Last updated: 2022-04-11
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 7983950 | Eric Tytell | 2022-04-11 | wflow_git_commit(c(“analysis/about.Rmd”, “analysis/index.Rmd”, |
| Rmd | 0be8f4f | Eric Tytell | 2021-12-30 | Updated the index file to link correctly |
| Rmd | 23908bd | Eric Tytell | 2021-12-30 | Test site build again |
| Rmd | b9f4976 | Eric Tytell | 2021-12-30 | Start workflowr project. |
Dana Baxter\(^1\) | Karly E. Cohen\(^3\) | Cassandra M. Donatelli\(^2\) | Eric D. Tytell\(^1\)
\(^1\)Tufts University, Department of Biology \(^2\)University of Ottawa, Department of Biology \(^3\)University of Washington, Friday Harbor Labs
Submitted to Ecology and Evolution April 12, 2022.
The initial measurements were made by Dana Baxter by clicking points on vertebrae from CT scans. The measurements are in MasterVert_Measurements_old.csv.
Dana processed the data from Cymatogaster aggregata a bit later, so we have to merge it into the main data set.
Input: data/MasterVert_Measurements_old.csv Output: data/MasterVert_Measurements.csv
Here is the process to merge the Cymatogaster data: 01-ProcessCymatogasterFiles.
Species are distributed somewhat randomly throughout the bony fishes. We use the phylogeny from Betancur-R et al 2017. Not every species we digitized is in their tree. For most of them, we can use another species in the same genus, since we don’t have many species in our data set that are in one genus.
Input: data/MasterVert_Measurements.csv Output: output/MasterVert_Measurements_Matched.csv This contains all of the measurements for all of the vertebrae, but with a new set of columns for “MatchSpecies” and “MatchGenus”, which are the matching species in the Betancur-R tree.
This notebook checks the match between our species and the one in the tree: 02-CheckSpeciesMatch.
Here, we take the data for each vertebra and produce summary values for each species. We first center the data set by finding the median value of any measurement for each vertebra across all of the species, then subtracting the actual value from that median.
Input: output/MasterVert_Measurements_Matched.csv Output:
output/vertdata_centered.csv: This contains the centered measurementsoutput/vertdata_summary.csv: This contains the summary maximum values and medians for each speciesTo represent the variation of the measurements along the vertebrae, we fit linear models to each measurement as a function of position along the body. Based on AIC, we use just an overall mean, a slope and a midpoint, or a quadratic fit.
We use midpoint rather than intercept. Midpoint is the value at 80% of the way down the body. If we use intercept, we sometimes end up with negative values, which is weird.
Input: output/vertdata_centered.csv, output/vertdata_summary.csv Output:
output/vertdata_summary_lm.csv: Contains the midpoint, slope, and quadratic coefficients as appropriate for each model.output/vertdata_summary_lm_models.Rds: Same data, but storing the actual models in an Rds file.Here, we run the phylogenetic generalized least squares models to determine which variables differ among species.
Input: output/vertdata_centered.csv, output/vertdata_summary.csv Output:
output/vertdata_summary_lm_species.csv: Contains the summary data with the matched tip and label from the phylogenetic treeoutput/vert_tree.rds: The phylogeny containing just our species in RData format. The CSV export wasn’t working properly for tree dataFigures showing the overall mean for foramen diameter, posterior cone angle, and centrum body length, along with the distribution of the parameters along the body.
Also generates the stats table.