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Export charts

All plots generated by Monolix can be exported

All plots generated by Monolix can be exported as a figure or as text files in order to be able to plot it in another way or with other software for more flexibility.
All the files can be exported in R for example using the following command

 read.table("/path/to/file.txt", sep = ",", comment.char = "")

Remarks

  • The separator is the one defined in the user preferences. We set “,” in this example as it is the one by default.
  • The command comment.char = "" is needed for some files because to define groups or color, we use the character # that can be interpreted as a comment character by R.

The list of plots below corresponds to all the plots that Monolix can generate. They are computed with the task “Plots”, and the list of plots to compute can be selected by clicking on the button next to the task as shown below, prior to running the task.
Exporting the charts data can be made through the Export menu or through the preferences as described here.

In the following, we describe all the files generated by the export function

Charts concerning the Data

Observed data (continuous, categorical, and count)

xxx_observations.txt

Description: observation values

Full output file description

Column Description Comment
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
time Observation time
y Observation value (loq) The name of the column is the observation name
censored 1 if the observation is censored, 0 otherwise
split Name of the split the subject belongs to
color Name of the color the observation is colored with
filter 1 if the subject is filtered, 0 otherwise

Observed data (event)

xxx_curves.txt

Description: observation values

Full output file description

Column Description Needed Task
time Observation times
survivalFunction Survival of first event
averageEventNumber Average number of event at that time
split Name of the split the subject occasion belongs to

xxx_censored.txt

Description: censored values

Full output file description

Column Description Needed Task
time Observation times
values Survival of first event
split Name of the split the subject occasion belongs to

Model for the observations

Individual Fits

xxx_observations.txt

Description: observation values

Full output file description

Column Description Comment
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
time Observation time
y Observation value (loq)
median Prediction interval median
piLower Lower percentile of the individual prediction interval
piUpper Upper percentile of the individual prediction interval
censored 1 if the observation is censored, 0 otherwise

xxx_fits.txt

Description: individual fits based on population parameters and individual parameters

Full output file description

Column Description Needed Task
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
time Continuous time grid used to compute fits
pop Individual fit base on population parameter values without taking the covariates into account
popPred Individual fit base on population parameter values
indivPredMean Individual prediction based on the individual parameter values estimated by conditional mean Conditional distribution need to be computed
indivPredMode Individual prediction based on the individual parameter values estimated by conditional mode EBEs need to be computed

Observation vs Prediction

xxx_obsVsPred.txt

Description: observation and prediction (pop & indiv) values

Full output file description

Column Description Needed Task
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
time time of the observation
y Observation value (loq)
y_simBlq Observation value (simulated blq)
popPred Predictions based on population parameter values
indivPredMean Predictions based on the individual parameter values estimated by conditional mean Conditional distribution need to be computed
indivPredMode Predictions based on the individual parameter values estimated by conditional mode EBEs need to be computed
censored 1 if the observation is censored, 0 otherwise
split Name of the split the subject occasion belongs to
color Name of the color the observation is colored with
filter 1 if the subject is filtered, 0 otherwise

xxx_obsVsSimulatedPred.txt

Description: observation and simulated prediction values

Full output file description

Column Description Needed Task
rep Replicate id
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
time time of the observation
y Observation value (loq)
y_simBlq Observation value (simulated blq)
indivPredSimulated Predictions based on the simulated individual parameter values estimated by conditional distribution Conditional distribution need to be computed
censored 1 if the observation is censored, 0 otherwise
split Name of the split the subject occasion belongs to
color Name of the color the observation is colored with
filter 1 if the subject is filtered, 0 otherwise

xxx_visualGuides.txt

Description: splines and confidence intervals for predictions

Full output file description

Column Description Needed Task
popPred Continuous grid over population prediction values
popPred_spline Spline ordinates for population predictions
popPred_piLower Lower percentile of prediction interval for population predictions
popPred_piUpper Upper percentile of prediction interval for population predictions
indivPred Continuous grid over individual prediction values
indivPred_spline Spline ordinates for individual predictions
indivPred_piLower Lower percentile of prediction interval for individual predictions
indivPred_piUpper Upper percentile of prediction interval for individual predictions
split Name of the split the visual guides belong to

