diff --git a/DESCRIPTION b/DESCRIPTION index a1a0df7..516b806 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -4,9 +4,10 @@ Title: Distributions for Ecological Models in 'nimble' Version: 0.5.0 Maintainer: Benjamin R. Goldstein Authors@R: c(person("Benjamin R.", "Goldstein", role = c("aut", "cre"), - email = "ben.goldstein@berkeley.edu"), + email = "bgoldst2@ncsu.edu"), person("Daniel", "Turek", role = "aut"), person("Lauren", "Ponisio", role = "aut"), + person("Wei", "Zhang", role = "ctb"), person("Perry", "de Valpine", role = "aut")) Date: 2024-06-24 Description: Common ecological distributions for 'nimble' models in the form of nimbleFunction objects. diff --git a/R/dNmixture.R b/R/dNmixture.R index 22726aa..4edaa23 100644 --- a/R/dNmixture.R +++ b/R/dNmixture.R @@ -2,7 +2,9 @@ #' #' \code{dNmixture_s} and \code{dNmixture_v} provide Poisson-Binomial mixture #' distributions of abundance ("N-mixture") for use in \code{nimble} models. -#' Overdispersion alternatives are also provided . +#' Overdispersion alternatives using the negative binomial distribution (for +#' the abundance submodel) and the beta binomial distribution (for the detection +#' submodel) are also provided. #' #' @name dNmixture #' @@ -80,8 +82,8 @@ #' Beta-binomial-Poisson: BBP N-mixture uses a beta binomial distribution for #' detection probabilities and a Poisson distribution for abundance. The beta #' binomial distribution has scalar overdispersion parameter s (0-Inf). We -#' parameterize such that the variance of the beta binomial is \code{N \* prob -#' \* (1-prob) \* (N + s) / (s + 1)}, with greater s indicating less variance +#' parameterize such that the variance of the beta binomial is \code{N * prob +#' * (1-prob) * (N + s) / (s + 1)}, with greater s indicating less variance #' (greater-than-binomial relatedness between observations at the site) and s -> #' 0 indicating the binomial. The BBP is available in three suffixed forms: #' \code{dNmixture_BBP_v} is used if \code{prob} varies between observations, diff --git a/man/dNmixture.Rd b/man/dNmixture.Rd index 44d6e96..76c5966 100644 --- a/man/dNmixture.Rd +++ b/man/dNmixture.Rd @@ -112,7 +112,9 @@ For \code{rNmixture_s} and \code{rNmixture_v}: a simulated detection history, \c \description{ \code{dNmixture_s} and \code{dNmixture_v} provide Poisson-Binomial mixture distributions of abundance ("N-mixture") for use in \code{nimble} models. -Overdispersion alternatives are also provided . +Overdispersion alternatives using the negative binomial distribution (for +the abundance submodel) and the beta binomial distribution (for the detection +submodel) are also provided. } \details{ These nimbleFunctions provide distributions that can be @@ -157,8 +159,8 @@ the site (so both x and prob are scalar). Beta-binomial-Poisson: BBP N-mixture uses a beta binomial distribution for detection probabilities and a Poisson distribution for abundance. The beta binomial distribution has scalar overdispersion parameter s (0-Inf). We -parameterize such that the variance of the beta binomial is \code{N \* prob -\* (1-prob) \* (N + s) / (s + 1)}, with greater s indicating less variance +parameterize such that the variance of the beta binomial is \code{N * prob +* (1-prob) * (N + s) / (s + 1)}, with greater s indicating less variance (greater-than-binomial relatedness between observations at the site) and s -> 0 indicating the binomial. The BBP is available in three suffixed forms: \code{dNmixture_BBP_v} is used if \code{prob} varies between observations,