diff --git a/R/colext.R b/R/colext.R index 194a130..72b9874 100644 --- a/R/colext.R +++ b/R/colext.R @@ -8,7 +8,7 @@ #' @param gammaformula Right-hand sided formula for colonization probability #' @param epsilonformula Right-hand sided formula for extinction probability #' @param pformula Right-hand sided formula for detection probability -#' @param data A \code{\link{unmarkedMultFrame}} object +#' @param data A \code{\link[unmarked]{unmarkedMultFrame}} object #' @param prior_intercept_psi Prior distribution for the intercept of the #' psi (initial occupancy probability) model; see \code{?priors} for options #' @param prior_coef_psi Prior distribution for the regression coefficients of @@ -29,7 +29,7 @@ #' @param log_lik If \code{TRUE}, Stan will save pointwise log-likelihood values #' in the output. This can greatly increase the size of the model. If #' \code{FALSE}, the values are calculated post-hoc from the posteriors -#' @param ... Arguments passed to the \code{\link{stan}} call, such as +#' @param ... Arguments passed to the \code{\link[rstan]{stan}} call, such as #' number of chains \code{chains} or iterations \code{iter} #' #' @return \code{ubmsFitColext} object describing the model fit. diff --git a/R/distsamp.R b/R/distsamp.R index f8995d8..5039cd0 100644 --- a/R/distsamp.R +++ b/R/distsamp.R @@ -6,7 +6,7 @@ #' #' @param formula Double right-hand side formula describing covariates of #' detection and occupancy in that order -#' @param data A \code{\link{unmarkedFrameDS}} object +#' @param data A \code{\link[unmarked]{unmarkedFrameDS}} object #' @param keyfun One of the following detection functions: #' \code{"halfnorm"} for half-normal, \code{"exp"} for negative exponential, #' or \code{"hazard"} for hazard-rate (see warning below) @@ -24,7 +24,7 @@ #' @param prior_intercept_scale Prior distribution for the intercept of the #' scale parameter (i.e., log(scale)) for Hazard-rate models #' @param prior_sigma Prior distribution on random effect standard deviations -#' @param ... Arguments passed to the \code{\link{stan}} call, such as +#' @param ... Arguments passed to the \code{\link[rstan]{stan}} call, such as #' number of chains \code{chains} or iterations \code{iter} #' #' @return \code{ubmsFitDistsamp} object describing the model fit. diff --git a/R/multinomPois.R b/R/multinomPois.R index 3728090..fca11c7 100644 --- a/R/multinomPois.R +++ b/R/multinomPois.R @@ -5,7 +5,7 @@ #' #' @param formula Double right-hand side formula describing covariates of #' detection and abundance in that order -#' @param data A \code{\link{unmarkedFrameMPois}} object +#' @param data A \code{\link[unmarked]{unmarkedFrameMPois}} object #' @param prior_intercept_state Prior distribution for the intercept of the #' state (abundance) model; see \code{?priors} for options #' @param prior_coef_state Prior distribution for the regression coefficients of @@ -18,7 +18,7 @@ #' @param log_lik If \code{TRUE}, Stan will save pointwise log-likelihood values #' in the output. This can greatly increase the size of the model. If #' \code{FALSE}, the values are calculated post-hoc from the posteriors -#' @param ... Arguments passed to the \code{\link{stan}} call, such as +#' @param ... Arguments passed to the \code{\link[rstan]{stan}} call, such as #' number of chains \code{chains} or iterations \code{iter} #' #' @return \code{ubmsFitMultinomPois} object describing the model fit. diff --git a/R/occu.R b/R/occu.R index 300ce8e..33486ba 100644 --- a/R/occu.R +++ b/R/occu.R @@ -5,7 +5,7 @@ #' #' @param formula Double right-hand side formula describing covariates of #' detection and occupancy in that order -#' @param data A \code{\link{unmarkedFrameOccu}} object +#' @param data A \code{\link[unmarked]{unmarkedFrameOccu}} object #' @param