Distribution of the residuals

xxx_pdf.txt

Description: probability density function of each residual type (pwres, iwres, npde)

Full output file description

Column Description Needed Task
pwRes_abscissa Abscissa for pwres pdf
pwRes_pdf Pdf of pwres
iwRes_abscissa Abscissa for iwres pdf
iwRes_pdf Pdf of the iwres
npde_abscissa Abscissa for npde pdf
npde_pdf Pdf of the npde
split

xxx_cdf.txt

Description: cumulative distribution function of each residual type (pwres, iwres, npde)

Full output file description

Column Description Needed Task
pwRes_abscissa Abscissa for pwres cdf
pwRes_cdf Cdf of pwres
iwRes_abscissa Abscissa for iwres cdf
iwRes_cdf Cdf of the iwres
npde_abscissa Abscissa for npde cdf
npde_cdf Cdf of the npde
split

theoreticalGuides.txt

Description: theoretical guides for the pdf and the cdf

Full output file description

Column Description Needed Task
abscissa,pdf,cdf Abscissa for the theoretical curves
pdf Theoretical value of the pdf
cdf Theoretical value of the cdf

Scatter plot of the residuals

xxx_prediction_percentiles_iwRes.txt

Description: prediction percentiles of the iwREs to plot iwRes w.r.t. the prediction. The same files exists with the pwres and the npde.

Full output file description

Column Description Needed Task
prediction Value of the prediction
empirical_median Empirical median of the iwRes
empirical_lower Empirical lower percentile of the iwRes
empirical_upper Empirical upper percentile of the iwRes
theoretical_median Theoretical median of the iwRes
theoretical_lower Theoretical lower of the iwRes
theoretical_upper Theoretical upper of the iwRes
theoretical_median_piLower Lower bound of the theoretical median prediction interval
theoretical_median_piUpper Upper bound of the theoretical median prediction interval
theoretical_lower_piLower Lower bound of the theoretical lower prediction interval
theoretical_lower_piUpper Upper bound of the theoretical lower prediction interval
theoretical_upper_piLower Lower bound of the theoretical upper prediction interval
theoretical_upper_piUpper Upper bound of the theoretical upper prediction interval
split Name of the split the subject occasion belongs to

xxx_time_percentiles_iwRes.txt

Description: time percentiles of the iwREs to plot iwRes w.r.t. the time. The same files exists with the pwres and the npde.

Full output file description

Column Description Needed Task
time Value of the time
empirical_median Empirical median of the iwRes
empirical_lower Empirical lower percentile of the iwRes
empirical_upper Empirical upper percentile of the iwRes
theoretical_median Theoretical median of the iwRes
theoretical_lower Theoretical lower of the iwRes
theoretical_upper Theoretical upper of the iwRes
theoretical_median_piLower Lower bound of the theoretical median prediction interval
theoretical_median_piUpper Upper bound of the theoretical median prediction interval
theoretical_lower_piLower Lower bound of the theoretical lower prediction interval
theoretical_lower_piUpper Upper bound of the theoretical lower prediction interval
theoretical_upper_piLower Lower bound of the theoretical upper prediction interval
theoretical_upper_piUpper Upper bound of the theoretical upper prediction interval
split Name of the split the subject occasion belongs to

xxx_residuals.txt

Description: residuals values (pwres, iwres, npde)

Full output file description

Column Description Needed Task
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
time Observation times
prediction_pwRes Predictions based on population parameter values SAEM
pwRes PwRes (computed with observations) SAEM
pwRes_blq PwRes (computed with simulated blq)
prediction_iwRes_mean Predictions based on the individual parameter values estimated by conditional mean (INDIVESTIM) if available, SAEM either
iwRes_mean IwRes (computed with observations and individual parameter values estimated by conditional mean (INDIVESTIM) if available, SAEM either)
iwRes_mean_simBlq IwRes (computed with simulated blq and individual parameter values estimated by conditional mean (INDIVESTIM) if available, SAEM either)
prediction_iwRes_mode Predictions based on the individual parameter values estimated by conditional mode (INDIVESTIM)
iwRes_mode IwRes (computed with observations and the individual parameter values estimated by conditional mode (INDIVESTIM))
iwRes_mean_simBlq IwRes (computed with simulated blq and the individual parameter values estimated by conditional mode (INDIVESTIM))
prediction_npde Predictions based on population parameter values
npde Npde (computed with observations)
npde_simBlq Npde (computed with simulated blq) SAEM – If there are some censored data in the data set
censored 1 if the observation is censored, 0 otherwise
split Name of the split the subject occasion belongs to
color Name of the color the observation is colored with
filter 1 if the subject is filtered, 0 otherwise

