pooledSPsurv: pooledSPsurv

In Nicolas-Schmidt/BayesSPsurv: Bayesian Spatial Split Population Survival Model

Description

Markov Chain Monte Carlo (MCMC) to run Bayesian split population survival model with no frailties.

Returns a summary of a SPsurv object via summary.mcmc.

Print method for a pooledSPsurv x.

Returns a plot of a pooledSPsurv object via plot.mcmc.

Usage

pooledSPsurv(
  duration,
  immune,
  Y0,
  LY,
  data,
  N,
  burn,
  thin,
  w = c(1, 1, 1),
  m = 10,
  ini.beta = 0,
  ini.gamma = 0,
  form = c("Weibull", "exponential", "loglog")
)

## S3 method for class 'SPsurv'
summary(object, parameter = character(), ...)

## S3 method for class 'SPsurv'
print(x, ...)

## S3 method for class 'SPsurv'
plot(x, parameter = character(), ...)

Arguments

duration	survival stage equation written in a formula of the form Y ~ X1 + X2 + ... where Y is duration until failure or censoring.
immune	split stage equation written in a formula of the form C ~ Z1 + Z2 + ... where C is a binary indicator of immunity.
Y0	the elapsed time since inception until the beginning of time period (t-1).
LY	last observation year (coded as 1; 0 otherwise) due to censoring or failure.
data	data.frame.
N	number of MCMC iterations.
burn	burn-in to be discarded.
thin	thinning to prevent from autocorrelation.
w	size of the slice in the slice sampling for (betas, gammas, rho). Write it as a vector. E.g. c(1,1,1).
m	limit on steps in the slice sampling. A vector of values for beta, gamma, rho.
ini.beta	initial value for the parameter vector beta. By default is 0.
ini.gamma	initial value for the parameter vector gamma. By default is 0.
form	type of parametric model (Weibull, Exponential, or Log-Logistic).
object	an object of class SPsurv, the output of pooledSPsurv.
parameter	one of Four parameters of the pooledSPsurv output. Indicate either "betas," "gammas", "rho" or "delta".
...	additional parameter.
x	an object of class SPsurv, the output of pooledSPsurv.

Value

pooledSPsurv returns an object of class "SPsurv".

A "pooledSPsurv" object has the following elements:

betas	matrix, numeric values of the posterior for each variable in the duration equation .
gammas	matrix, numeric values of the posterior for each variable in the immune equation.
rho	vector, numeric values of rho.
delta	vector, numeric values of delta.
X	matrix of X's variables.
Z	matrix of Z's variables.
Y	vector of ‘Y’.
Y0	vector of ‘Y0’.
C	vector of ‘C’.
ini.beta	numeric initial value of beta.
ini.gamma	numeric initial value of gamma.
form	character, type of distribution.
call	description for the model to be estimated.

list. Empirical mean, standard deviation and quantiles for each variable.

list. Empirical mean, standard deviation and quantiles for each variable.

Examples

walter <- spduration::add_duration(Walter_2015_JCR,"renewed_war",
                                   unitID = "ccode", tID = "year",
                                   freq = "year", ongoing = FALSE)

set.seed(123456)

model <-
    pooledSPsurv(
        duration = duration ~ fhcompor1 + lgdpl + comprehensive + victory +
                   instabl + intensityln + ethfrac + unpko,
        immune   = cured ~ fhcompor1 + lgdpl + victory,
        Y0       = 't.0',
        LY       = 'lastyear',
        data     = walter,
        N        = 100,
        burn     = 10,
        thin     = 10,
        w        = c(1,1,1),
        m        = 10,
        form     = "Weibull"
    )


print(model)

summary(model, parameter = "betas")

# plot(model)

Nicolas-Schmidt/BayesSPsurv documentation built on Sept. 17, 2021, 8:51 a.m.