stomata-scaling

The repository contains source code for analyses and simulations related to:

Bounds on stomatal size can explain scaling with stomatal density in forest plants

Congcong Liu, Christopher D. Muir, Lawren Sack, Ying Li, Jiahui Zhang, Guirui Yu, Li Xu, Mingxu Li, Zihao Zhang, Hugo Jan de Boer, Xingguo Han, Nianpeng He. Accepted in New Phytologist.

Downloading repository

1. Download or clone this repository to your machine.

git clone [email protected]:cdmuir/stomatal-scaling.git

2. Open stomata-scaling.Rproj in RStudio
3. Install R packages if necessary using r/install-packages.R

Brief description of R scripts in r/ directory

• functions.R: custom functions

• header.R: script to clear workspace and load packages

• 01_fit-phylolm.r: fit phylolm model to estimate scaling exponent

• 02_plot-hypotheses.R: make figure 1

• 03_plot-results.R: make figure 3 showing results from 01_fit-phylolm.r

• 04_fit-OUCH.R: estimate OU covariance between stomatal size and density

• 05_sim-OUCH.R: simulate synthetic data from OUCH model for parametric bootstrap

• 06_bootstrap-OUCH.R: fit synthetic data from OUCH model for parameteric bootstrap

• 07_summarize-OUCH.R: summarize OUCH parameter bootstrap (Table 3)

• 08_plot-ellipses.R: make figure 4

• 09_set-parameters.R: define baseline parameter sets for simulations

• 10_get-h1V*.R: derive among-species size-density covariance (hypothesis 1)

• 11_get-h2G*.R: derive within-species genetic covariance matrix, figures S2-S4 (hypothesis 2)

• 12_get-h2mu*.R: derive among-species trait means (hypothesis 2)

• 13_get-h2V*.R: derive among-species size-density covariance (hypothesis 2)

• 14_get-h3G*.R: derive within-species genetic covariance matrix, figures S5-S7 (hypothesis 3)

• 15_compare-vectors.R: make selection response vectors for figures S8-10

• 16_sim-h2-baseline.R: Recursion equations to determine stationary variance of V* under baseline scenario (hypothesis 2)

• 17_sim-h3-baseline.R: Recursion equations to determine stationary variance of V* under baseline scenario (hypothesis 3)

• 18_sim-h2-Mratio.R: simulate effect of M ratio on V* (hypothesis 2)

• 19_sim-h3-Mratio.R: simulate effect of M ratio on V* (hypothesis 3)

• 20_sim-h2-rM.R: simulate effect of mutational correlation on V* (hypothesis 2)

• 21_sim-h3-rM.R: simulate effect of mutational correlation on V* (hypothesis 3)

• 22_sim-h2-omega.R: simulate effect of $\omega$ (hypothesis 2)

• 23_sim-h3-omega.R: simulate effect of $\omega$ (hypothesis 3)

• 24_sim-h2-phi.R: simulate effect of $\phi_f$ on V* (hypothesis 2)

• 25_sim-h3-phi.R: simulate effect of $\phi_a$ on V* (hypothesis 3)

• 26_summarize-sims.R: summarize simulation results

• 27_plot-sims.R: make figures S11-S15

• 28_analyze-covariance.R: analysis for section S4

Raw data

• raw-data/stomatal-data.csv: stomatal size and density data
  • species
  • genus
  • family
  • stomatal density [1 / mm^2]
  • Stomatal length/size [um]
  • plant functional group/1-tree/2-shrub/3-herb
• raw-data/phylogeny.tre: phylogeny of species in stomatal data (newick format)