prior_intercept_state Prior distribution for the intercept of the #' state (occupancy probability) model; see \code{?priors} for options #' @param prior_coef_state Prior distribution for the regression coefficients of @@ -18,7 +18,7 @@ #' @param log_lik If \code{TRUE}, Stan will save pointwise log-likelihood values #' in the output. This can greatly increase the size of the model. If #' \code{FALSE}, the values are calculated post-hoc from the posteriors -#' @param ... Arguments passed to the \code{\link{stan}} call, such as +#' @param ... Arguments passed to the \code{\link[rstan]{stan}} call, such as #' number of chains \code{chains} or iterations \code{iter} #' #' @return \code{ubmsFitOccu} object describing the model fit. diff --git a/R/occuRN.R b/R/occuRN.R index 6a9a09b..c2fab1c 100644 --- a/R/occuRN.R +++ b/R/occuRN.R @@ -6,7 +6,7 @@ #' #' @param formula Double right-hand side formula describing covariates of #' detection and abundance in that order -#' @param data A \code{\link{unmarkedFrameOccu}} object +#' @param data A \code{\link[unmarked]{unmarkedFrameOccu}} object #' @param K Integer upper index of integration for N-mixture. This should be #' set high enough so that it does not affect the parameter estimates. #' Note that computation time will increase with K. @@ -22,7 +22,7 @@ #' @param log_lik If \code{TRUE}, Stan will save pointwise log-likelihood values #' in the output. This can greatly increase the size of the model. If #' \code{FALSE}, the values are calculated post-hoc from the posteriors -#' @param ... Arguments passed to the \code{\link{stan}} call, such as +#' @param ... Arguments passed to the \code{\link[rstan]{stan}} call, such as #' number of chains \code{chains} or iterations \code{iter} #' #' @return \code{ubmsFitOccuRN} object describing the model fit. diff --git a/R/occuTTD.R b/R/occuTTD.R index da18c65..945789a 100644 --- a/R/occuTTD.R +++ b/R/occuTTD.R @@ -12,7 +12,7 @@ #' Currently ignored as dynamic models are not yet supported. #' @param detformula Right-hand sided formula for mean time-to-detection. #' @param data \code{unmarkedFrameOccuTTD} object that supplies the data -#' (see \code{\link{unmarkedFrameOccuTTD}}). +#' (see \code{\link[unmarked]{unmarkedFrameOccuTTD}}). #' @param ttdDist Distribution to use for time-to-detection; either #' \code{"exp"} for the exponential, or \code{"weibull"} for the Weibull, #' which adds an additional shape parameter \eqn{k}. @@ -33,7 +33,7 @@ #' @param log_lik If \code{TRUE}, Stan will save pointwise log-likelihood values #' in the output. This can greatly increase the size of the model. If #' \code{FALSE}, the values are calculated post-hoc from the posteriors -#' @param ... Arguments passed to the \code{\link{stan}} call, such as +#' @param ... Arguments passed to the \code{\link[rstan]{stan}} call, such as #' number of chains \code{chains} or iterations \code{iter} #' #' @return \code{ubmsFitOccuTTD} object describing the model fit. diff --git a/R/pcount.R b/R/pcount.R index da98588..9d479ef 100644 --- a/R/pcount.R +++ b/R/pcount.R @@ -5,7 +5,7 @@ #' #' @param formula Double right-hand side formula describing covariates of #' detection and abundance in that order -#' @param data A \code{\link{unmarkedFramePCount}} object +#' @param data A \code{\link[unmarked]{unmarkedFramePCount}} object #' @param K Integer upper index of integration for N-mixture. This should be #' set high enough so that it does not affect the parameter estimates. #' Note that computation time will increase with K. @@ -22,7 +22,7 @@ #' @param log_lik If \code{TRUE}, Stan will save pointwise log-likelihood values #' in the output. This can greatly increase the size of the model. If #' \code{FALSE}, the values are calculated post-hoc from the posteriors -#' @param ... Arguments passed to the \code{\link{stan}} call, such as +#' @param ... Arguments passed to the \code{\link[rstan]{stan}} call, such as #' number of chains \code{chains} or iterations \code{iter} #' #' @return \code{ubmsFitPcount} object describing the model fit. diff --git a/man/stan_colext.Rd b/man/stan_colext.Rd index 05a1d4d..fe6b145 100644 --- a/man/stan_colext.Rd +++ b/man/stan_colext.Rd @@ -33,7 +33,7 @@ occupancy at each site} \item{pformula}{Right-hand sided formula for detection probability} -\item{data}{A \code{\link{unmarkedMultFrame}} object} +\item{data}{A \code{\link[unmarked]{unmarkedMultFrame}} object} \item{prior_intercept_psi}{Prior distribution for the intercept of the psi (initial occupancy probability) model; see \code{?priors} for options} @@ -65,7 +65,7 @@ the detection model} in the output. This can greatly increase the size of the model. If \code{FALSE}, the values are calculated post-hoc from the posteriors} -\item{...}{Arguments passed to the \code{\link{stan}} call, such as +\item{...}{Arguments passed to the \code{\link[rstan]{stan}} call, such as number of chains \code{chains} or iterations \code{iter}} } \value{ diff --git a/man/stan_distsamp.Rd b/man/stan_distsamp.Rd index ae016d5..88aa210 100644 --- a/man/stan_distsamp.Rd +++ b/man/stan_distsamp.Rd @@ -23,7 +23,7 @@ stan_distsamp( \item{formula}{Double right-hand side formula describing covariates of detection and occupancy in that order} -\item{data}{A \code{\link{unmarkedFrameDS}} object} +\item{data}{A \code{\link[unmarked]{unmarkedFrameDS}} object} \item{keyfun}{One of the following detection functions: \code{"halfnorm"} for half-normal, \code{"exp"} for negative exponential, @@ -51,7 +51,7 @@ scale parameter (i.e., log(scale)) for Hazard-rate models} \item{prior_sigma}{Prior distribution on random effect standard deviations} -\item{...}{Arguments passed to the \code{\link{stan}} call, such as +\item{...}{Arguments passed to the \code{\link[rstan]{stan}} call, such as number of chains \code{chains} or iterations \code{iter}} } \value{ diff --git a/man/stan_multinomPois.Rd b/man/stan_multinomPois.Rd index 06357bb..00e8735 100644 --- a/man/stan_multinomPois.Rd +++ b/man/stan_multinomPois.Rd @@ -20,7 +20,7 @@ stan_multinomPois( \item{formula}{Double right-hand side formula describing covariates of detection and abundance in that order} -\item{data}{A \code{\link{unmarkedFrameMPois}} object} +\item{data}{A \code{\link[unmarked]{unmarkedFrameMPois}} object} \item{prior_intercept_state}{Prior distribution for the intercept of the state (abundance) model; see \code{?priors} for options} @@ -40,7 +40,7 @@ the detection model} in the output. This can greatly increase the size of the model. If \code{FALSE}, the values are calculated post-hoc from the posteriors} -\item{...}{Arguments passed to the \code{\link{stan}} call, such as +\item{...}{Arguments passed to the \code{\link[rstan]{stan}} call, such as number of chains \code{chains} or iterations \code{iter}} } \value{ diff --git a/man/stan_occu.Rd b/man/stan_occu.Rd index 71b21b5..ebd4ed3 100644 --- a/man/stan_occu.Rd +++ b/man/stan_occu.Rd @@ -20,7 +20,7 @@ stan_occu( \item{formula}{Double right-hand side formula describing covariates of detection and occupancy in that order} -\item{data}{A \code{\link{unmarkedFrameOccu}} object} +\item{data}{A \code{\link[unmarked]{unmarkedFrameOccu}} object} \item{prior_intercept_state}{Prior distribution for the intercept of the state (occupancy probability) model; see \code{?priors} for options} @@ -40,7 +40,7 @@ the detection model} in the output. This can greatly increase the size of the model. If \code{FALSE}, the values are calculated post-hoc from the posteriors} -\item{...}{Arguments passed to the \code{\link{stan}} call, such as +\item{...