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multivariate model fit checking analysis should not use 'mixed_effects' as predictor for BT #79

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egouldo opened this issue Sep 3, 2024 · 1 comment
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@egouldo
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egouldo commented Sep 3, 2024

In fixing up downstream code after #42, noticed that the multivariate model selection checking analysis includes the predictor mixed_model for the blue tit analyses, but it shouldn't because we didn't pass preregistered threshold.

Note that this isn't a problem for the main targets pipeline because the function applied there fit_multivar_MA() checks and won't fit the model if the threshold isn't met (fixed in egouldo/ManyEcoEvo#147).

@egouldo egouldo added the bug an unexpected problem or unintended behavior label Sep 3, 2024
@egouldo egouldo added this to the Respond Peer Review Comments milestone Sep 3, 2024
@egouldo egouldo self-assigned this Sep 3, 2024
egouldo added a commit that referenced this issue Sep 4, 2024
egouldo added a commit that referenced this issue Sep 4, 2024
don't calculate importance weights, switch to rowwise() approach for mapping model checks, don't replace NA singularity values with TRUE
egouldo added a commit that referenced this issue Sep 4, 2024
…reporting

as opposed to model fit checking analysis results. Note have manually validated that model fits concur with those in package.
egouldo added a commit that referenced this issue Sep 4, 2024
… for multivar analyses

feat!: Also check whether SE and CI for random effects can be calculated
@egouldo egouldo closed this as completed Sep 4, 2024
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egouldo commented Sep 5, 2024

library(report)
library(ManyEcoEvo)
#> Loading required package: rmarkdown
#> Loading required package: bookdown
#> Registered S3 method overwritten by 'parsnip':
#>   method          from 
#>   print.nullmodel vegan
#> Registered S3 method overwritten by 'lava':
#>   method         from    
#>   print.estimate EnvStats
library(tidyverse)

ManyEcoEvo_yi_results %>%
  dplyr::filter(dataset == "blue tit") %>%
  pluck("MA_mod_mv", 1) %>%
  format_formula()
#> [1] "formula: box_cox_abs_deviation_score_estimate ~ RateAnalysis + PublishableAsIs + mean_diversity_index"

Created on 2024-09-05 with reprex v2.1.0

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