Facilities for Simulating from ODE-Based Models
log likelihood and derivatives for Unif distribution
log likelihood and derivatives for Weibull distribution
logit and inverse logit (expit) functions
lowergamma: upper incomplete gamma function
Leaky ReLU activation function
Calculate expected confidence bands or prediction intreval with normal...
Assign the model block in the rxode2 related object
Model block for rxode2/nlmixr models
Extract model lines from a rxui model
Conversion between character and integer ODE integration methods for r...
Cumulative distribution of standard normal
Plot rxode2 objects
Update Solved object with '+'
Parametric ReLU Activation Function
Print the rxCoef object
Print rxDll object
Print Values
Print information about the rxode2 object.
probit and inverse probit functions
Objects exported from other packages
Rectified Linear Unit (ReLU) Activation Function
Scaled Inverse Chi Squared distribution
One correlation sample from the LKJ distribution
Allow unloading of dlls
Append two rxui models together
Assign Control Variable
Assign pointer based on model variables
Simulate beta variable from threefry generator
Simulate Binomial variable from threefry generator
Creates a logical matrix for block matrixes.
Return the C file associated with the rxode2 object
Use cat when rxode2.verbose is TRUE
Return the md5 of an rxode2 object or file
Get the rxModels information
This gives the derivative table for rxode2
This function gets the currently assigned function pointer assignments
This function gets the currently assigned translations
Optimize rxode2 for computer evaluation
Simulate ordinal value
Parameters specified by the model
Prepare Error function for inclusion in rxode2
Parse PK function for inclusion in rxode2
Prepare Pred function for inclusion in rxode2
Silence some of rxode2's C/C++ messages
Respect suppress messages
Creates a package from compiled rxode2 models
Translate the model to C code if needed
This function is called when processing rxode2 user functions from the...
Return the control that is being processed or setup control for proces...
Return the data.frame that is being processed or setup data.frame for ...
Return the current estimation method for the UI processing
Get the rxode2 iniDf of the current UI being processed (or return NULL...
Return the lhs parsed language expression
Return the model variables that is being processed or setup model vari...
This gives the current number in the ui of the particular function bei...
Returns if the current ui function is being parsed
Reset the rxode2 ui environment variables
Compress/Decompress rxode2 ui
This function tests if this object is a iniDf as needed by the UI
Test if rxode2 uses linear solved systems
Test if the rxode2 model has any parameters with user defined boundari...
Convert event data to trial duration data A helper function to create ...
Update for rxUi
uppergamma: upper incomplete gamma function
Set random effects and residual error to zero
Assert properties of the rxUi models
Assert a variable exists in the model
Assert a variable would be new to the model
Calculate expected confidence bands with binomial sampling distributio...
boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions
Return the rxode2 coefficients
Sample a covariance Matrix from the Posterior Inverse Wishart distribu...
Derivatives of the Exponential Linear Unit (ELU) Activation Function
This uses simulations to match the rse
Derivatives of GELU
Derivative of Leaky ReLU activation function
This function asserts the requested rename makes sense
cbind Ome
Clear/Set pipeline
Collect warnings and just warn once.
Convert a factor/char to an id
This copies the rxode2 UI object so it can be modified
Expand parameters
Generate extraC information for rxode2 models
Get the extraCnow for compiling
Get the last idLvl
Get the internal breakdown of an evid
Handle the single error for normal or t distributions
This gets the append arg for the ini() piping
Reorder rows in iniDf
Update the iniDf of a model
Is the linear systems with gradients built-in
Check if a language object matches a template language object
Internal messaging statements
Handle model lines
Assign in the rxode2 pipeline
Returns quoted call information
Get a blank, theta1, or eta1 initialization block for iniDf
Return the C code of an internal function
Print out a table in the documentation
Get the upper boundary condition when the transformation it
Get the lambda value based on the pred information
Get the lower boundary condition when the transformation requires it
Get the Observation transformation
Get the prediction name
Get the prediction transformation
Get Variance for error type
Internal function to tell if the linCmt() is the model variables
Internal function for calculating the Jacobian
Internal function to generate the model variables for a linCmt() model
Get the rxode2 function pointers
Internal Pruning function
Return the equivalents symengine user functions from C
Sensitivity for model
rxode2 general transformation function
Get the information about the rxode2 derived parameter transformation
Temporarily set options then restore them while running code
With one sink, then release
Temporarily set options then restore them while running code
Register a method for a suggested dependency
Return symengineFs from user functions
This converts NONMEM-style EVIDs to classic RxODE events
Get the function name with the current arguments as a string
Lock/Unlock environment for getting R user functions
Setup the UDF environment (for querying user defined funtions)
Use the udf model variable information to get the environment where th...
