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mixed_model still present as predictor in blue tit multivariate models WHY #147

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egouldo opened this issue Sep 2, 2024 · 2 comments · Fixed by #148
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mixed_model still present as predictor in blue tit multivariate models WHY #147

egouldo opened this issue Sep 2, 2024 · 2 comments · Fixed by #148
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egouldo commented Sep 2, 2024 

dplyr::distinct(tidyr::unnest(dplyr::filter(dplyr::select(tidyr::hoist(
  dplyr::filter(
    ManyEcoEvo::ManyEcoEvo_viz,
    !!!rlang::exprs(exclusion_set == "complete", expertise_subset ==
      "All", publishable_subset == "All", collinearity_subset ==
      "All"), model_name == "MA_mod_mv"
  ), mod_fit_stats, "R2_conditional",
  "R2_marginal", "Sigma"
), dataset, model_params), dataset ==
  "blue tit"), model_params), Parameter)
#> Registered S3 method overwritten by 'parsnip':
#>   method          from 
#>   print.nullmodel vegan
#> Registered S3 method overwritten by 'lava':
#>   method         from    
#>   print.estimate EnvStats
#> # A tibble: 9 × 1
#>   Parameter                                     
#>   <chr>                                         
#> 1 (Intercept)                                   
#> 2 RateAnalysis                                  
#> 3 PublishableAsIspublishable as is              
#> 4 PublishableAsIspublishable with major revision
#> 5 PublishableAsIspublishable with minor revision
#> 6 mean_diversity_index                          
#> 7 mixed_model                                   
#> 8 SD (Intercept)                                
#> 9 SD (Observations)

Created on 2024-09-03 with reprex v2.1.0
@egouldo egouldo added the bug an unexpected problem or unintended behavior label Sep 2, 2024
@egouldo egouldo self-assigned this Sep 2, 2024
@egouldo egouldo added this to the Respond Reviewer Comments milestone Sep 2, 2024
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egouldo commented Sep 2, 2024

Related to: egouldo/ManyAnalysts#23

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egouldo commented Sep 3, 2024

Bingo, so the evaluation of whether the data frame passes the threshold for fitting counts number of observations on the data frame with untested review data such that each observation is replicated for every row in review_data. We need to call distinct() first:

image

egouldo added a commit that referenced this issue Sep 3, 2024
@egouldo
bug: fix threshold checking for multivariate model fitting #147
40d9ab7 
only count `mixed_model` after calling `distinct()` on analysis identifier column and `mixed_model` first.

Update argument checking to fail if any id columns not present.

docs: update `@details` section about required id column and add `any_of()` to `@importFrom`
This was referenced Sep 3, 2024
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@egouldo egouldo linked a pull request Sep 5, 2024 that will close this issue
fix bugs in package data regeneration for ManyAnalysts manuscript #148
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egouldo added a commit that referenced this issue Sep 5, 2024
@egouldo
fix bugs in package data regeneration for ManyAnalysts manuscript (#148)
967852b 
* Increment version number to 2.7.5.9000

* bug: fix threshold checking for multivariate model fitting #147

only count `mixed_model` after calling `distinct()` on analysis identifier column and `mixed_model` first.

Update argument checking to fail if any id columns not present.

docs: update `@details` section about required id column and add `any_of()` to `@importFrom`

* docs: rearrange headings in NEWS.md

* bug: ensure outlier subset creation occurs on all `exclusion_set` values in Zr #144

removed filter for `exclusion_set` == "complete"

* bug: exclude analysis with non-count-based dependent variable from `yi` analysis #145

* feat: #146 add function for excluding extreme estimates based on a multiplier threshold for population parameter estimates

* fix typo #146

* docs!: #146 `devtools::document()`

* bug: #146 export function

* build!: #146 apply exclusion function to Eucalyptus dataset in targets pipeline

Note that this functionality was previously included in the  manuscript

* #146 increment dev version and news before rebuilding package and targets pipeline

* - build!: don't forget to filter the corresponding diversity data after exclusions!

* - build!: fix #146 regenerate yi data after excluding extreme values

* Increment version number to 2.7.6
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fix bugs in package data regeneration for ManyAnalysts manuscript egouldo/ManyEcoEvo
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