Drosophila pseudoobscura aging 2026

<p>Data and analysis code for lifespan, development time, and body size assays in Drosophila pseudoobscura. </p>

<p>This data repository consist of nine data files, four code scripts, and this README document, with the following data and code filenames and variables</p>

<p>Data files and variables:</p>
<ol>
<li>Dpse_aging_strains_2025_01_10.txt
<ul>
<li> Strain - ID number for Strain </li>
<li> sex - sex of individual fly </li>
<li> Birth - date that the fly emerged from the pupal case </li>
<li> Death - date that the fly was observed dead or last observed alive</li>
<li> Age-at-death - days the fly lived until death </li>
<li> notes - information about the fly </li>
<li> censrec - if the fly was last observed dead (1) or alive (0)</li>
<li> winter_cens - estimate of age at death if winter holiday is censored </li>
<li> winter_death - estimate of age at death if averaging over winter holiday</li>
</ul>
</li>
<li> Dpse_aging_18C_2025_08_11.txt [same variables used in files 2,3,4] </li>
<li> Dpse_aging_22C_2025_07_01.txt [same variables used in files 2,3,4] </li>
<li> Dpse_aging_25C_2025_07_01.txt
<ul>
<li> Strain - ID number for Strain </li>
<li> Birth - date that the fly emerged from the pupal case </li>
<li> Death - date that the fly was observed dead or last observed alive</li>
<li> Age-at-death - days the fly lived until death </li>
<li> notes - information about the fly </li>
<li> censrec - if the fly was last observed dead (1) or alive (0) </li>
</ul>
</li>
<li> Dpse-devrate-18c_2025_08.txt [same variables used in files 5,6,7] </li>
<li> Dpse-devrate-22c_2025_08.txt [same variables used in files 5,6,7] </li>
<li> Dpse-devrate-25c_2025_08.txt
<ul>
<li> Strain - ID number for Strain </li>
<li> Date Laid - date when the mother laid the egg that developed into the fly </li>
<li> Vial - unique ID for each vial for a Strain on a Date </li>
<li> Sex - sex of individual fly that emerged </li>
<li> Date of Emergence - date when the fly emerged </li>
<li> time - days from when laid until emerged </li>
<li> Notes - information about fly </li>
</ul>
</li>
<li> Dpse-body-Gabe_2025_07_31.tab
<ul>
<li> Strain - ID number for Strain </li>
<li> Sex - sex of the fly</li>
<li> vial-setup - date when mother of the fly was put into a vial to lay eggs </li>
<li> len-um - length of the fly in micrometers </li>
<li> Emergence - date when the fly emerged from the pupa </li>
<li> age - length of time it took for the fly to develop from egg to adult </li>
<li> Notes - information about the fly </li>
</ul>
</li>
<li> Dpse-strains.tab
<ul>
<li> ID - strain ID </li>
<li> accession - Drosophila species stock center ID </li>
<li> arrangement - third chromosome arrangement carried by strain </li>
<li> isogen - internal strain ID number </li>
<li> balancer - chromosome used to extract arrangement onto a common background </li>
<li> strain - full strain information </li>
<li> count - running count of strains for each arrangement</li>
</ul>
</li>
</ol>

<p>Code scripts and workflow:</p>
<ol>
<li> _Dpse_aging_strains_2025_09.pdf <br>
Supplemental File S1 <br/>
Code for analyzing lifespan data at 22C (Trial 1)</li>
<li> _Dpse_aging_temp-strains_2025_09.pdf<br>
Supplemental File S2<br/>
Code for analyzing lifespan data at three temperatures (Trial 2)</li>
<li> _Dpse_devrate_2025_09.pdf<br>
Supplemental File S3<br>
Code for analyzing development time data </li>
<li> _Dpse_body_2025_09.pdf
Supplemental File S4<br>
Code for analyzing body size measurement data</li>
</ol>

<p>Data were analyzed using R version 4.5.1 (2025-06-13) -- "Great Square Root"<br>
Analysis was implemented in RStudio Version 2026.01.1+403 (2026.01.1+403) <br>
The following packages were used in the analysis and data visualization: </p>
<ul>
<li> cowplot version 1.2.0 </li>
<li> coxme version 2.2-22</li>
<li> dplyr version 1.1.4</li>
<li> flexsurv version 2.3.2 </li>
<li> ggfortify version 0.4.18</li>
<li> ggplot2 version 4.0.2 </li>
<li> ggridges version 0.5.6</li>
<li> lme4 version 1.1-37</li>
<li> nlme version 3.1-168</li>
<li> outliers version 0.15</li>
<li> survival version 3.8-3</li>
<li> survminer version 0.5.0</li>
<li> tidychangepoint version 1.0.1</li>
<li> tidyr version 1.3.1</li>
</ul>