Added the rmdhunks and roxygen code to use them.

R/nlmixr2.R

@@ -79,6 +79,9 @@ nlmixr2Version <- function() {
 #' @param envir Environment where the nlmixr object/function is
 #'   evaluated before running the estimation routine.
 #' @return Either a nlmixr2 model or a nlmixr2 fit object
+#' 
+#' @includeRmd man/rmdhunks/nlmixr2Keywords.Rmd
+#' 
 #' @author Matthew L. Fidler
 #' @examples
 #'

data-raw/nlmixr2_object.csv

@@ -1,42 +1,42 @@
-Field,Description,
-conditionNumber,"Condition number, that is the highest divided by the lowest eigenvalue in the population covariance matrix",
-cor,Correlation matrix,
-phiR,correlation matrix of each individual's eta (if present),
-objDF,"Data frame containing objective function information (AIC, BIC, etc.)",
-time,"Duration of different parts of the analysis (e.g. setup, optimization, calculation of covariance, etc.)","(TIME is the time in the dataset, so be careful with the case one this one)"
-theta,Estimates for eta for each individual,Are fixef and theta the same?
-etaObf,"Estimates for eta for each individual, This also includes the objective function for each individual",
-fixef,Estimates of fixed effects,
-foceiControl,Estimation options if focei was used,This is also the translated foceiControl options for an other method; the output option is generated by the focei step
-ui,Final estimates for the model,alias = finalUi
-dataMergeFull,Full data merge with the fit output and the original dataset; Also includes nlmixrLlikObs which includes the individual observation contribution to the likelihood,
-censInfo,Gives the censorng information abot the fit (the type of censoring that was seend and handled in the dataset),
-dataLloq,Gives the lloq from the dataset (average) when cesoring has occured; Requires the fit to have a table step,
-dataUloq,Gives the uloq from the dataset (average) when censoring has occured; requires the fit to have a table step,
-eta,IIV values for each indiviudal ,
-dataMergeInner,Inner data merge with the fit output and the original dataset; Also includes nlmixrLlikObs which includes the individual observation contribution to the likelihood,
-rxControl,Integration options used to control rxode2,
-dataMergeLeft,Left data merge with the fit output and the original dataset; Also includes nlmixrLlikObs which includes the individual observation contribution to the likelihood,
-omega,Matrix containing the estimates of the multivarte normal covariance matrix for between subject varaibilities (omega),
-covMethod,Method used to calculate covariance of the fixed effects,
-modelName,Name of the R object containing the model,
-origData,Original dataset ,
-phiRSE,Relative standard error of each individuals eta,
-dataMergeRight,Right data merge with the fit output and the original dataset; Also includes nlmixrLlikObs which includes the individual observation contribution to the likelihood,
-ipredModel,rxode2 estimation model for fit (internal will likely be removed from visibility,
-phiSE,Standard error of each individuals eta,
-parFixed,Table of parameter estimates (rounded and pretty looking),
-parFixedDF,Table of parameter estimates as a data frame,
-omegaR,The correlation matirx of omega with standard deviations for the diagonal pieces,
-iniUi,The initial model used to start the estimation,
-finalUi,The model with the estimates replaced as values,(alias is $ui)
-scaleInfo,"The scaling factors used for nlmixr2 estimation in focei; The can be changed by foceiControl(scaleC=...) if you think these are unreasonable.  It also tells the Gill83 outcome of trying to find the best step size (High gradient error, bad gradient etc)",
-table,"These are the table options that were used when generating the table output (were CWRES included, etc",
-shrink,This is a table of shrinkages for all the individual ETAs as well as the variance shrinkage as well as summary statistics for the ETAs and Residual Error,
-env,This is the environment where all the information for the fit is stored outside of the data-frame.  It is an R environment hence $env,
-seed,This is the initial seed used for saem,
-simInfo,"This returns a list of all the fit information used for a traditional rxode2 simulation, which you can tweak yourself if you wish",
-runInfo,This returns a list of all the warnings or fit information,Alais $warnings
