jibarozzo · May 20, 2026 · Apr 25, 2026 · Apr 27, 2026 · Apr 28, 2026 · Apr 28, 2026
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -70,11 +70,12 @@ jobs:
           extra-packages: |
             any::rcmdcheck
             any::tidyverse
+            any::devtools
           needs: check
 
       - name: Check package
         uses: r-lib/actions/check-r-package@v2
         with:
-          error-on: "\"error\""
+          error-on: '"error"'
           upload-snapshots: true
-          build_args: "c(\"--no-manual\",\"--compact-vignettes=gs+qpdf\")"
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -6,7 +6,7 @@ on:
       - main
       - develop
   release:
-    types: [ published ]
+    types: [published]
   workflow_dispatch:
 
 name: pkgdown.yaml

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   issue_comment:
-    types: [ created ]
+    types: [created]
 
 name: pr-commands.yaml
 

diff --git a/.github/workflows/render-rmarkdown.yaml b/.github/workflows/render-rmarkdown.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   pull_request:
-    branches: [ main ]
+    branches: [main]
   release:
-    types: [ published ]
+    types: [published]
   workflow_dispatch:
 
 name: render-rmarkdown.yaml

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,7 +1,6 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
-
   pull_request:
     branches:
       - main

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: BRCore
-Title: Unified Framework for Identification and Ecological Interpretation of Microbial Data from Bioenergy Research Centers
-Version: 2.0.4.9000
+Title: A Unified Framework for Identification and Ecological Interpretation of Microbial Data from Bioenergy Research Centers
+Version: 2.0.7.9000
 Authors@R: c(
     person("Bolívar", "Aponte Rolón",
            email = "bolaponte@pm.me", 
@@ -28,11 +28,9 @@ Authors@R: c(
            role = c("cph", "fnd"))
   )
 Description: A unified framework for identification and ecological interpretation of core microbiomes across time and space, enhancing robustness and reproducibility in microbiome data analysis. 'BRCore' implements the workflow proposed by Shade and Stopnisek (2019) and incorporates additional rarefaction steps. The proposed workflow aims to identify persistent microbiomes using abundance-occupancy distributions and neutral community model fitting. For more details on abundance-occupancy distributions see Shade A, Stopnisek N (2019) <doi:10.1016/j.mib.2019.09.008>, for neutral models, see Sloan et al. (2006) <doi:10.1111/j.1462-2920.2005.00956.x> and Burns et al. (2015) <doi:10.1038/ismej.2015.142>.
-License: MIT + file LICENSE
-Encoding: UTF-8
-Language: en-US
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
+Depends: 
+    R (>= 4.4)
+biocViews:
 Imports: 
     cli (>= 3.6.5),
     dplyr (>= 1.1.4),
@@ -42,24 +40,25 @@ Imports:
     Hmisc (>= 5.2.4),
     magrittr (>= 2.0.4),
     minpack.lm (>= 1.2.4),
-    phyloseq (>= 1.54.0),
+    phyloseq,
     rlang (>= 1.1.6),
     scales (>= 1.4.0),
-    stats4 (>= 4.5.2),
+    stats4,
     tibble (>= 3.3.0),
     tidyr (>= 1.3.1),
     vegan (>= 2.7.2)
 Suggests:
-    devtools (>= 2.4.5),
-    here (>= 1.0.1),
     knitr (>= 1.50),
     rmarkdown (>= 2.30),
     testthat (>= 3.2.3),
     tidyverse (>= 2.0.0),
     viridis (>= 0.6.5)
+License: MIT + file LICENSE
+Encoding: UTF-8
+Language: en-US
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
 Config/testthat/edition: 3
-Depends: 
-    R (>= 4.4)
 LazyData: true
 VignetteBuilder: knitr
 URL: https://github.com/germs-lab/BRCore, https://www.germslab.org/BRCore/

