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Rm analyses that shouldn't be run (BT random effects models) #23
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Sections C.6.1 and C.6.2 refer to the multivariate models for both Zr and yi, not the deviation from the analytic mean explained by inclusion of random effect models.
I may have misinterpreted the original preregistration if so. Depending on Tim's response I’ll update the code or leave as is. |
From Tim:
|
be0ae12 fixes this I think |
Yep: 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 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_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 And now check univariate mixed effects models 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_results %>%
dplyr::filter(dataset == "blue tit") %>%
pluck("uni_mixed_effects", 1)
#> [1] NA ManyEcoEvo_yi_results %>%
dplyr::filter(dataset == "blue tit") %>%
pluck("uni_mixed_effects", 1)
#> [1] NA Created on 2024-09-05 with reprex v2.1.0 |
Hey Tim,
I think this may potentially be a result of the way I repeated the analyses over each of the different data subsets, i'll look into it.
So, the models may have been fitted automatically, but I never extracted the results of the cases where we had < 5 analyses with random effects included.
Elliot.
On 1 Jun 2024, at 6:14 am, Tim Parker [email protected] wrote:
Hi Elliot,
In the supplement
C.6.1 Effect Sizes Zr
also
C.6.2 Out of sample predictions yi
It appears that the presence of mixed effects (whether or not the analyst included a random effect) was included in both the BT and the Euc models, but I thought that we only included this effect for Euc since there were too few BT analysts that did not include a random effect.
-Tim
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