Bayesian Spatial Survival Analysis with Parametric Proportional Hazards Models

Bayesian inference for parametric proportional hazards spatial survival models; flexible spatial survival models. See Benjamin M. Taylor, Barry S. Rowlingson (2017) .


Spatial Survival Analysis R Package

The GitHub Version of this package is the developmental version.

The latest checked and tested version is available on CRAN, click HERE.

News

CHANGES IN spatsurv VERSION 0.9-1

SIGNIFICANT USER-VISIBLE CHANGES

o There is now a facility for modelling the frailties on a grid, this allows for the analysis of large quantities of spatially referenced survival data. Please note that this functionality is still in the testing phase in this version of the package.

BUG FIXES

o There was an error in the acceptance probability in the function simsurv, this has now been corrected.

	
	
	
	CHANGES IN spatsurv VERSION 0.9-2

SIGNIFICANT USER-VISIBLE CHANGES

o There is now a facility for user-defined covariance functions, for example ExponentialCovFct(), and with more than 2 parameters for example, SpikedExponentialCovFct().

BUG FIXES

o There was an error in the proposal kernel and acceptance ratio in the function survspat. This has been fixed.



	CHANGES IN spatsurv VERSION 0.9-4

BUG FIXES

o There was an error in the transformation from gamma to Y in the non-gridded likelihood functions. This has been fixed.



	CHANGES IN spatsurv VERSION 0.9-5

SIGNIFICANT USER-VISIBLE CHANGES

o Coding of additional survival models has been made easier. The ability to cope with left and interval censored data has been partly coded. 



	CHANGES IN spatsurv VERSION 0.9-6

SIGNIFICANT USER-VISIBLE CHANGES

o Parametrisation of some of the weibull model has changed from (shape, scale) to (alpha, lambda) with hazard lambda x alpha x t^(alpha-1) 

o Additional baseline hazard models added: Gompertz (gompertzHaz), Gompertz-Makeham (makehamHaz), 'powers of t' (tpowHaz)

o Mechanism for specifying model has now been changed and improved

o Extensible user-defied baseline hazard functions

o package vignette now available by typing 'spatsurvVignette()'

BUG FIXES

o Various minor bugs have been fixed


    CHANGES IN spatsurv VERSION 0.9-7

BUG FIXES

o Fixed bug in naming beta paramters caused by factor variables.

    CHANGES IN spatsurv VERSION 0.9-8

SIGNIFICANT USER-VISIBLE CHANGES

o Added capability to use basis splines to model the baseline hazard
o Non-spatial modelling function, survspatNS, now included too.

    CHANGES IN spatsurv VERSION 0.9-8

BUG FIXES

o Fixed bug in posteriorcov when using RandomFields covariance functions

    CHANGES IN spatsurv VERSION 0.9-10

SIGNIFICANT USER-VISIBLE CHANGES

o Profiled code to get substantial speedup for gridded, polygonal and SPDE methods
o spplot1 function now has leaflet capability and also can produce static maps with an OpenStreetMap background via the function getBackground.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("spatsurv")

1.6 by Benjamin M. Taylor, 12 days ago


Browse source code at https://github.com/cran/spatsurv


Authors: Benjamin M. Taylor and Barry S. Rowlingson Additional contributions Ziyu Zheng


Documentation:   PDF Manual  


Task views:


GPL-3 license


Imports survival, sp, spatstat.geom, spatstat.core, spatstat, raster, iterators, RandomFields, fields, Matrix, stringr, rgeos, RColorBrewer, methods, lubridate

Suggests rgdal, rgl, OpenStreetMap


See at CRAN