See if the UI function exists in given environment.
Get the udf strings for creating model md5
Handle arguments for ui functions
Internal function to figure out if this session supports Unicode
Convert numeric vector to repeated data.frame
Derivatives Parametric ReLU Activation Function
Derivative of the Rectified Linear Unit (ReLU) Activation Function
Derivative of the Scaled Exponential Linear Unit (SELU) Activation Fun...
Default Softplus Activation Function
Derivative of the Swish Activation Function
Exponential Linear Unit (ELU) Activation Function
Error function
Event Table Function
Expand additional doses
Combining event tables
Repeat an rxode2 event table
Sequence of event tables
Event translation for rxode2
Create an event table object
Find the assignments in R expression
Force using base order for rxode2 radix sorting
Gammap: normalized lower incomplete gamma function
gammapDer: derivative of gammap
gammapInv and gammapInva: Inverses of normalized gammap function
Gammaq: normalized upper incomplete gamma function
gammaqInv and gammaqInva: Inverses of normalized gammaq function
GELU activation function
Generate an example (template) of a dosing regimen shiny app
Get the base simulation model for simulation with inis in the underlyi...
Get the base simulation model for simulation
Get the symengine for loading into symengine with rxS()
Get/Set the number of threads that rxode2 uses
Empty Guide
Assign the ini block in the rxode2 related object
Ini block for rxode2/nlmixr models
One correlation sample from the Inverse Wishart distribution
Check to see if this is an rxEt object.
Check to see if this is an rxSolve object.
Return if the object can be stacked
Linear model to replace in rxode2 ui model
Calculate the log likelihood of the binomial function (and its derivat...
Calculate the log likelihood of the binomial function (and its derivat...
log likelihood of Cauchy distribution and it's derivatives (from stan)
log likelihood and derivatives for chi-squared distribution
log likelihood and derivatives for exponential distribution
log likelihood and derivatives for F distribution
log likelihood and derivatives for Gamma distribution
log likelihood and derivatives for Geom distribution
Calculate the log likelihood of the negative binomial function (and it...
Calculate the log likelihood of the negative binomial function (and it...
Log likelihood for normal distribution
log-likelihood for the Poisson distribution
Log likelihood of T and it's derivatives (from stan)
Determine if the DLL associated with the rxode2 object is loaded
Left handed Variables
Lock/unlocking of rxode2 dll file
Verify that a compartment would be new to the model
This sets function gets the currently assigned function pointer assign...
This assigns the c level linkages for a roxde2 model
Set timing for progress bar
State variables
Recast model in terms of sum/prod
Get list of supported functions
Add dosing to eventTable
Verify that a value is a valid nlmixr2 compartment name
Add sampling to eventTable
Coerce object to data.frame
Turn into an ini block for initialization
Turn into a model expression
As rxode2 ui
Verify that the compartment exists in a model
Simulate Cauchy variable from threefry generator
Bind the study parameters and individual parameters
rxChain Chain or add item to solved system of equations
Second command in chaining commands
Simulate chi-squared variable from threefry generator
Cleanup anonymous DLLs by unloading them
Initial Values and State values for a rxode2 object
Combine Error Lines and create rxode2 expression
Compile a model if needed
Current Condition for rxode2 object
This updates the tolerances based on the sensitivity equations
This will create the cache directory for rxode2 to save between sessio...
