ethanplunkett · Oct 22, 2026 · Oct 22, 2026 · Oct 22, 2026 · Oct 22, 2026 · Oct 22, 2026
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -2,3 +2,5 @@
 ^\.Rproj\.user$
 ^\.github$
 ^data-raw$
+^LICENSE\.md$
+^cran-comments\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: BirdFlowExamples
-Title: Data package with example BirdFlowR models
+Title: Data Package with Example BirdFlowR Models
 Version: 0.0.1.9001
 Authors@R: 
       person("Ethan", "Plunkett",  email = "plunkett@umass.edu", 
@@ -15,10 +15,8 @@ LazyData: true
 LazyDataCompression: gzip
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends: 
     R (>= 3.5)
 Imports:
     Matrix
-Remotes:
-  birdflow-science/BirdFlowR
diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2026 birdflow-science
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2026
+COPYRIGHT HOLDER: birdflow-science
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 birdflow-science
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+## BirdFlowExamples 0.0.1.9001
+2026-10-22
+
+* Renamed package from `BirdFlowModels` to `BirdFlowExamples`. The data
+  object names (`amewoo`, `rewbla`, `rewbla_observations`,
+  `rewbla_intervals`, `states`) are unchanged.
+
+* Refit `amewoo` and `rewbla` and reduced their file size.
+
 ## BirdFlowModels 0.0.2.9003
 2025-04-08 
 

diff --git a/R/data.R b/R/data.R
@@ -1,8 +1,8 @@
 # This file documents data
 
-#' @name BirdFlowModels
-#' @rdname BirdFlowModels
-#' @aliases BirdFlowModels
+#' @name BirdFlowExamples
+#' @rdname BirdFlowExamples
+#' @aliases BirdFlowExamples
 #' @aliases amewoo
 #' @aliases rewbla
 #' @title Birdflow Example Models
@@ -12,13 +12,14 @@
 #'
 #' @format `BirdFlow` model
 #'
-#' @source Trained on eBird Status and Trends 2019 and 2021 Data.
+#' @source Trained on eBird Status and Trends 2023 Data.
 #'
-#' @references Fink, D., T. Auer, A. Johnston, M. Strimas-Mackey, S. Ligocki, O.
-#' Robinson, W. Hochachka, L. Jaromczyk, A. Rodewald, C. Wood, I. Davies, A.
-#' Spencer. 2022. eBird Status and Trends, Data Version: 2021; Released: 2022.
-#' Cornell Lab of Ornithology, Ithaca, New York.
-#' https://doi.org/10.2173/ebirdst.2021
+#' @references  Fink, D., T. Auer, A. Johnston, M. Strimas-Mackey, S. Ligocki, O. Robinson,
+#' W. Hochachka, L. Jaromczyk, C. Crowley, K. Dunham, A. Stillman, C. Davis, M. Stokowski,
+#' P. Sharma, V. Pantoja, D. Burgin, P. Crowe, M. Bell, S. Ray, I. Davies, V. Ruiz-Gutierrez,
+#' C. Wood, A. Rodewald. 2024.
+#' eBird Status and Trends, Data Version: 2023;
+#' Released: 2025. Cornell Lab of Ornithology, Ithaca, New York. https://doi.org/10.2173/WZTW8903
 #' @seealso [BirdFlowR::load_model()] will load a vetted model from a
 #' BirdFlow model collection.  `BirdFlowR::load_collection_index()` will
 #' return a data frame with information on available models.

diff --git a/R/states.R b/R/states.R
@@ -15,7 +15,7 @@
 #' class **data.frame** and has columns:
 #' \describe{
 #'   \item{name}{State name}
-#'   \item{geometry}{Contains polyon information}
+#'   \item{geometry}{Contains polygon information}
 #'
 #'  The code below was used to create this object:
 #'  ```

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
-# BirdFlowModels
+# BirdFlowExamples
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/birdflow-science/BirdFlowModels/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/birdflow-science/BirdFlowModels/actions/workflows/R-CMD-check.yaml)
+[![R-CMD-check](https://github.com/birdflow-science/BirdFlowExamples/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/birdflow-science/BirdFlowExamples/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 This is a "Data" R package that contains a fitted BirdFlow model for use with 
@@ -26,14 +26,14 @@ the data in the package will change frequently.
 Use the code below to install from github
 
 ```{r}
-devtools::install_github("birdflow-science/BirdFlowModels")
+devtools::install_github("birdflow-science/BirdFlowExamples")
 ```
 ## Use
 
