give.init {bayesSurv} | R Documentation

## Check and possibly fill in initial values for the G-spline, augmented observations and allocations for Bayesian models with G-splines

### Description

These functions are not to be called by ordinary users.

These are just sub-parts of `bayesBisurvreg.priorInit` and related functions to make them more readable for the programmer.

### Usage

    give.init.Gspline(prior, init, mcmc.par, dim)

    give.init.y(init.y, dim, y.left, y.right, status)

    give.init.y2(init.y, init2.y, dim, design, design2, doubly)

    give.init.r(init.r, init.y, dim, KK,
       gamma, sigma, c4delta, intcpt, scale)

### Arguments

`prior` | a~list as required by `prior` argument of the function `bayesHistogram` or `prior` and `prior2` arguments of the function `bayesBisurvreg`
`init` | a~list as required by `init` argument of the function `bayesHistogram` or by `init` and `init2` arguments of the function `bayesBisurvreg`
`mcmc.par` | a~list as required by `mcmc.par` argument of function `bayesHistogram` or by `mcmc.par` and `mcmc.par2` arguments of the function `bayesBisurvreg`
`dim` | dimension of the G-spline/response, 1 or 2.
`init.y` | initial (augmented) observations possibly given by the user. They are partially checked for consistency and these supplied by the user used in the resulting object. This should be either vector of length n where n is a~sample size if the dimension is one or a~matrix with 2 columns and n rows if the dimension is two.
`init2.y` | initial (augmented) times-to-event (if doubly censoring) possibly given by the user. They are partially checked for consistency and these supplied by the user used in the resulting object. This should be either vector of length n where n is a~sample size if the dimension is one or a~matrix with 2 columns and n rows if the dimension is two.
`design` | an~object as returned by the function `bayessurvreg.design` related to either the onset time if doubly censored observations or to the event time. Remark: `design$Y` contains original times and NOT their logarithmic transformations.
`design2` | an~object as returned by the function `bayessurvreg.design` related to time-to-event if doubly censored observations. Remark: `design2$Y` contains original times and NOT their logarithmic transformations.
`doubly` | logical indicating whether the response is doubly censored or not
`y.left` | observed, left or right censored log(event time) or the lower limit of the interval censored observation. Sorted in a~transposed order compared to `init.y`.
`y.right` | upper limit of the interval censored observation, whatever if the observation is not interval-censored sorted in a~transposed order compared to `init.y`.
`status` | status indicator vector/matrix. 1 for observed times, 0 for right censored times, 2 for left censored times, 3 for interval censored times.
`init.r` | initial allocations possibly given by the user. This should be a~vector of length n where n is a~sample size if `dim` is equal to 1 and a~matrix with n rows and 2 columns if `dim` is equal to 2. Values should be on the scale -K[j],...,K[j], j=1,...,dim
`init.y` | correctly computed initial observations the G-spline is estimated from. In the case of regression these should be replaced by residuals. This must be either a~vector or matrix (in the format as returned by the function `give.init.y`).
`KK` | vector of length `dim` with K coefficients defining the G-spline.
`gamma` | vector of length `dim` with initial gamma parameters of the G-spline.
`sigma` | vector of length `dim` with initial sigma parameters of the G-spline.
`c4delta` | vector of length `dim` with constants to compute the distance between two knots defining the G-spline.
`intcpt` | vector of length `dim` with initial values of the intercept term of the G-spline.
`scale` | vector of length `dim` with initial values of the scale parameters of the G-spline.

### Value

Some lists.

### Value for give.init.Gspline

A~list with the following components:

Gparmi
  integer parameters for the G-spline constructor in the C++ code
Gparmd
  double parameters for the G-spline constructor in the C++ code
specification
  specification of the G-spline model (1 or 2), see `bayesHistogram` for more detail

and the following attributes:

init
prior
mcmc.par

### Value for give.init.y

A~vector or matrix with the same structure as `init.y`, i.e. with 2~columns and n rows in the case of the bivariate data.

### Value for give.init.y2

A~list with the following components:

init.y
  a~vector of length n or a~matrix with 2 columns and n rows with initial log(onset times)
init2.y
  a~vector of length n or a~matrix with 2 columns and n rows with initial log(times-to-event). If the data are not doubly cdensored, this object is equal to 0.
y1.left
  lower limit of the log-response (or exact/right/left censored observation) as required by the C++ function `bayesBisurvreg`, related to the onset time in the case of doubly censoring and to the event time otherwise
y1.right
  upper limit of the log-response as required by the C++ function `bayesBisurvreg`, related to the onset time in the case of doubly censoring and to the event time otherwise
status1
  status vector as required by the C++ function `bayesBisurvreg` related to the onset time in the case of doubly censoring and to the event time otherwise
t2.left
  lower limit of the response as required by the C++ function `bayesBisurvreg`, related to time-to-event in the case of doubly censoring, equal to 0 if there is no doubly-censoring
t2.right
  upper limit of the response as required by the C++ function `bayesBisurvreg`, related to time-to-event in the case of doubly censoring, equal to 0 if there is no doubly-censoring
status2
  status vector related to time-to-event in the case of doubly censoring, equal to 0 otherwise.

### Value for give.init.r

### Author(s)

Arnost Komarek arnost.komarek@med.kuleuven.be

[Package bayesSurv version 0.4 Index]