Appendix A. Data and sources.

Data and sources

Knitr cache file

This cache file stores the results of running each of the code chunks in manuscript.Rmd and supplement.Rmd, see http://yihui.name/knitr for details on caching

Appendix B. Characterizing beta-binomial observation error in population data.

Characterizing beta-binomial observation error in population data

The feedback network affecting a stem cell in its niche.

<p>Here stem cells are clear circles, transit amplifying cells colored circles, and fully differentiated cells in black. A focal stem cell has positive feedback (+) on itself but shares inhibition and negative feedback (−) with other stem cells. Transit amplifying cells receive positive feedback from stem cells and exert positive feedback on fully differentiated cells. Both transit amplifying and fully differentiated cells exhibit negative feedback on stem cells. The symbols that characterize these processes are explained in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001591#s4" target="_blank">Materials and Methods</a>.</p

The stochastic trajectories for 100 simulations of the stem-transit amplifying-differentiated system described in the text and the solution of the differential equations 25–27 (red line).

<p>The stochastic trajectories for 100 simulations of the stem-transit amplifying-differentiated system described in the text and the solution of the differential equations 25–27 (red line).</p

The results of the stochastic simulation can be shown as phase plots of stem cells and transit amplifying cells (uppere panel) or stem cells and fully differentiated cells (lower panel)

<p>The results of the stochastic simulation can be shown as phase plots of stem cells and transit amplifying cells (uppere panel) or stem cells and fully differentiated cells (lower panel)</p

Parameters, Their Interpretations, and Values.

<p>Parameters, Their Interpretations, and Values.</p

CSV files for figures

All data tables used to generate figures as CSV files by figure name. (20 files, 13 MB). Note, all data are from simulations, not true observations, and can also be re-generated by running the code provided. See corresponding code blocks of Manuscript.Rmd and Supplement.Rmd for details

Data for the ms "Evolution of growth rates and resilience to massive mortality events"

<p>Data from simulations and code for ms "Evolution of growth rates and resilience to massive mortality events" submitted to the Journal of Fish Biology. The code clearly documents analyses and plots.</p

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