 After loading this package the dataset will be available for use.
 
 ```{r}
-library(BirdFlowModels)
+library(BirdFlowExamples)
 library(BirdFlowR)
 print(amewoo)
 species(amewoo)

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,29 @@
+# CRAN comments
+
+## Package size
+
+`R CMD check` reports an installed size of 6.3 MB (`data` subdirectory
+6.2 MB), driven by the example `BirdFlow` model objects the package
+exists to provide (`amewoo.rda` 3.9 MB, `rewbla.rda` 1.1 MB, plus
+`states.rda`, `rewbla_observations.rda`, and `rewbla_intervals.rda`
+together under 0.2 MB on disk). This is over the informal 5 MB
+guideline for source packages.
+
+These models and ancillary data are the package's sole purpose: fitted
+example models for testing and demonstrating the companion `BirdFlowR`
+package. They have already been fit at coarse spatial resolution
+(`amewoo` at 150 km, `rewbla` at 350 km) and, for `rewbla`, with heavy
+sparsification specifically to minimize size while still exercising the
+code paths they are used for (geometry mismatches and season wraparound
+in particular). `amewoo`'s resolution was kept finer than `rewbla`'s
+because it is also used in `BirdFlowR` vignette figures, where coarser
+resolution would visibly degrade example output.
+
+## Test environments
+
+* local macOS install, R 4.x
+* GitHub Actions: macOS, Windows, Ubuntu (release and devel)
+
+## R CMD check results
+
+0 errors | 0 warnings | 0 notes
diff --git a/data-raw/DATASET.R b/data-raw/DATASET.R
diff --git a/data-raw/models.R b/data-raw/models.R
@@ -0,0 +1,88 @@
+# Code to fit amewoo model on Unity Cluster. It is unlikely to work
+# in other contexts.
+
+# Currently there are two models the first amewoo is used in most examples.
+# It is not a sparse model.
+# The second rewbla was initial added to test evaluation code
+# e.g. BirdFlowR::interval_log_likelihood()
+# and is used in a few other tests. It is heavily sparsified.
+
+
+dir <- "/work/pi_plunkett_umass_edu/birdflowexamples/"
+
+library(BirdFlowR)
+library(BirdFlowPipeline)
+bf <- load_model("amewoo")
+
+species <- "amewoo"
+res <- 150
+hp <- bf$metadata$hyperparameters
+
+dir.create(dir, showWarnings = FALSE)
+batch_species(species = species,
+              grid_search_type = "old",
+              dist_pow = hp$dist_pow,
+              dist_weight = hp$dist_weight,
+              ent_weight = hp$ent_weight,
+              res = res,
+              hdf_path = dir,
+              base_output_path = dir,
+              clip = BirdFlowPipeline::americas_clip,
+              crs = as.character(BirdFlowPipeline::americas_crs)[2])
+
+
+
+result <- paste0(dir, species, "_", res, "km/", species,
+                 "_", ebirdst::ebirdst_version()$status_version_year[1], "_",
+                 res, "km_obs1.0_ent",
+                 hp$ent_weight,
+                 "_dist", hp$dist_weight,
+                 "_pow", hp$dist_pow, ".hdf5")
+
+
+bf <- import_birdflow(result)
+
+amewoo <- bf
+
+usethis::use_data(amewoo, compress = "xz")
+
+
+# Note I'm using the tuned parameters from AMEWOO for rewbla as well
+# This isn't best practice for models used for inference but
+# is fine for creating a second model
+species <- "rewbla"
+res <- 350
+hp <- bf$metadata$hyperparameters
+
+dir.create(dir, showWarnings = FALSE)
+batch_species(species = species,
+              grid_search_type = "old",
+              dist_pow = hp$dist_pow,
+              dist_weight = hp$dist_weight,
+              ent_weight = hp$ent_weight,
+              res = res,
+              hdf_path = dir,
+              base_output_path = dir,
+              clip = BirdFlowPipeline::americas_clip,
+              crs = as.character(BirdFlowPipeline::americas_crs)[2])
+
+
+
+result <- paste0(dir, species, "_", res, "km/", species,
+                 "_", ebirdst::ebirdst_version()$status_version_year[1], "_",
+                 res, "km_obs1.0_ent",
+                 hp$ent_weight,
+                 "_dist", hp$dist_weight,
+                 "_pow", hp$dist_pow, ".hdf5")
+
+
+
+bf <- import_birdflow(result)
+rewbla <- sparsify(bf, method = "conditional", p = .95, p_protected = 0.05)
+
+
+
+usethis::use_data(rewbla, compress = "xz", overwrite = TRUE)
+
+
+
diff --git a/data/amewoo.rda b/data/amewoo.rda
diff --git a/data/rewbla.rda b/data/rewbla.rda
diff --git a/data/rewbla_intervals.rda b/data/rewbla_intervals.rda
diff --git a/data/rewbla_observations.rda b/data/rewbla_observations.rda
diff --git a/data/states.rda b/data/states.rda
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,26 +1,35 @@
 Auer
-BSM
+birdflow
 BirdFlow
+BirdFlowModels
 BirdFlowR
 Birdflow
-CMD
+BSM
+Burgin
 Celis
+CMD
+Crowe
+doi
+Dunham
+eBird
+ebirdst
+github
 Hochachka
+https
 Jaromczyk
 Ligocki
 Mackey
 Malorodova
 Nakash
-Rodewald
-Strimas
-birdflow
-doi
-eBird
-ebirdst
-github
-https
 natively
+Pantoja
 preprocessed
 rewbla
 rnaturalearthhires
+Rodewald
+Sharma
+Stillman
+Stokowski
+Strimas
+WZTW