From 48c463680b51fa767b4cd7bd62865f192d0354ac Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 6 Feb 2021 18:30:32 +0100 Subject: Reintroduce interface to saemix Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed. --- NAMESPACE | 8 ++++++++ 1 file changed, 8 insertions(+) (limited to 'NAMESPACE') diff --git a/NAMESPACE b/NAMESPACE index 9776d2f3..f2497283 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -30,11 +30,15 @@ S3method(print,mkinmod) S3method(print,mmkin) S3method(print,nafta) S3method(print,nlme.mmkin) +S3method(print,saem.mmkin) S3method(print,summary.mkinfit) S3method(print,summary.nlme.mmkin) +S3method(print,summary.saem.mmkin) S3method(residuals,mkinfit) +S3method(saem,mmkin) S3method(summary,mkinfit) S3method(summary,nlme.mmkin) +S3method(summary,saem.mmkin) S3method(update,mkinfit) S3method(update,mmkin) S3method(update,nlme.mmkin) @@ -86,6 +90,9 @@ export(parms) export(plot_err) export(plot_res) export(plot_sep) +export(saem) +export(saemix_data) +export(saemix_model) export(sigma_twocomp) export(transform_odeparms) import(deSolve) @@ -126,5 +133,6 @@ importFrom(stats,residuals) importFrom(stats,rnorm) importFrom(stats,shapiro.test) importFrom(stats,update) +importFrom(stats,vcov) importFrom(utils,getFromNamespace) importFrom(utils,write.table) -- cgit v1.2.1 From c6eb6b2bb598002523c3d34d71b0e4a99671ccd6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 9 Jun 2021 16:53:31 +0200 Subject: Rudimentary support for setting up nlmixr models - All degradation models are specified as ODE models. This appears to be fast enough - Error models are being translated to nlmixr as close to the mkin error model as possible. When using the 'saem' backend, it appears not to be possible to use the same error model for more than one observed variable - No support yet for models with parallel formation of metabolites, where the ilr transformation is used in mkin per default - There is a bug in nlmixr which appears to be triggered if the data are not balanced, see nlmixrdevelopment/nlmixr#530 - There is a print and a plot method, the summary method is not finished --- NAMESPACE | 8 ++++++++ 1 file changed, 8 insertions(+) (limited to 'NAMESPACE') diff --git a/NAMESPACE b/NAMESPACE index f2497283..bb4f5f92 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -16,6 +16,7 @@ S3method(mixed,mmkin) S3method(mkinpredict,mkinfit) S3method(mkinpredict,mkinmod) S3method(nlme,mmkin) +S3method(nlmixr,mmkin) S3method(nobs,mkinfit) S3method(parms,mkinfit) S3method(parms,mmkin) @@ -30,6 +31,7 @@ S3method(print,mkinmod) S3method(print,mmkin) S3method(print,nafta) S3method(print,nlme.mmkin) +S3method(print,nlmixr.mmkin) S3method(print,saem.mmkin) S3method(print,summary.mkinfit) S3method(print,summary.nlme.mmkin) @@ -38,6 +40,7 @@ S3method(residuals,mkinfit) S3method(saem,mmkin) S3method(summary,mkinfit) S3method(summary,nlme.mmkin) +S3method(summary,nlmixr.mmkin) S3method(summary,saem.mmkin) S3method(update,mkinfit) S3method(update,mmkin) @@ -86,6 +89,8 @@ export(nafta) export(nlme) export(nlme_data) export(nlme_function) +export(nlmixr_data) +export(nlmixr_model) export(parms) export(plot_err) export(plot_res) @@ -102,6 +107,8 @@ importFrom(R6,R6Class) importFrom(grDevices,dev.cur) importFrom(lmtest,lrtest) importFrom(methods,signature) +importFrom(nlmixr,nlmixr) +importFrom(nlmixr,tableControl) importFrom(parallel,detectCores) importFrom(parallel,mclapply) importFrom(parallel,parLapply) @@ -135,4 +142,5 @@ importFrom(stats,shapiro.test) importFrom(stats,update) importFrom(stats,vcov) importFrom(utils,getFromNamespace) +importFrom(utils,packageVersion) importFrom(utils,write.table) -- cgit v1.2.1 From 0c9b2f0e3c8ce65cb790c9e048476784cbbea070 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 11 Jun 2021 11:14:45 +0200 Subject: Finished 'summary.nlmixr.mmkin', checks, docs --- NAMESPACE | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'NAMESPACE') diff --git a/NAMESPACE b/NAMESPACE index bb4f5f92..0f61396d 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -35,6 +35,7 @@ S3method(print,nlmixr.mmkin) S3method(print,saem.mmkin) S3method(print,summary.mkinfit) S3method(print,summary.nlme.mmkin) +S3method(print,summary.nlmixr.mmkin) S3method(print,summary.saem.mmkin) S3method(residuals,mkinfit) S3method(saem,mmkin) @@ -89,6 +90,7 @@ export(nafta) export(nlme) export(nlme_data) export(nlme_function) +export(nlmixr) export(nlmixr_data) export(nlmixr_model) export(parms) @@ -104,6 +106,7 @@ import(deSolve) import(graphics) import(nlme) importFrom(R6,R6Class) +importFrom(dplyr,"%>%") importFrom(grDevices,dev.cur) importFrom(lmtest,lrtest) importFrom(methods,signature) @@ -119,6 +122,7 @@ importFrom(stats,aggregate) importFrom(stats,as.formula) importFrom(stats,coef) importFrom(stats,coefficients) +importFrom(stats,confint) importFrom(stats,cov2cor) importFrom(stats,dist) importFrom(stats,dnorm) @@ -138,6 +142,7 @@ importFrom(stats,qnorm) importFrom(stats,qt) importFrom(stats,residuals) importFrom(stats,rnorm) +importFrom(stats,sd) importFrom(stats,shapiro.test) importFrom(stats,update) importFrom(stats,vcov) -- cgit v1.2.1 From 05baf3bf92cba127fd2319b779db78be86170e5e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Jun 2021 13:58:34 +0200 Subject: Let backtransform_odeparms handle nlmixr formation fractions Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr --- NAMESPACE | 2 ++ 1 file changed, 2 insertions(+) (limited to 'NAMESPACE') diff --git a/NAMESPACE b/NAMESPACE index 0f61396d..aa40b570 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -62,6 +62,7 @@ export(f_time_norm_focus) export(get_deg_func) export(ilr) export(invilr) +export(invtffm0) export(loftest) export(logistic.solution) export(lrtest) @@ -101,6 +102,7 @@ export(saem) export(saemix_data) export(saemix_model) export(sigma_twocomp) +export(tffm0) export(transform_odeparms) import(deSolve) import(graphics) -- cgit v1.2.1 From 5c15ef747568b3a9a9c094b6aa546dc80e3aa87a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 27 Sep 2021 20:10:01 +0200 Subject: intervals() methods, more DFOP/tc variants --- NAMESPACE | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'NAMESPACE') diff --git a/NAMESPACE b/NAMESPACE index aa40b570..aa3899ac 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -8,6 +8,8 @@ S3method(aw,mmkin) S3method(confint,mkinfit) S3method(f_time_norm_focus,mkindsg) S3method(f_time_norm_focus,numeric) +S3method(intervals,nlmixr.mmkin) +S3method(intervals,saem.mmkin) S3method(loftest,mkinfit) S3method(logLik,mkinfit) S3method(lrtest,mkinfit) @@ -61,6 +63,7 @@ export(endpoints) export(f_time_norm_focus) export(get_deg_func) export(ilr) +export(intervals) export(invilr) export(invtffm0) export(loftest) @@ -112,6 +115,7 @@ importFrom(dplyr,"%>%") importFrom(grDevices,dev.cur) importFrom(lmtest,lrtest) importFrom(methods,signature) +importFrom(nlme,intervals) importFrom(nlmixr,nlmixr) importFrom(nlmixr,tableControl) importFrom(parallel,detectCores) -- cgit v1.2.1