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Update recruitment, priors #42

Merged
merged 49 commits into from
Apr 16, 2024
Merged

Update recruitment, priors #42

merged 49 commits into from
Apr 16, 2024

Commits on Apr 5, 2024

  1. add johns orcid

    @sebdalgarno
    sebdalgarno committed Apr 5, 2024
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  2. move analytical methods to methods vignette and move bboufit details … 

    …to tutorial
    @sebdalgarno
    sebdalgarno committed Apr 5, 2024
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  3. fix predict ML for fixed with missing first year

    @sebdalgarno
    sebdalgarno committed Apr 5, 2024
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  4. add john orcid

    @sebdalgarno
    sebdalgarno committed Apr 5, 2024
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  5. loosen priors on fixed year effect survival, fixes #38

    @sebdalgarno
    sebdalgarno committed Apr 5, 2024
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Commits on Apr 6, 2024

  1. use sd of 2 for trend since year is scaled

    @sebdalgarno
    sebdalgarno committed Apr 6, 2024
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  2. use rounder number for recruitment b0 prior

    @sebdalgarno
    sebdalgarno committed Apr 6, 2024
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  3. loosen recruitment prior (especially for lower bound)

    @sebdalgarno
    sebdalgarno committed Apr 6, 2024
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  4. add vignette on priors

    @sebdalgarno
    sebdalgarno committed Apr 6, 2024
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  5. add example of bayes/ML and fixed/random

    @sebdalgarno
    sebdalgarno committed Apr 6, 2024
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  6. improve priors wording

    @sebdalgarno
    sebdalgarno committed Apr 6, 2024
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  7. add dplyr to suggests for vignettes

    @sebdalgarno
    sebdalgarno committed Apr 6, 2024
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Commits on Apr 7, 2024

  1. minor wording changes to methods vignette

    @sebdalgarno
    sebdalgarno committed Apr 7, 2024
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Commits on Apr 8, 2024

  1. add dplyr to suggests

    @sebdalgarno
    sebdalgarno committed Apr 8, 2024
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  2. add dplyr funs to namespace

    @sebdalgarno
    sebdalgarno committed Apr 8, 2024
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  3. add predict_calf_cow and change predict_recruitment to decesare recru… 

    …itment
    @sebdalgarno
    sebdalgarno committed Apr 8, 2024
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  4. only add bAnnual[1] if year not excluded

    @sebdalgarno
    sebdalgarno committed Apr 8, 2024
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  5. ensure that se join by correct term

    @sebdalgarno
    sebdalgarno committed Apr 8, 2024
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  6. document

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    sebdalgarno committed Apr 8, 2024
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  7. rebuild data with new priors and add fixed_ml for testing correct bAn… 

    …nual predictions
    @sebdalgarno
    sebdalgarno committed Apr 8, 2024
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  8. update tests and snapshots

    @sebdalgarno
    sebdalgarno committed Apr 8, 2024
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Commits on Apr 9, 2024

  1. ensure CaribouYear in order in case where year level intercept shuffled

    @sebdalgarno
    sebdalgarno committed Apr 9, 2024
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  2. add decesare ref to documentation and match terminology in bbouretro,… 

    … add link to predict_calf_cow_ratio, change y-axis title to just 'Recruitment' for plot
    @sebdalgarno
    sebdalgarno committed Apr 9, 2024
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  3. add sex_ratio arg for use in decesare recxruitment calculations

    @sebdalgarno
    sebdalgarno committed Apr 9, 2024
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  4. use special method to change intercept for ML fixed year models, sign… 

    …ificantly improves convergence
    @sebdalgarno
    sebdalgarno committed Apr 9, 2024
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Commits on Apr 11, 2024

  1. move calf-cow text

    @sebdalgarno
    sebdalgarno committed Apr 11, 2024
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  2. add calf-cow prediction tests

    @sebdalgarno
    sebdalgarno committed Apr 11, 2024
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  3. pass sex_ratio through generic predict recruitment

    @sebdalgarno
    sebdalgarno committed Apr 11, 2024
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  4. trend model does adjusted recruitment prediction

    @sebdalgarno
    sebdalgarno committed Apr 11, 2024
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  5. year trend recruitment y-axis title without calves/adult female

    @sebdalgarno
    sebdalgarno committed Apr 11, 2024
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  6. add sex ratio tests for lambda and pop change

    @sebdalgarno
    sebdalgarno committed Apr 11, 2024
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  7. add sex ratio arg to internal functions

    @sebdalgarno
    sebdalgarno committed Apr 11, 2024
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  8. use inherited params for survival/recruitment

    @sebdalgarno
    sebdalgarno committed Apr 11, 2024
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  9. remove smart_intercept arg no longer used

    @sebdalgarno
    sebdalgarno committed Apr 11, 2024
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Commits on Apr 12, 2024

  1. update snapshots

    @sebdalgarno
    sebdalgarno committed Apr 12, 2024
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  2. add magrittr

    @sebdalgarno
    sebdalgarno committed Apr 12, 2024
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  3. document

    @sebdalgarno
    sebdalgarno committed Apr 12, 2024
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Commits on Apr 13, 2024

  1. use binomial model aggregated by year

    @sebdalgarno
    sebdalgarno committed Apr 13, 2024
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  2. update priors to reflect binomial model

    @sebdalgarno
    sebdalgarno committed Apr 13, 2024
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  3. update survival priors in vignette model

    @sebdalgarno
    sebdalgarno committed Apr 13, 2024
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  4. update docs to new binomical recruitment model

    @sebdalgarno
    sebdalgarno committed Apr 13, 2024
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  5. update to describe binomial recruitment model instead of poisson

    @sebdalgarno
    sebdalgarno committed Apr 13, 2024
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  6. update recruitment priors now on logit scale

    @sebdalgarno
    sebdalgarno committed Apr 13, 2024
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  7. log-odds scale now not log

    @sebdalgarno
    sebdalgarno committed Apr 13, 2024
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  8. update data and snapshots

    @sebdalgarno
    sebdalgarno committed Apr 13, 2024
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  9. chceks pass dplyr global vars

    @sebdalgarno
    sebdalgarno committed Apr 13, 2024
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Commits on Apr 14, 2024

  1. run styler

    @sebdalgarno
    sebdalgarno committed Apr 14, 2024
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  2. run linter

    @sebdalgarno
    sebdalgarno committed Apr 14, 2024
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Commits on Apr 16, 2024

  1. minor correction to year_start arg documentation

    @sebdalgarno
    sebdalgarno committed Apr 16, 2024
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