-parHistStacked,Value of objective function and parameters at each iteration (tall format),
-parHist ,Value of objective function and parameters at each iteration (wide format),
-cov,Variance-covariance matrix,
+Field,Description
+conditionNumber,"Condition number, that is the highest divided by the lowest eigenvalue in the population covariance matrix"
+cor,Correlation matrix
+phiR,correlation matrix of each individual's eta (if present)
+objDF,"Data frame containing objective function information (AIC, BIC, etc.)"
+time,"Duration of different parts of the analysis (e.g. setup, optimization, calculation of covariance, etc.)"
+theta,Estimates for eta for each individual
+etaObf,"Estimates for eta for each individual, This also includes the objective function for each individual"
+fixef,Estimates of fixed effects
+foceiControl,Estimation options if focei was used
+ui,Final estimates for the model
+dataMergeFull,Full data merge with the fit output and the original dataset; Also includes nlmixrLlikObs which includes the individual observation contribution to the likelihood
+censInfo,Gives the censorng information abot the fit (the type of censoring that was seend and handled in the dataset)
+dataLloq,Gives the lloq from the dataset (average) when cesoring has occured; Requires the fit to have a table step
+dataUloq,Gives the uloq from the dataset (average) when censoring has occured; requires the fit to have a table step
+eta,IIV values for each indiviudal 
+dataMergeInner,Inner data merge with the fit output and the original dataset; Also includes nlmixrLlikObs which includes the individual observation contribution to the likelihood
+rxControl,Integration options used to control rxode2
+dataMergeLeft,Left data merge with the fit output and the original dataset; Also includes nlmixrLlikObs which includes the individual observation contribution to the likelihood
+omega,Matrix containing the estimates of the multivarte normal covariance matrix for between subject varaibilities (omega)
+covMethod,Method used to calculate covariance of the fixed effects
+modelName,Name of the R object containing the model
+origData,Original dataset 
+phiRSE,Relative standard error of each individuals eta
+dataMergeRight,Right data merge with the fit output and the original dataset; Also includes nlmixrLlikObs which includes the individual observation contribution to the likelihood
+ipredModel,rxode2 estimation model for fit (internal will likely be removed from visibility
+phiSE,Standard error of each individuals eta
+parFixed,Table of parameter estimates (rounded and pretty looking)
+parFixedDF,Table of parameter estimates as a data frame
+omegaR,The correlation matirx of omega with standard deviations for the diagonal pieces
+iniUi,The initial model used to start the estimation
+finalUi,The model with the estimates replaced as values
+scaleInfo,"The scaling factors used for nlmixr2 estimation in focei; The can be changed by foceiControl(scaleC=...) if you think these are unreasonable.  It also tells the Gill83 outcome of trying to find the best step size (High gradient error, bad gradient etc)"
+table,"These are the table options that were used when generating the table output (were CWRES included, etc"
+shrink,This is a table of shrinkages for all the individual ETAs as well as the variance shrinkage as well as summary statistics for the ETAs and Residual Error
+env,This is the environment where all the information for the fit is stored outside of the data-frame.  It is an R environment hence $env
+seed,This is the initial seed used for saem
+simInfo,"This returns a list of all the fit information used for a traditional rxode2 simulation, which you can tweak yourself if you wish"
+runInfo,This returns a list of all the warnings or fit information
+parHistStacked,Value of objective function and parameters at each iteration (tall format)
+parHist ,Value of objective function and parameters at each iteration (wide format)
+cov,Variance-covariance matrix

data-raw/nlmixr2_object_add.R

@@ -1,3 +1,3 @@
 library(usethis)
 nlmixr2Keywords <- read.csv("nlmixr2_object.csv");
-usethis::use_data(nlmixr2Keywords)
+usethis::use_data(nlmixr2Keywords, overwrite=TRUE)

man/rmdhunks/nlmixr2Keywords.Rmd

@@ -0,0 +1,5 @@
+The nlmixr object has the following fields:
+
+```{r echo=FALSE}
+knitr::kable(nlmixr2Keywords)
+```