Add to rxode2's derivative tables
Delete the DLL for the model
Demote the error type
Calculate derived parameters for the 1-, 2-, and 3- compartment linear...
Jacobian and parameter derivatives
Return the DLL associated with the rxode2 object
Load rxode2 object
Unload rxode2 object
Combine transformations and error structures
Dispatch solve to 'rxode2' solve
EVID formatting for tibble and other places.
Convert a positive base
Convert a positive integer to a letter series
Invert matrix using RcppArmadillo.
Simulate exponential variable from threefry generator
Expand d(f)/d(eta)
Expand grid internal function
Faster expand.grid
Expand if/else clauses into multiple different types of lines.
Expand sensitivity
Expand second order sensitivity
Simulate F variable from threefry generator
Apply the fixed population estimated parameters
Clear memoise cache for rxode2
Add/Create C functions for use in rxode2
Add user function to rxode2
Simulate gamma variable from threefry generator
Check the type of an object using Rcpp
Checks if the rxode2 object was built with the current build
Simulate geometric variable from threefry generator
rxGetControl option from ui
This is a S3 method for getting the distribution lines for a rxode2 si...
Get the linear compartment model true function
Get model properties without compiling it.
Get rxode2 model from object
Get the rxode2 seed
Format rxSolve and related objects as html.
Set the preferred factoring by state
This sets the inductive linearization strategy for matrix building
All model variables for a rxode2 object
Simulate Binomial variable from threefry generator
Get the normalized model
Simulate random normal variable from threefry generator
Set the function body of an rxUi object while retaining other object i...
Create an ODE-based model specification
Internal translation to get model variables list
Control the packages that are loaded when a rxode2 model dll is load...
Simulate random Poisson variable from threefry generator
Simulate a from a Poisson process
Change distribution name to the preferred distribution name term
rxode2 progress bar functions
Prune branches (ie if/else) from rxode2
Creates a rxRateDur object
Reload rxode2 DLL
rxRemoveControl options for UI object
Respect suppress messages
Rename items inside of a rxode2 ui model
Rep R0 for foce
Require namespace, otherwise throw error.
Simulate from a (truncated) multivariate normal
Load a model into a symengine environment
This seeds the engine based on the number of cores used in random numb...
rxSetControl options for UI object
Assign covariates for piping
Set Initial conditions to time zero instead of the first observed/dose...
Set the variables for the model piping automatic covarite selection
Defunct setting of product
Set the parallel seed for rxode2 random number generation
Silence some of rxode2's C/C++ messages
Defunct setting of sum
Setup the initial conditions.
Setup the initial conditions.
Use Shiny to help develop an rxode2 model
Simulate Parameters from a Theta/Omega specification
Options, Solving & Simulation of an ODE/solved system
Free the C solving/parsing information.
See if the memory is installed for a solve
This function splits a function based on + or - terms
Stack a solved object for things like default ggplot2 plot
Get Omega^-1 and derivatives
Creates an object for calculating Omega/Omega^-1 and derivatives
Return the dimension of the built-in derivatives/inverses
Sync options with rxode2 variables
Simulate student t variable from threefry generator
Get the rxode2 temporary directory
rxTheme is the ggplot2 theme for rxode2 plots
rxode2 to symengine environment
This is a generic function for deparsing certain objects when printing...
S3 for getting information from UI model
Simulate uniform variable from threefry generator
Unloads all rxode2 compiled DLLs
Use model object in your package
Validate rxode2 This allows easy validation/qualification of nlmixr by...
Version and repository for this dparser package.
Simulate Weibull variable from threefry generator
Preserved seed and possibly set the seed
Scaled Exponential Linear Unit (SELU) Activation Function
Softplus Activation Function
Dosing/Amt geom/stat
Censoring geom/stat
Summary of rxDll object
Print expanded information about the rxode2 object.
Swaps the matrix list with a cube
Switch Activation Function
Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.
Useful links