xxx_simulatedResiduals.txt

Description: simulated residuals values

Full output file description

Column Description Needed Task
rep replicate
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
time Observation times
prediction_iwRes Predictions based on the simulated individual parameter values based on the conditional distribution
iwRes_simulated IwRes (computed with observations and the simulated individual parameter values)
iwRes_simulated_simBlq IwRes (computed with simulated blq and the simulated individual parameter values)
censored 1 if the observation is censored, 0 otherwise
split Name of the split the subject occasion belongs to
color Name of the color the observation is colored with
filter 1 if the subject is filtered, 0 otherwise

xxx_spline.txt

Description: splines (residuals values against time and prediction)

Full output file description

Column Description Needed Task
time_pwRes Time grid for pwRes spline SAEM
time_pwRes_spline pwRes against time spline SAEM
time_iwRes Time grid for iwRes spline At least SAEM
time_iwRes_spline iwRes against time spline At least SAEM
time_npde Time grid for npde spline SAEM
time_npde_spline npde against time spline SAEM
prediction_pwRes Prediction grid for pwRes spline SAEM
prediction_pwRes_spline pwRes against population prediction spline SAEM
prediction_iwRes Prediction grid for iwRes spline At least SAEM
prediction_iwRes_spline iwRes against individual prediction spline At least SAEM
prediction_npde Prediction grid for npde spline SAEM
prediction_npde_npde npde against population prediction spline SAEM
split Name of the split the visual guides belong to If the chart is splitted

xxx_{time,population,individual}Bins.txt

Description: bins values for the corresponding axis.

Full output file description

Column Description Needed Task
binsValues Abscissa bins values
split Name of the split the bins refer to If the chart is splitted

Model for the individual parameters

Distribution of the individual parameters

cdf.txt

Full output file description

Column Description Needed Task
param_abscissa Abscissa of the cdf of the individual parameter param
param_cdf Empirical cdf of the individual parameter param
split Name of the split the subject occasion belongs to

pdf.txt

Full output file description

Column Description Needed Task
param_abscissa Abscissa of the pdf of the individual parameter param
param_pdf Empirical pdf of the individual parameter param
split Name of the split the subject occasion belongs to

visualGuides.txt

Full output file description

Column Description Needed Task
param_abscissa Abscissa of the pdf and the pdf of the individual parameter param
param_pdf Theoretical pdf of the individual parameter param
param_cdf Theoretical cdf of the individual parameter param

Distribution of the random effects

cdf.txt

Full output file description

Column Description Needed Task
param_abscissa Abscissa of the cdf of the standardized random effect of  param
param_cdf Empirical cdf of the standardized random effect of  param
split Name of the split the subject occasion belongs to

pdf.txt

Full output file description

Column Description Needed Task
param_abscissa Abscissa of the pdf of the standardized random effect of  param
param_pdf Empirical pdf of the standardized random effect of  param
split Name of the split the subject occasion belongs to

StandardizedEta.txt

Description: standardized random effects of the individual parameters

Full output file description

Column Description Needed Task
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
standEta_X_method Standardized random effects values on each individual parameter with variability.

