From 4a3fc2766376ec9ebe36de10c03ebaa265a5747c Mon Sep 17 00:00:00 2001 From: athowes Date: Thu, 1 Aug 2024 14:27:37 +0100 Subject: [PATCH 1/5] Add README.Rmd to Rbuildignore --- .Rbuildignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.Rbuildignore b/.Rbuildignore index 3f48a5497..dbd82beab 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -13,3 +13,4 @@ ^pkgdown$ ^doc$ ^Meta$ +README.Rmd From 828163a6231969bffa5c12702b48575572a79bee Mon Sep 17 00:00:00 2001 From: athowes Date: Thu, 1 Aug 2024 14:28:20 +0100 Subject: [PATCH 2/5] Move bayesplot and posterior to Suggests rather than Imports --- DESCRIPTION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3bf1a27ea..b1e41e913 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,14 +28,12 @@ Imports: cmdstanr, data.table, ggplot2, - posterior, purrr, ggridges, stats, cli, checkmate, - rstan, - bayesplot + rstan Suggests: bookdown, testthat (>= 3.0.0), @@ -45,7 +43,9 @@ Suggests: dplyr, knitr, roxyglobals, - tibble + tibble, + bayesplot, + posterior Remotes: stan-dev/cmdstanr, Rdatatable/data.table, From bb0126643e554071524976a0368f0224d7f576b0 Mon Sep 17 00:00:00 2001 From: athowes Date: Thu, 1 Aug 2024 14:29:39 +0100 Subject: [PATCH 3/5] Add tidyr (use in vignette) --- DESCRIPTION | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index b1e41e913..fa6eb774f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -45,7 +45,8 @@ Suggests: roxyglobals, tibble, bayesplot, - posterior + posterior, + tidyr Remotes: stan-dev/cmdstanr, Rdatatable/data.table, From c1bb3f9d199241a7c214d99ff9ad5e4b0b21a338 Mon Sep 17 00:00:00 2001 From: athowes Date: Thu, 1 Aug 2024 14:41:35 +0100 Subject: [PATCH 4/5] Perhaps do need posterior -- confusing checks --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index fa6eb774f..7b2d17399 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -33,7 +33,8 @@ Imports: stats, cli, checkmate, - rstan + rstan, + posterior Suggests: bookdown, testthat (>= 3.0.0), @@ -45,7 +46,6 @@ Suggests: roxyglobals, tibble, bayesplot, - posterior, tidyr Remotes: stan-dev/cmdstanr, From 70b380b895a1f5e992c3285eb4c5daed0bf1e048 Mon Sep 17 00:00:00 2001 From: athowes Date: Fri, 2 Aug 2024 12:11:37 +0100 Subject: [PATCH 5/5] Add explicit stats::update --- R/latent_individual.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/latent_individual.R b/R/latent_individual.R index ea14e6359..900c77c98 100644 --- a/R/latent_individual.R +++ b/R/latent_individual.R @@ -149,13 +149,14 @@ epidist_family.epidist_latent_individual <- function(data, #' @method epidist_formula epidist_latent_individual #' @family latent_individual #' @importFrom brms brmsterms +#' @importFrom stats update #' @export epidist_formula.epidist_latent_individual <- function(data, family, formula, ...) { epidist_validate(data) formula <- brms:::validate_formula(formula, data = data, family = family) - formula <- update( + formula <- stats::update( formula, delay_central | vreal(obs_t, pwindow_upr, swindow_upr) ~ . )