diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 0cab5a68..6d14af22 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -43,11 +43,13 @@ jobs: with: extra-packages: | any::rcmdcheck + any::BH + any::RcppEigen needs: check - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true - args: c("--ignore-vignettes", "--no-manual", "--as-cran") - build_args: c("--no-build-vignettes") + # args: c("--ignore-vignettes", "--no-manual", "--as-cran") + # build_args: c("--no-build-vignettes") diff --git a/R/helpers.R b/R/helpers.R index ef3bdead..e48b9e1c 100644 --- a/R/helpers.R +++ b/R/helpers.R @@ -189,7 +189,8 @@ release_questions <- function() { c( "Have you updated references?", "Have you updated inst/CITATION?", - "Have you updated the vignettes?" + "Have you updated the vignettes?", + "Have you tested building the vignettes on GitHub Actions?" ) } # nocov end diff --git a/vignettes/loo2-lfo.Rmd b/vignettes/loo2-lfo.Rmd index 905558e7..23ba7459 100644 --- a/vignettes/loo2-lfo.Rmd +++ b/vignettes/loo2-lfo.Rmd @@ -281,7 +281,7 @@ preds <- cbind( ) ggplot(cbind(df, preds), aes(x = year, y = Estimate)) + - geom_smooth(aes(ymin = Q5, ymax = Q95), stat = "identity", size = 0.5) + + geom_smooth(aes(ymin = Q5, ymax = Q95), stat = "identity", linewidth = 0.5) + geom_point(aes(y = y)) + labs( y = "Water Level (ft)", @@ -321,7 +321,7 @@ The initial step for the exact computation is to calculate the log-predictive densities by refitting the model many times: ```{r exact_loglik, results="hide"} -loglik_exact <- matrix(nrow = nsamples(fit), ncol = N) +loglik_exact <- matrix(nrow = ndraws(fit), ncol = N) for (i in L:(N - 1)) { past <- 1:i oos <- i + 1 @@ -514,7 +514,7 @@ predict. ```{r exact_loglikm, results="hide"} M <- 4 -loglikm <- matrix(nrow = nsamples(fit), ncol = N) +loglikm <- matrix(nrow = ndraws(fit), ncol = N) for (i in L:(N - M)) { past <- 1:i oos <- (i + 1):(i + M) diff --git a/vignettes/loo2-non-factorized.Rmd b/vignettes/loo2-non-factorized.Rmd index a48b0256..fb79ea03 100644 --- a/vignettes/loo2-non-factorized.Rmd +++ b/vignettes/loo2-non-factorized.Rmd @@ -569,7 +569,7 @@ is strong. In fact, summing over the pointwise ELPD values and leaving out the fourth observation yields practically equivalent results for approximate and exact LOO-CV: -````{r pt4} +```{r pt4} without_pt_4 <- c( approx = sum(psis_loo$pointwise[-4, "elpd_loo"]), exact = sum(exact_elpds[-4])