User's Reference (SBPOP)
Most uptodate information

Functions  Overview
Simulates a given SBmodel with a given SBPOPdosing scheme.Simulates the application of a dosing schedule to a model that has been prepared for it (using the mergemoddosSBPOP function) and either plots or returns the simulation resultsInstallation of SBPD  

installSBPOP  Installation script for the SBPOP package. 
lookforSBPOP  Searches SBPOP functions for strings and opens the documents in which these strings appear. 
newscriptSBPOP  Function creating a template file for a new script. 
newfunctionSBPOP  Function creating a template file for a new function. 
setseedSBPOP  Set the seed. 
Dosing schedule related functions  
SBPOPdosing  Creates an SBPOPdosing object defining a dosing schedule. 
SBPOPstruct  Returns the internal data structure of an object. 
isSBPOPdosing  Checks if input argument is an SBPOPdosing object. 
SBPOPcreateDOSfile  Creates a *.dos file with the dosing text description. 
SBPOPcreateDOSING  Creating a desired SBPOPdosing scheme. 
SBPOPdoseupdatevalue  Allows to update the dosing amount for a given input, defined in an SBPOPdosing object. 
SBPOPsimulate  . 
SBPOPmergemoddos  Based on a model and dosing object, a new SBmodel is generated, that implements the defined dosings. Multiple dosing schedules are realized by updating the parameters of subsequent dosings using events. 
mergemoddosSBPOP  This function takes an SBmodel and an SBPOPdosing scheme as inputs. It adds necessary elements to the model that are required to implement the different dosing inputs (bolus, infusion, absorption0, absorption1) for simulation purposes (e.g. by the SBPOPsimdosing function). 
SBPOPsimdosing  . 
getmoddosinputinfoSBPOP  Checks the availability of dosing input definitions used in the model in the dosing object and returns a structure similar to the "input" field structure of an SBmodel, augmented with the dosing information, defined in the SBPOPdosing object. 
dosing2doseeventSBPOP  This function takes an SBPOP dosing object as input and returns a structure in which the dosing events, happening, are sorted according to the times at which they happen. Additionally, the output structure contains information about the dosing amount and the names of the parameters in a model to change in order to apply the dosing. 
doseinputsSBPOP  Extracts names and types of dosing inputs from a SBPOPdosing object. 
General data file handling  
SBPOPloadCSVdataset  Loads a CSV dataset as a MATLAB dataset. 
SBPOPloadNONCSVdataset  Loads a nonCSV dataset as a MATLAB dataset. Example: NONMEM and Monolix output tables. 
SBPOPexportCSVdataset  Exports a MATLAB dataset as a CSV file. 
SBPOPdataset2wide  Expands a dataset from a row based format to a column based format. 
SBPOPsas7bdat2csv  Convert a sas7bdat file to a CSV file (Requires presence of SAS on your systems command line). 
Plotting Tools  
SBPOPplotCovarianceCat  This function plots the covariance relationship between a list of continuous variables and a list of categorical variabels. 
SBPOPplotfacetgrid  This function allows to generate facetgrid plot with many different settings. 
SBPOPplotfill  Function allowing to plot shaded areas with transparency. 
SBPOPplotHistogram  This function plots histograms of the data provided, allows grouping and plotting several histograms on top of each other. 
SBPOPplotpairwiseCorr  Plots pairwise correlations of data. 
SBPOPplotQQ  QQ plot for provided input data. 
SBPOPplottrellis  Nice function to do Trellis plots with many different settings. 
SBPOPplotXY  This function plots Ydata vs. Xdata with many different settings. 
Monolix related functions  
SBPOPcreateMLXTRANfile  Create MLXTRAN structural model based on SBmodel and SBPOPdosing scheme. 
SBPOPcreateMONOLIXproject  Create Monolix project (includes structural model creation). 
SBPOPrunMONOLIXproject  Runs specified Monolix project. 
SBPOPsampleMONOLIXparam  Samples population and individual parameters from a Monolix fitting result. The resulting population and individual parameters can be used for model simulations. 
Figure export tools  
printFigureSBPOP  Exports MATLAB figures as JPG, PNG, or PS files. For PS files it appends them in same file. 
startNewPrintFigureSBPOP  Removes PS file (windows) or PDF file (unix) if it exists (so new figures are not appended). 
convert2pdfSBPOP  Converts PS to PDF files on unix/linux. 
Other  
getcolorsSBPOP  Function returns color settings and linestyles, etc. Useful for plots to be able to use better colors than the MATLAB default. 
usernameSBPOP  Get the name of the current user. 
popPKPD Toolbox  
Please note that the functions in the popPKPD Toolbox within SBPOP assume a standard dataset format. Nothing really exciting but some standard is needed in order to simplify things.
This data format is documented in the help text of the function SBPOPcheckDataFormat and at every place where the user needs to see it. Most available functions are general for both popPK and popPKPD. However, there are some which only deal with popPK. Please note that the functions assume that fits have been done with Monolix. NONMEM is out of scope (for now)  sorry!  
popPK specific functions  
SBPOPcreatePopPKproject  Setup of a popPK workflow, automatically creating documented template scripts that can be used. 
SBPOPexplorePopPKdata  Creates a wide range of data exploration plots specific for popPK analyses. 
SBPOPcleanPopPKdata  Supports simple data cleaning specific for popPK analyses. 
SBPOPconvert2popPKdataset  Convert dataset to popPK dataset. Removing placebo patients, keeping only certain columns, keeping only dose and PK in the dataset. 
SBPOPbuildPopPKModelSpace  Function allowing to generate a PK model subspace, running all the estimations, generating tables for comparison of models, and generating a wide range of fit analysis plots. For current limitations of possible models, please look at the help text to this function. 
