v2.5.1

bbsBayes version 2.5.1 has been released and is available for immediate download from CRAN: https://cran.r-project.org/web/packages/bbsBayes/index.html

New to This Release

• Access to 2022 Release of Breeding Bird Survey data
• missing random intercept for stratum in slope models added in
• minor fixes to fix CRAN notes

Note that we have now moved to a major.minor.patch version number, rather than the previous major.minor.patch.year, where year specified the data year.

v2.4.0.2020

bbsBayes version 2.4.0.2020 has been released on CRAN as of 10 March 2022.

The most major change since the last update was updated model definitions and argument names. See this thread for details: #187

v2.3.7.2020

v2.3.7.2020 of bbsBayes has been released on CRAN as of 23 June 2021. https://cran.r-project.org/package=bbsBayes

This release note highlights the key changes since v2.3.6.2020:

Line width argument in plot_indices()

Now you can specify an increase or decrease in line width on all plots produced by plot_indices() using the line_width argument

Add clearer messages during JAGS modelling

When JAGS models run, the jagsUI package takes over the console messages. We have added a message stating such

Add viridis option for mapping

By setting col_viridis = TRUE one can use the viridis colour palette for generate_map

Add load_map() function

This function allows the user to load the sf shapefile of any of the 5 stratification options directly into their environment

Deprecate prepare_jags_data() in favour of prepare_data()

In preparation for the eventual option of using a Stan model rather than a JAGS model, we have generalized this function to allow for preparation of data for either JAGS or (in the future) for Stan. For now, since bbsBayes only supports JAGS, we have set the default of sampler = "jags".

v2.3.4.2020

v2.3.4.2020 of bbsBayes has been released on CRAN as of 22 October 2020. See the CRAN release here: https://cran.r-project.org/web/packages/bbsBayes/index.html

This version modifies the patch done for 2.3.3.2020 that deals with stop-level data. The upstream version of the data has been repaired, so the patch was no longer needed.

v2.3.3.2020

v2.3.3.2020

bbsBayes v2.3.3.2020 has been released on CRAN as of 8 July 2020. See release on CRAN here: https://cran.r-project.org/web/packages/bbsBayes/index.html

This version patches a bug from v2.3.2.2020 where fetch_bbs_data() encounters an unexpected column in a data frame for the wrong data level and crashes. This has been repaired in the new version.

v2.3.2.2020

v2.3.2.2020

bbsBayes v2.3.2.2020 has been released on CRAN as of 27 June 2020. See release on CRAN here: https://cran.r-project.org/web/packages/bbsBayes/index.html

The following minor changes have been made to bbsBayes since 2.2.2

2020 USGS Breeding Bird Survey Data Set Release

• The United States Geological Survey has released the 2020 version of the Breeding Bird Survey data set, which now includes data spanning 1966 - 2019
• USGS has opted to host the data on ScienceBase rather than FTP, thus fetch_bbs_data() had to be updated
• fetch_bbs_data() now uses functionality from the R package sbtools to fetch data from Science Base. The user should notice no difference in functionality
• IMPORTANT In order to run analyses on this new data set, users must run fetch_bbs_data(force = TRUE) in order to overwrite their previous 2019 data set (that spanned 1966-2018).

Stratify() now lumps some species

• by default, stratify() now lumps species forms for 13 species/groups that have been lumped or split since the beginning of the BBS, including the following:
  • unid Dusky Grouse/Sooty Grouse --> Blue Grouse (Dusky/Sooty)
  • (unid. race) Dark-eyed Junco --> Dark-eyed Junco (all forms)
  • (unid. Red/Yellow-shafted) Northern Flicker --> Northern Flicker (all forms)
  • unid. Bullock's Oriole / Baltimore Oriole --> Northern Oriole (all forms)
  • Red-tailed Hawk --> Red-tailed Hawk (all forms)
  • unid. sapsucker --> Sapsuckers (Yellow-bellied/Red-naped/Red-breasted/Williamson's)
  • Snow Goose --> Snow Goose (all forms)
  • unid. Cassin's Vireo / Blue-headed Vireo --> Solitary Vireo (Blue-headed/Cassin's)
  • unid. Alder Flycatcher / Willow Flycatcher --> Traill's Flycatcher (Alder/Willow)
  • unid. Cordilleran / Pacific-slope Flycatcher --> Western Flycatcher (Cordilleran/Pacific-slope)
  • unid. Western Grebe / Clark's Grebe --> Western Grebe (Clark's/Western)
  • (unid. Myrtle/Audubon's) Yellow-rumped Warbler --> Yellow-rumped Warbler (all forms)
  • unid. Common Redpoll / Hoary Redpoll --> Redpoll (Common/Hoary)
• users can choose to NOT lump species by setting lump_species_forms = FALSE when calling stratify()

Update in version numbering

• Version numbering changing from major.minor.patch to major.minor.patch.data_version
• In this case, we are now 2.3.2.2020, indicating that bbsBayes now accesses the 2020 release of the BBS data set
• We will update the data_version each time USGS releases a new data set

Thank you for your continued use of bbsBayes! Now, go make some pretty plots of all the new data!

v2.2.2

Patch error where stratum weights are not guaranteed to sum to 1, which they should.

Also modified CITATION to reflect preprint now on bioRxiv.

v2.2.1

CRAN RELEASE!!!!

bbsBayes has finally made it into the CRAN universe. See: https://cran.r-project.org/web/packages/bbsBayes/index.html

Deprecated functions since v2.2.1

The following functions have been deprecated as WAIC is no longer used in the Breeding Bird Survey for model selection:

• waic()
• p_waic()

Additionally, the following functions have been deprecated...

• plot_cont_indices()
• generate_regional_trends()
• generate_regional_indices()
• generate_strata_indices()
• generate_strata_trends()
• generate_cont_indices()
• generate_cont_trend()

...in favour of functions that combine functionality of above. For example, the shiny new "generate_trends()" function takes over the functionality of the regional, strata, and cont trends function above, using an argument for specifying the region.

Additional Notes

Most other commits since v2.2.0 have been minor fixes to the documentation for CRAN. Many tests were added.

v2.1.0

New functions and updated functionality for status and trend visualizations. Fixed some CRAN Check notes.

v2.0.0

Functionality for 2018 release of North American Breeding Bird Survey data.