Fix vignettes and add pkgdown GA

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,47 @@
+## Copied this workflow from: https://github.com/waldronlab/bugphyzz/blob/main/.github/workflows/pkgdown.yaml
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    container: bioconductor/bioconductor_docker:RELEASE_3_19
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Install apt dependencies
+        run: |
+          sudo apt-get update && sudo apt-get install -y rsync
+
+      - name: Install R dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
+          install.packages("pkgdown", dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Build site 
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: gh-pages
+          clean: false
+          folder: docs

_pkgdown.yml

@@ -1,4 +1 @@
 url: http://waldronlab.io/MicrobiomeBenchmarkDataAnalyses/
-template:
-  bootstrap: 5
-

vignettes/articles/HMP_2012_WMS_gingival.Rmd

@@ -61,36 +61,40 @@ ps
 Select methods for DA:
 
 ```{r, message=FALSE, warning=FALSE}
-# ps <- runNormalizations(set_norm_list(), ps, verbose = FALSE)
-# zw <- weights_ZINB(ps, design = conditions_col)
-# DA_methods <- set_DA_methods_list(conditions_col, conditions)
-# 
-# for (i in seq_along(DA_methods)) {
-#     if (grepl("Seurat", names(DA_methods)[i])) {
-#         names(DA_methods[[i]]$contrast) <- NULL
-#     } else {
-#         next
-#     }
-# }
-# names(DA_methods)
-```
-
-
-
-# Run DA
-
-```{r, message=FALSE, warning=FALSE}
-## DA_output <- run_DA(ps, conditions_col, conditions)
 ps <- runNormalizations(set_norm_list(), ps, verbose = FALSE)
 zw <- weights_ZINB(ps, design = conditions_col)
 DA_methods <- set_DA_methods_list(conditions_col, conditions)
 
+for (i in seq_along(DA_methods)) {
+    if (grepl("Seurat", names(DA_methods)[i])) {
+        names(DA_methods[[i]]$contrast) <- NULL
+    } else {
+        next
+    }
+}
 # These methods throw an error, so they must be removed
-DA_methods <- DA_methods[!names(DA_methods) == 'DA_ALDEx2.1']
-DA_methods <- DA_methods[!names(DA_methods) == 'DA_corncob.1']
+# DA_methods <- DA_methods[!names(DA_methods) == 'DA_ALDEx2.1']
+# DA_methods <- DA_methods[!names(DA_methods) == 'DA_corncob.1']
+DA_methods <- DA_methods[!names(DA_methods) == 'DA_edgeR.1']
+names(DA_methods)
+```
 
-# run methods
-DA_output <- runDA(DA_methods, ps, weights = zw, verbose = FALSE)
+```{r, warning=FALSE, message=TRU}
+tim <- system.time({
+    DA_output <- vector("list", length(DA_methods))
+    for (i in seq_along(DA_output)) {
+        message(
+            "Running method ", i, ": ", names(DA_methods)[i], " - ", Sys.time()
+        )
+        DA_output[[i]] <- tryCatch(
+            error = function(e) NULL,
+            runDA(DA_methods[i], ps, weights = zw, verbose = FALSE) 
+        )
+    }
+    DA_output <- purrr::list_flatten(DA_output, name_spec = "{inner}")
+    DA_output <- purrr::discard(DA_output, is.null)
+})
+tim
 ```
 
 # Enrichment
@@ -159,7 +163,7 @@ positives <- createPositives(
 
 ## Plot TP - FP 
 
-```{r, fig.height = 6, fig.width=10}
+```{r, fig.height = 10, fig.width=15}
 positive_plots <- plot_positives(positives)
 grid.arrange(grobs = positive_plots, ncol = 3)
 ```
@@ -169,5 +173,3 @@ grid.arrange(grobs = positive_plots, ncol = 3)
 ```{r session info}
 sessionInfo()
 ```
-
-

vignettes/articles/Ravel_2011_16S_BV.Rmd

@@ -94,19 +94,61 @@ methods added to the original workflow and modified plots.
 
 ## Run differential abundance analysis
 
+
 DA analysis:
 
-```{r run DA benchdamic, message=FALSE, warning=FALSE}
+```{r}
 ps <- runNormalizations(set_norm_list(), ps, verbose = FALSE)
 zw <- weights_ZINB(ps, design = conditions_col)
 DA_methods <- set_DA_methods_list(conditions_col, conditions)
 
+for (i in seq_along(DA_methods)) {
+    if (grepl("Seurat", names(DA_methods)[i])) {
+        names(DA_methods[[i]]$contrast) <- NULL
+    } else {
+        next
+    }
+}
+# These methods throw an error, so they must be removed
+# DA_methods <- DA_methods[!names(DA_methods) == 'DA_ALDEx2.1']
+# DA_methods <- DA_methods[!names(DA_methods) == 'DA_corncob.1']
+# DA_methods <- DA_methods[!names(DA_methods) == 'DA_edgeR.1']
+names(DA_methods)
+```
+
+
+
+```{r, warning=FALSE, message=TRUE}
+tim <- system.time({
+    DA_output <- vector("list", length(DA_methods))
+    for (i in seq_along(DA_output)) {
+        message(
+            "Running method ", i, ": ", names(DA_methods)[i], " - ", Sys.time()
+        )
+        DA_output[[i]] <- tryCatch(
+            error = function(e) NULL,
+            runDA(DA_methods[i], ps, weights = zw, verbose = FALSE) 
+        )
+    }
+    DA_output <- purrr::list_flatten(DA_output, name_spec = "{inner}")
+    DA_output <- purrr::discard(DA_output, is.null)
+})
+tim
+```
+
+
+
+```{r run DA benchdamic, message=FALSE, warning=FALSE}
+# ps <- runNormalizations(set_norm_list(), ps, verbose = FALSE)
+# zw <- weights_ZINB(ps, design = conditions_col)
+# DA_methods <- set_DA_methods_list(conditions_col, conditions)
+
 ## These methods throw an error, so they must be removed
-DA_methods <- DA_methods[!names(DA_methods) == 'DA_ALDEx2.1']
-DA_methods <- DA_methods[!names(DA_methods) == 'DA_corncob.1']
+# DA_methods <- DA_methods[!names(DA_methods) == 'DA_ALDEx2.1']
+# DA_methods <- DA_methods[!names(DA_methods) == 'DA_corncob.1']
 
 ## run methods
-DA_output <- runDA(DA_methods, ps, weights = zw, verbose = FALSE) 
+# DA_output <- runDA(DA_methods, ps, weights = zw, verbose = FALSE) 
 ```
 
 # Enrichment
@@ -179,7 +221,7 @@ positives <- createPositives(
 
 Create putative positives plot
 
-```{r plot positves, fig.width=10, fig.height=6}
+```{r plot positves, fig.width=15, fig.height=10}
 plots <- plot_positives(positives)
 grid.arrange(grobs = plots, ncol = 3)
 ```
@@ -205,7 +247,8 @@ assay(tse_genus, 'TSS + CLR') <- apply(assay(tse_genus, 'TSS'), 2, function(x) {
     # log(x / exp(mean(log(x))))
 })
 
-data <- tidySummarizedExperiment::as_tibble(tse_genus) |> 
+data <- tse_genus |> 
+    as_tibble() |> 
     rename(taxon_name = .feature, sample = .sample) |> 
     mutate(
         taxon_annotation = ifelse(