SBPOPfitanalysisPopPK  Function generating GOF plots for a range of PK models. No need to call it yourself. The function "SBPOPbuildPopPKModelSpace" does it already for you. 
General popPK/popPKPD functions  
SBPOPcheckDataFormat  Checking the data format and reporting problems. 
SBPOPexploreIndivData  This function allows to plot individual data from a standardized PKPD dataset. 
SBPOPexploreSummaryStats  This function produces summary statistics for the provided dataset. 
SBPOPexplorePopPDdata  Creates a wide range of data exploration plots specific for popPD analyses. 
SBPOPcleanPopPDdata  Supports simple data cleaning specific for popPD analyses. 
SBPOPconvert2popPDparametersDataset  Convert dataset to popPD dataset, including individual PK parameters for simulation of the PK. 
SBPOPconvert2popPDconcentrationDataset  Convert dataset to popPD dataset, including individual concentrations to use as regression variable. 
SBPOPconvert2popPKPDsimultaneousDataset  Convert dataset to popPKPD dataset, allowing simultaneous popPKPD fit. 
SBPOPcleanImputeCovariates  Covariate imputation. 
SBPOPcleanRemoveFewObsSubjects  Removal of subjects with not more than Nobs observations. 
SBPOPcleanRemovePlaceboSubjects  Removal of placebo subjects. 
SBPOPcleanRemoveRecordsIDs  Removal of user defined IDs and records. 
SBPOPgetMonolixDataHeader  Determination of Monolix header types. 
SBPOPfitanalysisETAvsCOV  Plots the individual variations over covariates and categorical covariates. 
SBPOPfitanalysisGOFplots  Produces several plots that can be used for checking the goodness of fit. 
SBPOPfitanalysisIndividualFits  Plots individual fits and population prediction against observed data over time. 
SBPOPfitanalysisOutlierDetection  Considers PWRES and searches for outliers and displays info about them. 
SBPOPfitanalysisRandomEffects  Plots information about the random effects in different ways. 
SBPOPcovariateChangeAssessment  Assesses the changes that a covariates introduces on the model parameters, based on the contents of the dataset (without uncertainty). 
SBPOPcovariateAssessmentUncertainty  Assesses the changes that a covariates introduces on the model parameters, based on the contents of the dataset (with uncertainty). 
SBPOPcompareModels  This function allows to compare the same structural model for different estimation results from Monolix. 
SBPOPcomparePopPKmodels  This function allows to compare different popPK models created with the PKPD toolbox in SBPOP. 
SBPOPassessInformationContent  This function allows to predict the information content in data of (a) future study/ies, given the planned dosing and observation schedule. 
SBPOPcreateVPC  Generation and plotting of simple VPC. 
SBPOPcreateStratifiedVPC  Allows to generate a stratified VPC. 
SBPOPcreatePopPKstratifiedVPC  Allows to generate a stratified VPC with even less input arguments, but limited to popPK models built with the popPKPD toolbox in SBPOP. 
SBPOPrunMONOLIXprojectFolder  Runs all models in specified folder. 
SBPOPfitanalysisProjectsFolderPlots  Creates fit analysis plots for all Monolix project folders in specified folder. The underlying models do not need to contain the same parameters. 
SBPOPfitanalysisProjectsFolderInfo  Creates model comparison tables for all Monolix project folders in specified folder. The underlying models do not need to contain the same parameters. 
SBPOPfitanalysisGeneralPlots  Plots fit analysis plots for a single specified Monolix project folder. 
EXPLORATORY functions  NOT yet included in public version of SBPOP  
Early Biologics Modeling  
standard_Drug_LigandTarget_model.txtbc  This is a TEXTBC format model, implementing a 3 compartment standard model to be used for antibody modeling when the target/targets are ligands. It is build in a modular way, can easily be simplified and extended if needed. The advantage of a standardized model are standard parameter, state, and variable names, that can be assumed and used in associated functions. 
SBPOPcreateDRUGligandTargetModel  This function just copies the standard model (drug vs. ligand as target) to the current folder under the given name and makes it available to the user to edit, modify, and customize. 
SBPOPtissuedata  This function is simply a collection of literature data from two references, that stores the volumes of different tissues and the corresponding volumes of the interstitial spaces (human values only). 
SBPOPplotDoseEffectCurve  This function plots a dose/effect curve for given input arguments. 
SBPOPplotDoseParamCurve  This function plots a dose/parameter curve for given input arguments. Different effect levels are used as parameters for the different curves. 
SBPOPoptimizeDRUGkinetics  This function will estimate parameters of the standard model to adjust the kinetics of a drug molecule (mAb, nanobody, etc.) to desired properties (alpha and beta halflife and percentage of steadystate distribution between disease tissue and plasma). 
SBPOPoptimizeLigandTARGETkinetics  This function will estimate parameters of the standard model to adjust the kinetics of a target (ligand) to desired properties (alpha and beta halflife). 
SBPOPoptimizeLigandTARGETsynthesis  This function will estimate parameters of the standard model to adjust the steadystate concentrations of a target (ligand) to desired properties (plasma/disease tissue/peripheral tissue concentrations). 
PBPK model simulation and parameter fit  
Not all PBPK model functions in SBPOP are documented here below. Functions for building complete PBPK models are available but some work is needed on them.  
SBPOPsimpbpk  This function simulates a PBPK model and plots the results. If the results are not plotted (when an output argument is given) then the results are returned to the MATLAB workspace. 
SBPOPfitpbpk  This function estimates defined parameters in the given PBPK model in order to fit the model simulation to the provided measurements. It returns the fitted model. 