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@AdamCSmithCWS AdamCSmithCWS released this 04 Oct 17:35
· 13 commits to main since this release
v1.1.2
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What's Changed

2024 release. Includes access to the 2024 release of the BBS database (observations from 1966 through to 2023).
adds options to generate spaghetti plots of population trajectories in plot_indices. Spaghetti plots show a selection of posterior draws of the population trajectories as many distinct lines. These lines provide a different way to summarise the uncertainty of the population trajectories that separates the uncertainty of the trends (shape of the population trajectory) from the uncertainty in the mean abundance (vertical placement on the graphs).

adds options to estimate trends from any model using a gam-based smooth. The gam_smooths argument in the generate_indices(gam_smooths = TRUE) function creates an array of posterior draws of gam smooths through the population trajectory. These posterior draws can be used in the generate_trends(gam = TRUE) function to estimate trends and their uncertainties based on these smooths, for any custom range of dates. These smooth trends provide an alternative to the end-point trends that are the default in bbsBayes2. If the gam argument is set to TRUE, all of the trend and population change calculations are based on the posterior array of smooths, rather than the posterior array of annual indices. Calculating the smooths in generate_indices requires significantly more time and so the gam_smooths option is set to FALSE by default.

adds informative error messages to: a) identify challenges with interpreting the observed annual means relative to estimate trajectories for composite regions (all except stratum); b) identify species and time-periods where analyses may be complicated by changes in species taxonomy (see bbsBayes2::species_notes); and c) identify when the strata_custom optional sf object passed to stratify does not have the correct crs and strata_name column type.

prepare_data now exports columns including latitude and longitude of each BBS route start-location in the raw_data component of the output list.

fix a number of errors and issues identified in version 1.1.1.

Full Changelog: v1.1.1...v1.1.2

Contributors

AdamCSmithCWS
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