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Missing variables to be coded in mean/sd parameter lookup table #80

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egouldo opened this issue Feb 9, 2023 · 1 comment · Fixed by #87
Closed
6 tasks

Missing variables to be coded in mean/sd parameter lookup table #80

egouldo opened this issue Feb 9, 2023 · 1 comment · Fixed by #87
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@egouldo
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egouldo commented Feb 9, 2023

  • Missing variables from ManyAnalysts:::analysis_data_param_tables
  response_id       submission_id analysis_id split_id response_variable_name      
  <chr>                     <dbl>       <dbl>    <dbl> <chr>                       
1 R_3dWjjdkDbTRCUqs             1           1        1 SMI                         
2 R_3eemYAT4onCCt0N             1           1        1 residual_day14_weight       
3 R_PvSAhRE12PvmEJb             1           1        1 SMI                         
4 R_SDyCfmAPuL4gcKZ             5           5        1 residual_day_14_weight_males

And also: euc_sdlgs50cm_2m

Originally posted by @egouldo in https://github.com/egouldo/ManyAnalysts/issues/162#issuecomment-1423526812

  • @hannahsfraser to Edit script /data-raw/analysis_datasets/osf_load_analyst_dataset.R, calculating variables SMI and residual_day14_weight and residual_day_14_weight_males

  • @egouldo ManyAnalysts::blue_tit_data & ManyAnalysts::euc_data to be regenerated by running /data-raw/analysis_datasets/osf_load_analyst_dataset.R

  • @egouldo Rebuild package (will update ManyAnalysts::blue_tit_data & ManyAnalysts::euc_data)

  • @egouldo In /data-raw/ run script: analysis_data_param_tables (which will run functions make_param_table on both ManyAnalysts::blue_tit_data and ManyAnalysts::euc_data.

  • @egouldo Rebuild package (will update analysis_data_param_tables)

  • @egouldo Rerun pipeline and check if missing back_transformed_data tables for the above cases are resolved egouldo/ManyAnalysts#162

  • 🗒️ Related to Constructed Variables are ignored when standardising (no average values in param table) #82

@egouldo egouldo added the bug an unexpected problem or unintended behavior label Feb 9, 2023
@egouldo egouldo closed this as completed Sep 1, 2023
@egouldo egouldo reopened this Sep 1, 2023
@egouldo egouldo transferred this issue from another repository Oct 27, 2023
@egouldo egouldo transferred this issue from another repository Aug 5, 2024
@egouldo egouldo transferred this issue from another repository Aug 5, 2024
@egouldo egouldo added this to the Respond Reviewer Comments milestone Aug 5, 2024
@egouldo
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egouldo commented Aug 5, 2024

Note that the above issue has been transferred from the repository with identifiable data so some issues / will not display / link correctly without appropriate permissions.

How were the variables constructed?

variable name construction
residual_day14_weight I took day_14_weight and adjusted for body size using a LMM including day_14_tarsus_length as a fixed effect and day14_measurer as a random intercept. I then took the residuals of this model and divided by 14 to give a daily chick growth rate. This was then used as my response.
lmer(day_14_weight ~ day_14_tarsus_length + (1 | day14_measurer), data = titdata)
titdata$day_14_weight_SA <- as.vector(resid(model.mass)) #SA = size adjusted
titdata$chick_growth_rate <- titdata$day_14_weight_SA / 14
residual_day_14_weight_males residuals of the regression:
day_14_weight ~ day_14_tarsus_length 
SMI I calculated scaled body mass based on body mass (day_14_weight) and tarsus length (day_14_tarsus_length) to have an estimate of chicks’ body mass independently of body size following the method of Peig and Green (2009).

Given these constructed variables are so specific to the specific datasets utilised by the analysts, as well as their models, I think we should not do this for the Many Analysts manuscript, if we want to do this for the software package, we can but there are marginal gains in doing this for the manuscript, and it will simply take too much work to implement this.

Marking as wontfix for the manuscript. We can get to this for the software manuscript if we really really really want, but I think there are more urgent and important tasks.

@egouldo egouldo added the wontfix label Aug 5, 2024
egouldo added a commit that referenced this issue Aug 5, 2024
- identified in the course of #80
egouldo added a commit that referenced this issue Aug 5, 2024
And explain implicit exclusions from yi meta-analysis
egouldo added a commit that referenced this issue Aug 5, 2024
egouldo added a commit that referenced this issue Aug 5, 2024
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@egouldo egouldo linked a pull request Aug 5, 2024 that will close this issue
egouldo added a commit that referenced this issue Aug 5, 2024
Close #80 param lookup tables for constructed variables
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