Simulate from ODE-Based Models


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Documentation for package ‘mrgsolve’ version 0.9.0

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A B C D E F G H I L M N O P R S T U V misc

mrgsolve-package mrgsolve

-- A --

aboutsolver About the ODEPACK differential equation solver used by mrgsolve
allparam Create and work with parameter objects
as.ev Coerce an object to class ev
as.ev-method Coerce an object to class ev
as.list-method Coerce a model object to list
as.list-method Coerce an mrgsims object to list
as.tbl.mrgsims Methods for handling output with dplyr verbs
assign_ev Replicate a list of events into a data set
as_bmat Coerce R objects to block or diagonal matrices
as_bmat-method Coerce R objects to block or diagonal matrices
as_cmat Coerce R objects to block or diagonal matrices
as_data_frame.mrgsims Methods for handling output with dplyr verbs
as_data_set Create a simulation data set from ev objects
as_data_set-method Create a simulation data set from ev objects
as_deslist Create a list of designs from a data frame
as_dmat Coerce R objects to block or diagonal matrices
as_dmat-method Coerce R objects to block or diagonal matrices
as_tibble.mrgsims Methods for handling output with dplyr verbs

-- B --

blocks Return the code blocks from a model specification file
blocks-method Return the code blocks from a model specification file
BLOCK_PARSE Functions to parse code blocks
bmat Create matrices from vector input

-- C --

c-method Operations with matlist objects
c-method Operations with tgrid objects
CAPTURE Functions to parse code blocks
carry.out Select items to carry into simulated output
carry_out Select items to carry into simulated output
cmat Create matrices from vector input
CMT Functions to parse code blocks
cmtn Get the compartment number from a compartment name
cmtn-method Get the compartment number from a compartment name
code Extract the code from a model

-- D --

data_set Select and modify a data set for simulation
data_set-method Select and modify a data set for simulation
design Set observation designs for the simulation
details Extract model details
distinct.mrgsims Methods for handling output with dplyr verbs
dmat Create matrices from vector input
do.mrgsims Methods for handling output with dplyr verbs
dorender Render a model to a document
do_mrgsim Simulate from a model object

-- E --

env_eval Re-evaluate the code in the ENV block
env_get Return model environment
env_get_env Return model environment
env_ls List objects in the model environment
env_update Update objects in model environment
ev Event objects for simulating PK and other interventions
ev-method Event objects for simulating PK and other interventions
ev_assign Replicate a list of events into a data set
ev_days Schedule dosing events on days of the week
ev_rep Replicate an event object
ev_repeat Repeat a block of dosing events
ev_rx Create intervention objects from Rx input
ev_rx-method Create intervention objects from Rx input
ev_seq Schedule a series of event objects
exBoot Example input data sets
exdatasets Example input data sets
exidata Example input data sets
expand.ev Create template data sets for simulation
expand.idata Create template data sets for simulation
expand_observations Insert observations into a data set
exTheoph Example input data sets
extran1 Example input data sets
extran2 Example input data sets
extran3 Example input data sets

-- F --

filter_.ev dplyr verbs for event objects
filter_.mrgsims Methods for handling output with dplyr verbs
filter_sims Methods for handling output with dplyr verbs
FIXED Functions to parse code blocks

-- G --

group_by.mrgsims Methods for handling output with dplyr verbs

-- H --

house Return a pre-compiled, PK/PD model

-- I --

idata_set Select and modify a idata set for simulation
idata_set-method Select and modify a idata set for simulation
INIT Functions to parse code blocks
init Methods for working with the model compartment list
init-method Methods for working with the model compartment list
inventory Check whether all required parameters needed in a model are present in an object
is.mrgmod Check if an object is a model object
is.mrgsims Check if an object is mrgsim output

-- L --

lctran Convert select upper case column names to lower case to conform to mrgsolve data expectations
loadso Load the model shared object
loadso.mrgmod Load the model shared object

