inst/doc/so.R

In libsoc: Read, Create and Write 'PharmML' Standard Output (so) XML Files

## ----read_so------------------------------------------------------------------
filename <- system.file("extdata", "pheno.SO.xml",  package="libsoc")
so <- libsoc::so_SO_read(filename)

## ----estimates----------------------------------------------------------------
param <- so$SOBlock[[1]]$Estimation$PopulationEstimates$MLE
param

## ----parameter_estimates------------------------------------------------------
so$all_population_estimates()

## ----parameter_types----------------------------------------------------------
cols <- colnames(param)
so$variability_type(cols)

## ----correlations-------------------------------------------------------------
so$correlation_parameters(cols)

## ----random_variables---------------------------------------------------------
so$random_variable_from_variability_parameter(cols)

## ----covariance_matrix--------------------------------------------------------
so$SOBlock[[1]]$Estimation$PrecisionPopulationEstimates$MLE$CovarianceMatrix

## ----standard_error-----------------------------------------------------------
so$SOBlock[[1]]$Estimation$PrecisionPopulationEstimates$MLE$StandardError

## ----standard_error2----------------------------------------------------------
so$all_standard_errors()

## ----relative_standard_error--------------------------------------------------
so$SOBlock[[1]]$Estimation$PrecisionPopulationEstimates$MLE$RelativeStandardError

## ----OFV----------------------------------------------------------------------
so$SOBlock[[1]]$Estimation$OFMeasures$Deviance

## ----predictions--------------------------------------------------------------
pred <- so$SOBlock[[1]]$Estimation$Predictions
head(pred, 20)

## ----columnType---------------------------------------------------------------
attributes(pred)$columnType

## ----id_column----------------------------------------------------------------
libsoc::id_column(pred)

## ----id_column_name-----------------------------------------------------------
libsoc::id_column_name(pred)

## ----idv_column---------------------------------------------------------------
libsoc::idv_column(pred)

## ----idv_column_name----------------------------------------------------------
libsoc::idv_column_name(pred)

## ----residuals----------------------------------------------------------------
res <- so$SOBlock[[1]]$Estimation$Residuals$ResidualTable
head(res, 20)

## ----messages-----------------------------------------------------------------
messages <- so$SOBlock[[1]]$TaskInformation$Message
messages[[1]]$Name
messages[[1]]$Content
messages[[1]]$Severity
messages[[1]]$Toolname
messages[[13]]$Content

## ----iofv---------------------------------------------------------------------
iofv <- so$SOBlock[[1]]$Estimation$OFMeasures$IndividualContribToLL
head(iofv)