R/cyclomort.R

In cyclomort: Survival Modeling with a Periodic Hazard Function

#' Cyclomort: periodic survival modeling
#' 
#' @description This package allows users to estimate parametric hazard functions 
#' with a known periodicity and one of more peak seasons of heightened mortality risk. 
#' It was motivated by the strongly seasonal mortality signal observed in many wild 
#' animal populations, but the model may be useful for any periodic time-to-event process.  
#' 
#' 
#' @details The central estimation function \code{\link{fit_cyclomort}} produces estimates 
#' for timing, duration and intensity of mortality peaks from right-censored survival data. 
#' Other functions simulate survival data from periodic hazard functions 
#' (\code{\link{simulate_cycloSurv}}), perform model selection to identify the number of 
#' seasons (\code{\link{select_seasons}}), perform simple hypothesis tests 
#' (\code{\link{factorfit_cyclomort}}), and various methods for visualizing and summarizing 
#' fits and model predictions.  Several data sets are also included. 
#' 
#' Details of the underlying model, motivation, and examples of implementation on mortality 
#' data are in the Gurarie et al. (2020). An active development version is on GitHub at 
#' \url{https://github.com/EliGurarie/cyclomort}. The vignette provides several examples 
#' of the functionality of the package.
#' 
#' @keywords internal
#' @references E. Gurarie, P. Thompson, A. Kelly, N. Larter, W. Fagan and K. Joly. 2020. 
#' For Everything There is a Season: Estimating periodic hazard functions with the cyclomort 
#' R package. \emph{Methods in Ecology and Evolution}, 11(1):129-139. <doi:10.1111/2041-210X.13305>
#' 
#' @import stats
#' @import magrittr
#' @import plyr
#' @import mvtnorm
#' @import survival
#' @import flexsurv
#' @import graphics
#' @import grDevices
#' 
"_PACKAGE"