User's Reference (SBPOP)
Most up-to-date information
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Functions - Overview
| Installation 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 | . | Simulates a given SBmodel with a given SBPOPdosing scheme.
| 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 | . | 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 results
| 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 non-CSV 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 facet-grid 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 | Set-up 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 steady-state 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 steady-state 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. |
