small tweaks to docos

DESCRIPTION

@@ -2,7 +2,7 @@ Package: bayesnec
 Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
 Version: 2.1.3.0
 Authors@R: c(person("Rebecca", "Fisher", email = "[email protected]", role = c("aut", "cre"),comment = c(ORCID = "0000-0001-5148-6731")), person("Diego R.","Barneche",role="aut",comment = c(ORCID = "0000-0002-4568-2362")), person("Gerard F.","Ricardo",role="aut",comment = c(ORCID = "0000-0002-2220-3971")), person("David R.","Fox",role="aut",comment = c(ORCID = "0000-0002-3178-7243")))
-Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). A full description of this package can be found in Fisher 'et al.' (2024)<doi:10.18637/jss.v110.i05>. This package expands and supersedes an original version implemented in R2jags (see Su and Yajima (2020)<https://CRAN.R-project.org/package=R2jags>; Fisher et al. (2020)<doi:10.5281/ZENODO.3966864>).
+Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). A full description of this package can be found in Fisher 'et al.' (2024)<doi:10.18637/jss.v110.i05>. This package expands and supersedes an original version implemented in 'R2jags' (see Su and Yajima (2020)<https://CRAN.R-project.org/package=R2jags>; Fisher et al. (2020)<doi:10.5281/ZENODO.3966864>).
 Depends:
     R (>= 4.1),
     brms,

R/check_priors.R

@@ -6,8 +6,9 @@
 #' @param filename An optional \code{\link[base]{character}} vector to be used
 #' as a pdf filename in the case of a \code{\link{bayesmanecfit}}. Any non
 #' empty character string will indicate the user wants to save the plots.
-#' @param ask Should the user be asked to hit enter for next page for a 
-#' \code{\link{bayesmanecfit}} object?
+#' @param ask Should the user be asked to hit enter for next page? Defaults to
+#' \code{TRUE}. Only relevant if \code{object} is of class
+#' \code{\link{bayesmanecfit}}.
 #'
 #' @seealso \code{\link{bnec}}
 #'
@@ -21,11 +22,10 @@
 #' }
 #'
 #' @export
-check_priors <- function(object, filename = NA, ask = ask) {
+check_priors <- function(object, filename = NA, ask = TRUE) {
   UseMethod("check_priors")
 }
 
-
 #' Plots the prior and posterior parameter probability densities from an
 #' object of class \code{\link{bayesnecfit}}.
 #'
@@ -43,7 +43,7 @@ check_priors <- function(object, filename = NA, ask = ask) {
 #' @noRd
 #'
 #' @export
-check_priors.bayesnecfit <- function(object, filename = NA) {
+check_priors.bayesnecfit <- function(object, filename = NA, ask = TRUE) {
   if (!is.na(filename)) {
     chk_character(filename)
   }

R/pull_brmsfit.R

@@ -1,4 +1,4 @@
-#' Extract and object of class \code{\link{brmsfit}} from
+#' Extract and object of class \code{\link[brms]{brmsfit}} from
 #' \code{\link{bayesnecfit}} or \code{\link{bayesmanecfit}}.
 #'
 #' @param object An object of class \code{\link{bayesnecfit}} or
@@ -7,7 +7,7 @@
 #'
 #' @seealso \code{\link{bnec}}
 #'
-#' @return A plot of the prior and posterior parameter probability densities.
+#' @return An object of class \code{\link[brms]{brmsfit}}.
 #'
 #' @examples
 #' library(bayesnec)