covariates {pomp} | R Documentation |

## Covariates

### Description

Incorporating time-varying covariates using lookup tables.

### Usage

```
## S4 method for signature 'numeric'
covariate_table(..., order = c("linear", "constant"), times)
## S4 method for signature 'character'
covariate_table(..., order = c("linear", "constant"), times)
repair_lookup_table(table, t, order)
```

### Arguments

`...` |
numeric vectors or data frames containing time-varying covariates. It must be possible to bind these into a data frame. |

`order` |
the order of interpolation to be used.
Options are “linear” (the default) and “constant”.
Setting |

`times` |
the times corresponding to the covariates. This may be given as a vector of (non-decreasing, finite) numerical values. Alternatively, one can specify by name which of the given variables is the time variable. |

`table` |
a ‘covartable’ object created by a call to |

`t` |
numeric vector;
times at which interpolated values of the covariates in |

### Details

If the ‘pomp’ object contains covariates (specified via the `covar`

argument), then interpolated values of the covariates will be available to each of the model components whenever it is called.
In particular, variables with names as they appear in the `covar`

covariate table will be available to any C snippet.
When a basic component is defined using an **R** function, that function will be called with an extra argument, `covars`

, which will be a named numeric vector containing the interpolated values from the covariate table.

An exception to this rule is the prior (`rprior`

and `dprior`

):
covariate-dependent priors are not allowed.
Nor are parameter transformations permitted to depend upon covariates.

`repair_lookup_table`

applies `lookup`

at the provided values of `t`

and returns the resulting lookup table.
If `order`

is unsupplied, the interpolation-order from `table`

is preserved.
** repair_lookup_table should be considered experimental: its interface may change without notice**.

### Value

`covariate_table`

returns a lookup table suitable for inclusion of covariates in a ‘pomp’ object.
Specifically, this is an object of class ‘covartable’.

`repair_lookup_table`

returns a lookup table with entries at the provided values of `t`

.

### Extrapolation

If `t`

is outside the range of the lookup table, the values will be extrapolated, and a warning will be issued.
The type of extrapolation performed will be constant or linear according to the `order`

flag used when creating the table.

### See Also

More on implementing POMP models:
`Csnippet`

,
`accumvars`

,
`basic_components`

,
`betabinomial`

,
`dinit_spec`

,
`dmeasure_spec`

,
`dprocess_spec`

,
`emeasure_spec`

,
`eulermultinom`

,
`parameter_trans()`

,
`pomp-package`

,
`pomp_constructor`

,
`prior_spec`

,
`rinit_spec`

,
`rmeasure_spec`

,
`rprocess_spec`

,
`skeleton_spec`

,
`transformations`

,
`userdata`

,
`vmeasure_spec`

More on interpolation:
`bsplines`

,
`lookup()`

*pomp*version 5.10.0.1 Index]