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,34 @@
 # BRCore (development version)
-* Fixes to quote 'BRCore' in DESCRIPTION and typo fix of `sncm.fit` in _pkgdown.yaml
+
+# BRCore 2.0.7
+2026-05-19
+
+*  [a43bc71](https://github.com/germs-lab/BRCore/commit/a43bc71d779c5b1b11b1291056570c6e00124212) Typo and instructions fixes to README and DESCRIPTION files.
+
+# BRCore 2.0.5
+2026-05-18
+
+## Bug Fixes
+
+* Relaxed version requirements for `phyloseq` and `stats4` to improve compatibility.
+
+* [5ba7a7c](https://github.com/germs-lab/BRCore/commit/5ba7a7c3067a2044c34aee812795dc427869eb4b) Added `biocViews` field to DESCRIPTION to allow installation of Bioconductor dependencies via `install.packages()`.
+* [40d79e4](https://github.com/germs-lab/BRCore/commit/40d79e448c632f590e4e52cbf16537496b29529f) Fixes to quote 'BRCore' in DESCRIPTION and typo fix of `sncm.fit` in _pkgdown.yaml
+
+## Refactoring
+
+* [95a42db](https://github.com/germs-lab/BRCore/commit/95a42db482675450157ec2099a658e0ce538901c) `sncm.fit()`: replaced `suppressWarnings()` with targeted warning capture via new internal helper `.internal_warn_sncm()`.
+* [46eff6f](https://github.com/germs-lab/BRCore/commit/46eff6fb691fd370e5b3723e285bb3882760d742) `plot_neutral_model()`: refined plot axis styling and formatted y-axis as percent. Resized box annotation.
+* [b275861](https://github.com/germs-lab/BRCore/commit/b275861e8434204d66dc4962d10499488d738513) Removed redundant `data("bcse")` calls from examples and README vignette.
+
+## Documentation
+
+* [46ef2ba](https://github.com/germs-lab/BRCore/commit/46ef2ba1ebb006736f9b86bfa7b06f3adca40f49) Updated vignette output.
+* [b275861](https://github.com/germs-lab/BRCore/commit/b275861e8434204d66dc4962d10499488d738513) Removed deprecated `num_iter` parameter from README examples.
+* Reordered DESCRIPTION fields.
 
 # BRCore 2.0.4
-Date: 2026-04-30
+2026-04-30
 
 * Fixes to documentation: 
     * DOI links updated to correct format
@@ -13,20 +39,20 @@ Date: 2026-04-30
     * New APA 7th edition style for references
 
 # BRCore 2.0.2
-Date: 2026-04-28
+2026-04-28
 
 * Fixes to vignette and function documentation prior to CRAN submission.
 * Removed "multiple rarefaction" concept from documentation.
 * Removed `parallel_helpers.R` since we have moved away from parallel implementations.
 * Cleaned NAMESPACE and DESCRIPTION.
 
 # BRCore 2.0.1
-Date: 2026-04-25
+2026-04-25
 
 * Resubmission to CRAN to address auto-check issues on Debian and Windows.
 
 # BRCore 2.0.0
-Date: 2026-04-24
+2026-04-24
 
 ## Breaking Changes
 
@@ -68,7 +94,7 @@ Date: 2026-04-24
 @jibarozzo @Gian77
 
 # BRCore 1.0.2
-Date: 2026-02-25
+2026-02-25
 
 ## Bug Fixes
 

diff --git a/R/add_rarefaction_metrics.R b/R/add_rarefaction_metrics.R
@@ -35,8 +35,6 @@
 #' library(phyloseq)
 #' library(BRCore)
 #'
-#' data("bcse", package = "BRCore")
-#'
 #' # Adding metrics to a "phyloseq" object
 #' bcse_metrics <- add_rarefaction_metrics(data = bcse)
 #' sample_data(bcse_metrics)|>

diff --git a/R/brcore_theme.R b/R/brcore_theme.R
@@ -78,7 +78,7 @@
       # Axes ----
       axis.title = element_text(
         size = base_size,
-        face = "bold",
+        face = "plain",
         colour = "black"
       ),
       axis.text = element_text(

