Initial roxygen pass

.gitignore

@@ -16,3 +16,8 @@ vignettes/*.html
 vignettes/*_files
 .DS_Store
 revdep/*
+*.o
+*.cc
+*.h
+src/Makevars
+R/stanmodels.R

DESCRIPTION

@@ -79,4 +79,4 @@ UseLTO: true
 NeedsCompilation: yes
 URL: https://mc-stan.org/rstanarm/, https://discourse.mc-stan.org
 BugReports: https://github.com/stan-dev/rstanarm/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

NAMESPACE

@@ -14,7 +14,13 @@ S3method(as_draws_rvars,stanreg)
 S3method(bayes_R2,stanreg)
 S3method(coef,stanmvreg)
 S3method(coef,stanreg)
+S3method(collapse_within_groups,default)
+S3method(collapse_within_groups,matrix)
 S3method(confint,stanreg)
+S3method(evaluate_log_survival,default)
+S3method(evaluate_log_survival,matrix)
+S3method(extract_pars,stanmvreg)
+S3method(extract_pars,stansurv)
 S3method(family,stanmvreg)
 S3method(family,stanreg)
 S3method(fitted,stanmvreg)
@@ -23,6 +29,8 @@ S3method(fixef,stanmvreg)
 S3method(fixef,stanreg)
 S3method(formula,stanmvreg)
 S3method(formula,stanreg)
+S3method(get_model_data,stanmvreg)
+S3method(get_model_data,stansurv)
 S3method(get_surv,stanjm)
 S3method(get_surv,stansurv)
 S3method(get_x,default)
@@ -35,6 +43,15 @@ S3method(get_z,lmerMod)
 S3method(get_z,stanmvreg)
 S3method(kfold,stanreg)
 S3method(launch_shinystan,stanreg)
+S3method(linear_predictor,default)
+S3method(linear_predictor,matrix)
+S3method(linkinv,character)
+S3method(linkinv,family)
+S3method(linkinv,stanmvreg)
+S3method(linkinv,stanreg)
+S3method(ll_args,stanjm)
+S3method(ll_args,stanreg)
+S3method(ll_args,stansurv)
 S3method(log_lik,stanjm)
 S3method(log_lik,stanmvreg)
 S3method(log_lik,stanreg)
@@ -73,6 +90,7 @@ S3method(pp_check,stanreg)
 S3method(predict,stanreg)
 S3method(predictive_error,matrix)
 S3method(predictive_error,ppd)
+S3method(predictive_error,stanmvreg)
 S3method(predictive_error,stanreg)
 S3method(predictive_interval,matrix)
 S3method(predictive_interval,ppd)
@@ -87,18 +105,28 @@ S3method(print,summary.stanreg)
 S3method(print,survfit.stanjm)
 S3method(print,survfit.stansurv)
 S3method(prior_summary,stanreg)
+S3method(psis,stanreg)
+S3method(quadrature_sum,default)
+S3method(quadrature_sum,matrix)
 S3method(ranef,stanmvreg)
 S3method(ranef,stanreg)
+S3method(rename_loos,stanreg)
+S3method(rename_loos,stanreg_list)
 S3method(residuals,stanmvreg)
 S3method(residuals,stanreg)
 S3method(se,stanmvreg)
 S3method(se,stanreg)
 S3method(sigma,stanmvreg)
 S3method(sigma,stanreg)
+S3method(split2,matrix)
+S3method(split2,vector)
 S3method(summary,stanmvreg)
 S3method(summary,stanreg)
 S3method(terms,stanmvreg)
 S3method(terms,stanreg)
+S3method(truncate,numeric)
+S3method(unpad_reTrms,array)
+S3method(unpad_reTrms,default)
 S3method(update,stanjm)
 S3method(update,stanmvreg)
 S3method(update,stanreg)
@@ -115,13 +143,17 @@ export(as_draws_matrix)
 export(as_draws_rvars)
 export(bayes_R2)
 export(cauchy)
+export(collapse_within_groups)
 export(compare_models)
 export(decov)
 export(default_prior_coef)
 export(default_prior_intercept)
 export(dirichlet)
+export(evaluate_log_survival)
 export(exponential)
+export(extract_pars)
 export(fixef)
+export(get_model_data)
 export(get_surv)
 export(get_x)
 export(get_y)
@@ -133,7 +165,10 @@ export(kfold)
 export(laplace)
 export(lasso)
 export(launch_shinystan)
+export(linear_predictor)
+export(linkinv)
 export(lkj)
+export(ll_args)
 export(log_lik)
 export(logit)
 export(loo)
@@ -166,7 +201,9 @@ export(prior_options)
 export(prior_summary)
 export(product_normal)
 export(ps_check)
+export(quadrature_sum)
 export(ranef)
+export(rename_loos)
 export(se)
 export(sigma)
 export(stan_aov)
@@ -196,6 +233,7 @@ export(stanmvreg_list)
 export(stanreg_list)
 export(student_t)
 export(tve)
+export(unpad_reTrms)
 export(waic)
 if(getRversion()>='3.3.0') importFrom(stats, sigma) else
   importFrom(lme4,sigma)