It can be StandEta_SAEM, StandEta_Mean, StandEta_Mode

filter 1 if the subject is filtered, 0 otherwise

SimulatedStandardizedEta.txt

Description: simulated standardized random effects of the individual parameters

Full output file description

Column Description Needed Task
rep Replicate id
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
standEta_X_simulated Standardized random effects values on each individual parameter with variability.
filter 1 if the subject is filtered, 0 otherwise

Correlation between Random Effects

eta.txt

Description: standard error on individual parameter predictions

Full output file description

Column Description Needed Task
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
eta_X_method Random effects values on each individual parameter with variability. It can be

eta_SAEM, eta_Mean, or eta_Mode

color Name of the color the ID is colored with
filter 1 if the subject is filtered, 0 otherwise

simulatedEta.txt

Description: standard error on individual parameter predictions

Full output file description

Column Description Needed Task
rep Replicate number
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
eta_X_simulated Simulated random effects values on each individual parameter
color Name of the color the ID is colored with
filter 1 if the subject is filtered, 0 otherwise

visualGuides.txt

Description: spline and linear regression for each couple of individual parameters plotted one against the other

This is done for each combination of parameter p1 and p2 to have p1 w.r.t. p2

Full output file description

Column Description Needed Task
p1_vs_p2_abscissa Abscissa
p1_vs_p2_spline Spline ordinates
p1_vs_p2_regression Linear regression ordinates

Individual Parameters Vs Covariates

covariates.txt

Description: individual parameters and random effects and covariate value for each subject

Full output file description

Column Description Needed Task
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
X_method Individual parameter value. It can be X_SAEM, X_mean, or X_mode
eta_X_method Random effects values. It can be  eta_X_SAEM, eta_Mean, or eta_Mode
covariate Covariates values
split
color Name of the color the observation is colored with
filter 1 if the subject is filtered, 0 otherwise

simulatedCovariates.txt

Description: simulated individual parameters and random effects and covariate value for each subject

Full output file description

Column Description Needed Task
rep Replicate of the simulation
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
X_method Individual parameter value. It can be X_SAEM, X_mean, or X_mode
eta_X_method Random effects values. It can be  eta_X_SAEM, eta_Mean, or eta_Mode
covariate Covariates values
split
color Name of the color the observation is colored with
filter 1 if the subject is filtered, 0 otherwise

Predictive checks and prediction

Visual Predictive Checks (continuous)

xxx_observations.txt

Description: observation values

Full output file description

Column Description Needed Task
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
time Observation times
y Observation values (loq)
y_simBlq Observation values (simulated blq)
censored 1 if the observation is censored, 0 otherwise
split Name of the split the subject occasion belongs to
color Name of the color the observation is colored with
filter 1 if the subject is filtered, 0 otherwise

xxx_bins.txt

Description: bins values for the corresponding axis.

Full output file description

Column Description Needed Task
binsValues Abscissa bins values
split Name of the split the bins refer to If the chart is splitted

xxx_percentiles.txt

Description: empirical and theoretical percentiles values (lower, median & upper) + confidence interval on theoretical percentiles (lower & upper)

Full output file description

Column Description Needed Task
bins_middles Abscissa bin middles
empirical_median Empirical median
empirical_lowerPercentile Empirical lower percentile
empirical_upperPercentile Empirical upper percentile
theoretical_median Theoretical median
theoretical_median_piLower Lower percentile of prediction interval  of theoretical median
theoretical_median_piUpper Upper percentile of prediction interval  of theoretical median
theoretical_lowerPercentile Median of the prediction interval for the lower percentile
theoretical_lower_piLower Lower percentile of the prediction interval for the lower percentile
theoretical_lower_piUpper Upper percentile of the prediction interval for the lower percentile
theoretical_upperPercentile median of the prediction interval for the upper percentile
theoretical_upper_piLower Lower percentile of the prediction interval for the upper percentile
theoretical_upper_piUpper Upper percentile of the prediction interval for the upper percentile
split Name of the split the visual guides belong to If the chart is splitted

Visual Predictive Checks (discrete)

xxx_distribution.txt

Description: discrete observation modalities theoretical distribution (among continuous time grid)

Full output file description

Column Description Needed Task
binsTimeBefore Abscissa bins time value before this time
binsTimeAfter Abscissa bins time value after this time
propCategory_empirical Empirical proportion of the modality set represented by the subchart
propCategory_median Median of the prediction interval for the proportion of the modality set represented by the subchart
propCategory_piLower Lower percentile of the prediction interval for proportion of the modality set represented by the subchart
propCategory_piUpper Upper percentile of the prediction interval for proportion of the modality set represented by the subchart
category Label for modality sets
split Name of the split the distributions refer to

xxx_xBins.txt

Description: bins values for the x-axis.

