mrgsolve: idata_set – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

idata_set

Select and modify a idata set for simulation

Description

The individual data set (idata_set) is a data frame with one row for each individual in a population, specifying parameters and other individual-level data.

Usage

idata_set(x, data, ...)

## S4 method for signature 'mrgmod,data.frame'
idata_set(
  x,
  data,
  .subset = TRUE,
  .select = TRUE,
  object = NULL,
  need = NULL,
  ...
)

## S4 method for signature 'mrgmod,ANY'
idata_set(x, data, ...)

## S4 method for signature 'mrgmod,missing'
idata_set(x, object, ...)

Arguments

`x`	model object
`data`	a data set that can be coerced to data.frame
`...`	passed along
`.subset`	an unquoted expression passed to `dplyr::filter`; retain only certain rows in the data set
`.select`	passed to `dplyr::select`; retain only certain columns in the data set; this should be the result of a call to `dplyr::vars()`
`object`	character name of an object existing in `$ENV` to use for the data set
`need`	passed to `inventory`

Details

The idata_set is a data.frame that specifies individual-level data for the problem. An ID column is required and there can be no more than one row in the data frame for each individual.

In most cases, the columns in the idata_set have the same names as parameters in the param list. When this is the case, the parameter set is updated as the simulation proceeds once at the start of each individual. The 'idata_set' can also be used to set initial conditions for each individual: for a compartment called CMT, make a column in idata_set called CMT_0 and make the value the desired initial value for that compartment. Note that this initial condition will be over-ridden if you also set the CMT_0 in $MAIN.

The most common application of idata_set is to specify a population or batch of simulations to do. We commonly use idata_set with an event object (see ev). In that case, the event gets applied to each individual in the idata_set.

It is also possible to provide both a data_set and a idata_set. In this case, the idata_set is used as a parameter lookup for IDs found in the data_set. Remember in this case, it is the data_set (not the idata_set) that determines the number of individuals in the simulation.

An error will be generated if any parameter columns in the input idata set contain NA.

Examples

mod <- mrgsolve::house()

data(exidata)

exidata

mod %>% 
  idata_set(exidata, ID <= 2) %>% 
  ev(amt = 100) %>%
  mrgsim() %>% 
  plot()

mod %>% 
  idata_set(exidata) %>% 
  ev(amt = 100) %>%
  mrgsim()

mod %>% ev(amt = 100) %>% mrgsim(idata=exidata)

mrgsolve

Simulate from ODE-Based Models

v0.11.1

GPL (>= 2)

Authors

Kyle T Baron [aut, cre] (<https://orcid.org/0000-0001-7252-5656>), Bill Gillespie [ctb], Charles Margossian [ctb], Devin Pastoor [ctb], Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>), Dilawar Singh [ctb], Felicien Le Louedec [ctb] (<https://orcid.org/0000-0003-3699-2729>), Timothy Waterhouse [ctb] (<https://orcid.org/0000-0002-0954-9660>), Metrum Research Group [cph]

Initial release