diff --git a/R/identify_core.R b/R/identify_core.R
@@ -101,9 +101,6 @@
 #' \donttest{
 #' library(BRCore)
 #'
-#' data("switchgrass", package = "BRCore")
-#' data("bcse", package = "BRCore")
-#'
 #' # With rarefied data
 #' res <- identify_core(
 #'   physeq_obj     = switchgrass,

diff --git a/R/multi_rarefy.R b/R/multi_rarefy.R
@@ -28,7 +28,7 @@
 #'
 #' @examples
 #' library(BRCore)
-#' data("bcse", package = "BRCore")
+#'
 #'
 #' # Example rarefaction (single iteration, single core to keep examples fast)
 #' otu_table_rare <- multi_rarefy(

diff --git a/R/plot_identified_core.R b/R/plot_identified_core.R
@@ -69,12 +69,12 @@ plot_identified_core <- function(
   prop_range <- max_prop - min_prop
 
   # Dynamic y positions for labels
-  elbow_y <- min_prop + 0.15 * prop_range
+  elbow_y <- min_prop + 0.1 * prop_range
   lastCall_y <- min_prop + 0.35 * prop_range
 
   # Adjust x position for labels if too close to edges
   elbow_x_offset <- ifelse(
-    elbow < max_rank * 0.1,
+    elbow < max_rank * 1.2,
     elbow + max_rank * 0.02,
     elbow - max_rank * 0.02
   )
@@ -86,7 +86,7 @@ plot_identified_core <- function(
 
   # Base plot
   p <- ggplot(new_data, aes(x = rank_num, y = proportionBC)) +
-    geom_point(size = 1.5, alpha = 0.7) +
+    geom_point(size = 2, alpha = 0.7) +
     geom_vline(
       xintercept = elbow,
       linetype = "dashed",
@@ -162,9 +162,10 @@ plot_identified_core <- function(
         " OTUs)"
       ),
       x = "Ranked OTUs",
-      y = "% Bray-Curtis similarity"
+      y = "Bray-Curtis similarity"
     ) +
     .brcore_theme() +
+    scale_y_continuous(labels = scales::label_percent(accuracy = 1)) +
     scale_x_continuous(breaks = seq(0, max(new_data$rank_num), by = 5))
 
   return(list(

diff --git a/R/plot_neutral_model.R b/R/plot_neutral_model.R
@@ -205,7 +205,7 @@ plot_neutral_model <- function(fit_result) {
       parse = TRUE,
       hjust = 1,
       vjust = -0.75,
-      size = 3,
+      size = 4.5,
       fill = "white",
       alpha = 0.9,
       lineheight = 1.05
@@ -214,7 +214,8 @@ plot_neutral_model <- function(fit_result) {
       title = "Neutral model",
       x = "Log10(mean abundance)",
       y = "Occupancy"
-    )
+    ) +
+    scale_y_continuous(labels = scales::label_percent(accuracy = 1))
   # change legend shape to avoid confusion with the scatter points.
   p <- p +
     guides(

diff --git a/R/plot_rarefaction_metrics.R b/R/plot_rarefaction_metrics.R
@@ -15,8 +15,6 @@
 #' library(phyloseq)
 #' library(BRCore)
 #'
-#' data("bcse", package = "BRCore")
-#'
 #' # Add rarefaction metrics to the phyloseq object
 #' bcse_metrics <- add_rarefaction_metrics(bcse)
 #'

diff --git a/R/plot_variance_propagation.R b/R/plot_variance_propagation.R
@@ -23,7 +23,6 @@
 #' library(phyloseq)
 #' library(BRCore)
 #' # Example comparing hill q=1 between Poplar and Switchgrass plots
-#' data("bcse", package = "BRCore")
 #' bcse_filt <- bcse |>
 #' subset_samples(Crop %in% c("Poplar", "Switchgrass"))
 #'