Fix check issues

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.

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.

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.

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.

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.

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.

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.

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.