}{Arguments passed to the \code{\link[rstan]{stan}} call, such as number of chains \code{chains} or iterations \code{iter}} } \value{ diff --git a/man/stan_occuRN.Rd b/man/stan_occuRN.Rd index 8ab8442..1d7ed62 100644 --- a/man/stan_occuRN.Rd +++ b/man/stan_occuRN.Rd @@ -21,7 +21,7 @@ stan_occuRN( \item{formula}{Double right-hand side formula describing covariates of detection and abundance in that order} -\item{data}{A \code{\link{unmarkedFrameOccu}} object} +\item{data}{A \code{\link[unmarked]{unmarkedFrameOccu}} object} \item{K}{Integer upper index of integration for N-mixture. This should be set high enough so that it does not affect the parameter estimates. @@ -45,7 +45,7 @@ the detection model} in the output. This can greatly increase the size of the model. If \code{FALSE}, the values are calculated post-hoc from the posteriors} -\item{...}{Arguments passed to the \code{\link{stan}} call, such as +\item{...}{Arguments passed to the \code{\link[rstan]{stan}} call, such as number of chains \code{chains} or iterations \code{iter}} } \value{ diff --git a/man/stan_occuTTD.Rd b/man/stan_occuTTD.Rd index 0091dcb..7e56e47 100644 --- a/man/stan_occuTTD.Rd +++ b/man/stan_occuTTD.Rd @@ -35,7 +35,7 @@ Currently ignored as dynamic models are not yet supported.} \item{detformula}{Right-hand sided formula for mean time-to-detection.} \item{data}{\code{unmarkedFrameOccuTTD} object that supplies the data -(see \code{\link{unmarkedFrameOccuTTD}}).} +(see \code{\link[unmarked]{unmarkedFrameOccuTTD}}).} \item{ttdDist}{Distribution to use for time-to-detection; either \code{"exp"} for the exponential, or \code{"weibull"} for the Weibull, @@ -66,7 +66,7 @@ shape parameter (i.e., log(shape)) for Weibull TTD models} in the output. This can greatly increase the size of the model. If \code{FALSE}, the values are calculated post-hoc from the posteriors} -\item{...}{Arguments passed to the \code{\link{stan}} call, such as +\item{...}{Arguments passed to the \code{\link[rstan]{stan}} call, such as number of chains \code{chains} or iterations \code{iter}} } \value{ diff --git a/man/stan_pcount.Rd b/man/stan_pcount.Rd index 6a1459c..6ea1bec 100644 --- a/man/stan_pcount.Rd +++ b/man/stan_pcount.Rd @@ -22,7 +22,7 @@ stan_pcount( \item{formula}{Double right-hand side formula describing covariates of detection and abundance in that order} -\item{data}{A \code{\link{unmarkedFramePCount}} object} +\item{data}{A \code{\link[unmarked]{unmarkedFramePCount}} object} \item{K}{Integer upper index of integration for N-mixture. This should be set high enough so that it does not affect the parameter estimates. @@ -48,7 +48,7 @@ the detection model} in the output. This can greatly increase the size of the model. If \code{FALSE}, the values are calculated post-hoc from the posteriors} -\item{...}{Arguments passed to the \code{\link{stan}} call, such as +\item{...}{Arguments passed to the \code{\link[rstan]{stan}} call, such as number of chains \code{chains} or iterations \code{iter}} } \value{ diff --git a/vignettes/ubms.Rmd b/vignettes/ubms.Rmd index 061dd4e..01dbd8a 100644 --- a/vignettes/ubms.Rmd +++ b/vignettes/ubms.Rmd @@ -195,7 +195,7 @@ To get the corresponding probabilities, you can use the `predict` function, whic For each parameter, the mean and standard deviation of the posterior distribution are given. Unlike `unmarked` output, there is no $Z$ or $p$-value. -Instead, there is a 95% [uncertainty interval](https://statmodeling.stat.columbia.edu/2016/11/26/reminder-instead-confidence-interval-lets-say-uncertainty-interval/) provided. +Instead, there is a 95% uncertainty interval provided. The final two columns in each summary table `n_eff` and `Rhat` are MCMC diagnostics. We will discuss their meaning later.