-- M --

matrix_helpers Create matrices from vector input
mcode Write, compile, and load model code
mcode_cache Write, compile, and load model code
mcRNG Set RNG to use L'Ecuyer-CMRG
modlib Internal model library
modlib_details modlib: PK/PD Model parameters, compartments, and output variables
modlib_pk modlib: Pharmacokinetic models
modlib_pkpd modlib: Pharmacokinetic / pharmacodynamic models
modlib_tmdd modlib: Target mediated disposition model
modlib_viral modlib: HCV viral dynamics models
mread Read a model specification file
mread_cache Read a model specification file
mread_file Read a model specification file
mrgsim Simulate from a model object
mrgsims_dplyr Methods for handling output with dplyr verbs
mrgsim_0 mrgsim variant functions
mrgsim_d mrgsim variant functions
mrgsim_df Simulate from a model object
mrgsim_di mrgsim variant functions
mrgsim_e mrgsim variant functions
mrgsim_ei mrgsim variant functions
mrgsim_i mrgsim variant functions
mrgsim_q Simulate from a model object with quicker turnaround
mrgsim_variants mrgsim variant functions
mrgsolve mrgsolve
mutate.ev dplyr verbs for event objects
mutate.mrgsims Methods for handling output with dplyr verbs
mutate_sims Methods for handling output with dplyr verbs

-- N --

names-method Get all names from a model object
NMXML Get THETA, OMEGA and SIGMA from a completed NONMEM run
nmxml Get THETA, OMEGA and SIGMA from a completed NONMEM run
numerics_only Prepare data.frame for input to mrgsim

-- O --

obsaug Augment observations in the simulated output
obsonly Collect only observations in the simulated output
omat Manipulate OMEGA matrices
omat-method Manipulate OMEGA matrices
OMEGA Manipulate OMEGA matrices
omega Manipulate OMEGA matrices

-- P --

PARAM Functions to parse code blocks
param Create and work with parameter objects
param-method Create and work with parameter objects
parse_rx Create intervention objects from Rx input
PKMODEL Parse PKMODEL BLOCK data
plot-method Plot method for mrgsims objects
plot-method Generate a quick plot of simulated data
plot_mrgsims Generate a quick plot of simulated data
plot_sims Plot data as an mrgsims object
pull.mrgsims Methods for handling output with dplyr verbs

-- R --

read_nmext Extract estimates from NONMEM ext file
realize_addl Make addl doses explicit in an event object or data set
realize_addl.data.frame Make addl doses explicit in an event object or data set
realize_addl.ev Make addl doses explicit in an event object or data set
render Render a model to a document
render-method Render a model to a document
Req Request simulated output
req Request simulated output
Req-method Request simulated output
req-method Request simulated output
reserved Reserved words
revar Get model random effect variances and covariances
revar-method Get model random effect variances and covariances

-- S --

see Print model code to the console
see-method Print model code to the console
select.ev dplyr verbs for event objects
select.mrgsims Methods for handling output with dplyr verbs
seq.ev Schedule a series of event objects
SIGMA Manipulate SIGMA matrices
sigma Manipulate SIGMA matrices
simargs Access or clear arguments for calls to mrgsim
slice.mrgsims Methods for handling output with dplyr verbs
smat Manipulate SIGMA matrices
smat-method Manipulate SIGMA matrices
soloc Return the location of the model shared object
solversettings Optional inputs for DLSODA
summarise.each Methods for handling output with dplyr verbs
summarise.mrgsims Methods for handling output with dplyr verbs

-- T --

tgrids_*_numeric Operations with tgrid objects
tgrids_+_numeric Operations with tgrid objects
tgrid_*_numeric Operations with tgrid objects
tgrid_+_numeric Operations with tgrid objects
THETA Functions to parse code blocks
tscale Re-scale time in the simulated output

-- U --

update Update the model object
update-method Update the model object

-- V --

valid_data_set Validate and prepare a data sets for simulation
valid_data_set.matrix Validate and prepare a data sets for simulation
valid_idata_set Validate and prepare idata data sets for simulation

-- misc --

$-method Select parameter values from a model object
*-method Operations with tgrid objects
+-method Operations with tgrid objects
[-method Select parameter values from a model object
[[-method Select parameter values from a model object