simulations.R' 'func_stepwise.R' 'main.R' 'main_estep.R'\n'main_initialiseMainAlgo.R' 'main_mstep.R' 'stepwise.R' 'zzz.R'", "Packaged": { "Date": "2026-05-26 06:39:25 UTC", "User": "root" }, "Author": "Emmanuelle Comets [aut, cre], Audrey Lavenu [aut], Marc\nLavielle [aut], Belhal Karimi [aut], Maud Delattre [ctb],\nAlexandra Lavalley-Morelle [ctb], Marilou Chanel [ctb],\nJohannes Ranke [ctb] (ORCID:\n), Sofia Kaisaridi\n[ctb], Lucie Fayette [ctb]", "Maintainer": "Emmanuelle Comets ", "Repository": "https://ecomets.r-universe.dev", "Date/Publication": "2026-02-25 15:14:41 UTC", "RemoteUrl": "https://github.com/cran/saemix", "RemoteRef": "HEAD", "RemoteSha": "651c0eb246604331836537af7cc989d55fb0b05a", "MD5sum": "00f2f6700cd986edc1466ebeb9d45e2b", "_user": "ecomets", "_type": "src", "_file": "saemix_3.5.tar.gz", "_fileid": "50af726b116ed3637d9f6963846679d8b9e0e082c46d04f18303a710bcfe449c", "_filesize": 2979248, "_sha256": "50af726b116ed3637d9f6963846679d8b9e0e082c46d04f18303a710bcfe449c", "_created": "2026-05-26T06:39:25.000Z", "_published": "2026-05-26T06:45:09.000Z", "_distro": "noble", "_jobs": [ { "job": 77821066516, "time": 158, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7210522823" }, { "job": 77821066506, "time": 157, "config": "linux-release-x86_64", 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called by the user", "topics": [ "readSaemix,SaemixData", "readSaemix,SaemixData-method" ] }, { "page": "replaceData", "title": "Replace the data element in an SaemixObject object", "topics": [ "replaceData", "replaceData-methods", "replaceData.saemixObject" ] }, { "page": "resid.saemix", "title": "Extract Model Residuals", "topics": [ "resid", "resid.saemix", "resid.SaemixObject", "resid.SaemixRes", "residuals", "residuals.saemix", "residuals.SaemixObject", "residuals.SaemixRes" ] }, { "page": "saemix", "title": "Stochastic Approximation Expectation Maximization (SAEM) algorithm", "topics": [ "estep", "initialiseMainAlgo", "mstep", "saemix" ] }, { "page": "saemix.bootstrap", "title": "Bootstrap for saemix fits", "topics": [ "saemix.bootstrap" ] }, { "page": "saemix.plot.data", "title": "Functions implementing each type of plot in SAEM", "topics": [ "compute.eta.map", "compute.sres", "saemix.plot.convergence", "saemix.plot.correlations", "saemix.plot.data", "saemix.plot.distpsi", "saemix.plot.distribresiduals", "saemix.plot.fits", "saemix.plot.llis", "saemix.plot.mirror", "saemix.plot.npde", "saemix.plot.obsvspred", "saemix.plot.parcov", "saemix.plot.parcov.aux", "saemix.plot.randeff", "saemix.plot.randeffcov", "saemix.plot.scatterresiduals", "saemix.plot.vpc" ] }, { "page": "saemix.plot.select", "title": "Plots of the results obtained by SAEM", "topics": [ "saemix.plot.select" ] }, { "page": "saemix.plot.setoptions", "title": "Function setting the default options for the plots in SAEM", "topics": [ "replace.data.options", "replace.plot.options", "saemix.data.setoptions", "saemix.plot.setoptions" ] }, { "page": "saemix.predict", "title": "Compute model predictions after an saemix fit", "topics": [ "saemix.predict" ] }, { "page": "saemixControl", "title": "List of options for running the algorithm SAEM", "topics": [ "saemixControl" ] }, { "page": "saemixData", "title": "Function to create an SaemixData object", "topics": [ "saemixData" ] }, { "page": "SaemixData-class", "title": "Class \"SaemixData\"", "topics": [ "print,SaemixData", "SaemixData", "SaemixData-class", "SaemixRepData", "SaemixRepData-class", "SaemixSimData", "SaemixSimData-class", "show,SaemixData", "showall,SaemixData" ] }, { "page": "saemixModel", "title": "Function to create an SaemixModel object", "topics": [ "saemixModel" ] }, { "page": "SaemixModel-class", "title": "Class \"SaemixModel\"", "topics": [ "print,SaemixModel", "SaemixModel", "SaemixModel-class", "show,SaemixModel", "showall,SaemixModel", "summary,SaemixModel", "[<-,SaemixModel-method" ] }, { "page": "SaemixObject-class", "title": "Class \"SaemixObject\"", "topics": [ "predict,SaemixObject", "print,SaemixObject", "SaemixObject", "SaemixObject-class", "show,SaemixObject", "showall,SaemixObject", "summary,SaemixObject", "[<-,SaemixObject-method" ] }, { "page": "saemixPredictNewdata", "title": "Predictions for a new dataset", "topics": [ "estimateIndividualParametersNewdata", "estimateMeanParametersNewdata", "saemixPredictNewdata" ] }, { "page": "SaemixRes-class", "title": "Class \"SaemixRes\"", "topics": [ "plot,SaemixRes", "print,SaemixRes", "SaemixRes", "SaemixRes-class", "show,SaemixRes", "showall,SaemixRes" ] }, { "page": "show-methods", "title": "Methods for Function show", "topics": [ "show,SaemixData-method", "show,SaemixModel-method", "show,SaemixObject-method", "show,SaemixRepData-method", "show,SaemixRes-method", "show,SaemixSimData-method", "show-methods" ] }, { "page": "showall-methods", "title": "Methods for Function showall", "topics": [ "showall", "showall,SaemixData-method", "showall,SaemixModel-method", "showall,SaemixObject-method", "showall,SaemixRes-method", "showall-methods" ] }, { "page": "simulate.SaemixObject", "title": "Perform simulations under the model for an saemixObject object", "topics": [ "simul.saemix", "simulate.SaemixObject", "simulateContinuousSaemix", "simulateIndividualParameters" ] }, { "page": "simulateDiscreteSaemix", "title": "Perform simulations under the model for an saemixObject object defined by its log-likelihood", "topics": [ "simulateDiscreteSaemix", "simulateTTESaemix" ] }, { "page": "step.saemix", "title": "Stepwise procedure for joint selection of covariates and random effects", "topics": [ "step.saemix" ] }, { "page": "stepwise.procedure", "title": "Stepwise procedure for joint selection of covariates and random effects", "topics": [ "stepwise.procedure" ] }, { "page": "subset", "title": "Data subsetting", "topics": [ "subset", "subset-methods", "subset.SaemixData" ] }, { "page": "summary-methods", "title": "Methods for Function summary", "topics": [ "summary", "summary,ANY-method", "summary,SaemixData", "summary,SaemixData-method", "summary,SaemixModel-method", "summary,SaemixObject-method", "summary,SaemixRes-method", "summary-methods" ] }, { "page": "testnpde", "title": "Tests for normalised prediction distribution errors", "topics": [ "kurtosis", "skewness", "testnpde" ] }, { "page": "theo.saemix", "title": "Pharmacokinetics of theophylline", "topics": [ "theo.saemix" ] }, { "page": "toenail.saemix", "title": "Toenail data", "topics": [ "toenail.saemix" ] }, { "page": "transform", "title": "Transform covariates", "topics": [ "transform", "transform.numeric" ] }, { "page": "transformCatCov", "title": "Transform categorical covariates", "topics": [ "transformCatCov" ] }, { "page": "transformContCov", "title": "Transform continuous covariates", "topics": [ "transform.SaemixData", "transformContCov" ] }, { "page": "validate.covariance.model", "title": "Validate the structure of the covariance model", "topics": [ "validate.covariance.model" ] }, { "page": "validate.names", "title": "Name validation (## )Helper function not intended to be called by the user)", "topics": [ "validate.names" ] }, { "page": "vcov", "title": "Extracts the Variance-Covariance Matrix for a Fitted Model Object", "topics": [ "vcov", "vcov.SaemixObject", "vcov.SaemixRes" 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