R/doc-rstanarm-package.R

@@ -104,4 +104,4 @@
 #' @template reference-bayesvis
 #' @template reference-muth
 #'
-NULL
+"_PACKAGE"

R/jm_make_assoc_terms.R

@@ -376,21 +376,36 @@ get_element <- function(parts, m = 1, which = "eta", ...) {
   }
 }
 
-# Collapse the linear predictor across the lower level units
-# clustered an individual, using the function specified in the
-# 'grp_assoc' argument
-#
-# @param eta The linear predictor evaluated for all lower level groups
-#   at the quadrature points.
-# @param grp_idx An N*2 array providing the indices of the first (col 1)
-#   and last (col 2) observations in eta that correspond to individuals
-#   i = 1,...,N.
-# @param grp_assoc Character string, the function to use to collapse
-#   across the lower level units clustered within individuals.
-# @return A vector or matrix, depending on the method called.
+#' Collapse the linear predictor across the lower level units
+#' clustered an individual, using the function specified in the
+#' 'grp_assoc' argument
+#'
+#' @param eta The linear predictor evaluated for all lower level groups
+#'   at the quadrature points.
+#' @param grp_idx An N*2 array providing the indices of the first (col 1)
+#'   and last (col 2) observations in eta that correspond to individuals
+#'   i = 1,...,N.
+#' @param grp_assoc Character string, the function to use to collapse
+#'   across the lower level units clustered within individuals.
+#' @return A vector or matrix, depending on the method called.
+#' @export
 collapse_within_groups <- function(eta, grp_idx, grp_assoc = "sum") {
   UseMethod("collapse_within_groups")
 }
+
+#' Collapse the linear predictor across the lower level units
+#' clustered an individual, using the function specified in the
+#' 'grp_assoc' argument
+#'
+#' @param eta The linear predictor evaluated for all lower level groups
+#'   at the quadrature points.
+#' @param grp_idx An N*2 array providing the indices of the first (col 1)
+#'   and last (col 2) observations in eta that correspond to individuals
+#'   i = 1,...,N.
+#' @param grp_assoc Character string, the function to use to collapse
+#'   across the lower level units clustered within individuals.
+#' @return A vector or matrix, depending on the method called.
+#' @export
 collapse_within_groups.default <- function(eta, grp_idx, grp_assoc) {
   N <- nrow(grp_idx)
   val <- rep(NA, N)
@@ -400,6 +415,19 @@ collapse_within_groups.default <- function(eta, grp_idx, grp_assoc) {
   }
   val
 }
+#' Collapse the linear predictor across the lower level units
+#' clustered an individual, using the function specified in the
+#' 'grp_assoc' argument
+#'
+#' @param eta The linear predictor evaluated for all lower level groups
+#'   at the quadrature points.
+#' @param grp_idx An N*2 array providing the indices of the first (col 1)
+#'   and last (col 2) observations in eta that correspond to individuals
+#'   i = 1,...,N.
+#' @param grp_assoc Character string, the function to use to collapse
+#'   across the lower level units clustered within individuals.
+#' @return A vector or matrix, depending on the method called.
+#' @export
 collapse_within_groups.matrix <- function(eta, grp_idx, grp_assoc) {
   N <- nrow(grp_idx)
   val <- matrix(NA, nrow = nrow(eta), ncol = N)