Full output file description

Column Description Needed Task
binsValues Abscissa bins values
split Name of the split the bins refer to If the chart is splitted

Visual Predictive Checks (event)

xxx_curves.txt

Description: observation values

Full output file description

Column Description Needed Task
time Observation times
survivalFunction_empirical Empirical survival of first event
survivalFunction_median Survival median
survivalFunction_pXX Survival percentile XX
averageEventNumber_empirical Empirical mean number of events
averageEventNumber_median Median mean number of events
averageEventNumber_pXX Percentile XX mean number of events
split Name of the split the subject occasion belongs to If the chart is splitted

xxx_censored.txt

Description: censored values

Full output file description

Column Description Needed Task
time Observation times
values Survival of first event
split Name of the split the subject occasion belongs to

BLQ Predictive Checks

xxx_cumulatedBLQfrequencies.txt

Description: censored simulated observations cumulated frequency

Full output file description

Column Description Needed Task
time Time
empiricalCumulatedFrequencies Empirical fraction of data that is BLQ between time 0 and time t
median Prediction interval median
piLower Lower bound of prediction interval
piUpper Upper bound of prediction interval
split Name of the split the visual guides belong to

Numerical Predictive Check

xxx_cdf.txt

Description: empirical and theoretical cumulative distribution function of observations

Full output file description

Column Description Needed Task
time Cdf continuous grid time
empiricalCdf Empirical cdf based on observations
theoreticalCdf Median of prediction interval for cdf
piLower Lower percentile of prediction interval for cdf
piUpper Upper percentile of prediction interval for cdf
split Name of the split the visual guides belong to

Prediction distribution (continuous)

xxx_observations.txt

Description: observation values

Full output file description

Column Description Needed Task
id Subject identifier
OCC Occasion value (optional) if there is IOV in the data set
time Observation times
y Observation values (loq)
censored 1 if the observation is censored, 0 otherwise
split Name of the split the subject occasion belongs to
color Name of the color the observation is colored with
filter 1 if the subject occasion is filtered, 0 otherwise

xxx_percentiles.txt

Description: theoretical percentiles computed on continuous grid

Full output file description

Column Description Needed Task
time Continuous time grid used for simulation
median Median
pPercentile Percentile
split Name of the split the visual guides belong to If the chart is splitted

Prediction distribution (discrete)

xxx_distribution.txt

Description: discrete observation modalities theoretical distribution (among continuous time grid)

Full output file description

Column Description Needed Task
binsTimeBefore Abscissa bins time value before this time
binsTimeAfter Abscissa bins time value after this time
propCategory_empirical Empirical proportion of the modality set represented by the subchart
propCategory_median Median of the prediction interval for the proportion of the modality set represented by the subchart
propCategory_piLower Lower percentile of the prediction interval for proportion of the modality set represented by the subchart
propCategory_piUpper Upper percentile of the prediction interval for proportion of the modality set represented by the subchart
category Label for modality sets
split Name of the split the distributions refer to

xxx_xBins.txt

Description: bins values for the x-axis.

Full output file description

Column Description Needed Task
binsValues Abscissa bins values
split Name of the split the bins refer to If the chart is splitted

Convergence diagnosis

SAEM

CvParam.txt

Description: evolution of the parameters during SAEM iterations

Full output file description

Column Description Needed Task
iteration Iteration number
convergenceIndicator Convergence Indicator
phase 1 for exploratory and 2 for smoothing
X Parameter X

MCMC

convergences.txt

Description: evolution of the convergence with respect to the MCMC iterations

Full output file description

Column Description Needed Task
iteration Iteration number
E_X Conditional expectation of the parameter X
sd_X Conditional standard error of the parameter X

bounds.txt

Description: bounds for each parameter corresponding to the bounds on the graph. The first line corresponds to the minimum and the second one corresponds to the maximum.

Full output file description

Column Description Needed Task
E_X Conditional expectation of the parameter X
sd_X Conditional standard error of the parameter X

Standard errors of the estimates

rse.txt

Description: Standards errors for each parameter

Full output file description

Column Description Needed Task
X parameter
rse_lin Relative standard error with linearization method
rse_sa Relative standard error with linearization method