Export charts data
All plots generated by Monolix can be exported
All plots generated by Monolix can be exported as figures or as text files in order to be able to plot them in another way or with other softwares for more flexibility.
Exporting the charts data can be made through the Export menu or through the preferences as described here.
The list of files in the next sections corresponds to all the charts data that Monolix can generate. They are computed with the task “Plots”, and the list of plots to compute in that task can be selected by clicking on the button next to the task prior to running it.
https://www.youtube.com/watch?v=JMyKwv9btbw
All the files can then be exported in R, for example using the following command:
read.table("/path/to/file.txt", sep = ",", comment.char = "", header = T)
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.
Charts concerning the Data
Observed data (continuous, categorical, and count)
xxx_observations.txt
Description: observation values
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
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
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
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
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 | Prediction using population parameter values and average covariate value from the population (continuous) or reference covariate value (categorical). | – |
popPred | Prediction using population parameter values and individual covariates. | – |
indivPredMean | Prediction based on the individual parameter values estimated by conditional mean | Conditional distribution need to be computed |
indivPredMode | 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
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
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
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)
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)
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
Column | Description | Needed Task |
abscissa,pdf,cdf | Abscissa for the theoretical curves | – |
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.
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.
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)
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
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)
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.
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
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
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
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
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
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
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
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
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
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
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
Column | Description | Needed Task |
id | Subject identifier | – |
OCC | Occasion value | (optional) if there is IOV in the data set |
trans_X_method | Individual parameter value in the transformed space. 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
Column | Description | Needed Task |
rep | Replicate of the simulation | |
id | Subject identifier | – |
OCC | Occasion value | (optional) if there is IOV in the data set |
trans_X_simulated | Simulated transformed individual parameter value. | – |
eta_X_simulated | Simulated random effects values. | – |
covariate | Covariates values | |
split | ||
color | Name of the color the observation 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 against a covariate
This is done for each combination of parameter param and covariate cov to have param w.r.t. cov
Column | Description | Needed Task |
param_vs_cov_abscissa | Abscissa | – |
param_vs_cov_spline | Spline ordinates | – |
param_vs_cov_regression | Linear regression ordinates | – |
Predictive checks and prediction
Visual Predictive Checks (continuous)
xxx_observations.txt
Description: observation values
Column | Description | Needed Task |
ID | Subject identifier | – |
OCC | Occasion value | (optional) if there is IOV in the data set |
time | Observation times | – |
timeAfterLastDose | Observation times after the last dose | – |
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.
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)
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 |
xxx_simulations.txt
Description: simulated values. This file is not exported by default with the charts data, but it can be exported by clicking on “Export > Export VPC simulations” in the application menu. Moreover, if the option “Export VPC simulations” is enabled in the Preferences, it is exported each time the VPC is generated.
Column | Description | Needed Task |
rep | Simulation replicate | – |
ID | Subject identifier | – |
OCC | Occasion value | (optional) if there is IOV in the data set |
time / timeAfterLastDose | Observation times or times after last dose | timeAfterLastDose if the corresponding option is used in the VPC |
sim_y | Simulated 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 is filtered, 0 otherwise | – |
Visual Predictive Checks (discrete)
xxx_distribution.txt
Description: discrete observation modalities theoretical distribution (among continuous time grid)
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.
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
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
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
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
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
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
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)
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.
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
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
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.
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
Column | Description | Needed Task |
X | parameter | – |
rse_lin | Relative standard error with linearization method | – |
rse_sa | Relative standard error with linearization method |