Code and simulation output from:
Letten, Yamamichi, Richardson and Ke. Microbial dormancy supports multi-species coexistence under resource fluctuations.
dormancy-tradeoff-fig1acd.R - Simulate competition between a gleaner
and a dormancy strategist (Fig 1a,c&d in ms).
dormancy-tradeoff-fig1b.R - Simulate competition between a gleaner and
a dormancy strategist with different parameter combinations for the
dormancy strategist’s growth and dormant phase mortality (Fig 1b in ms).
dormancy-tradeoff-fig2.R - Simulate competition between a gleaner, an
opportunist and a dormancy strategist for one resource supply
concentration and pulsing frequency (Fig 2 in ms).
dormancy-tradeoff-3sppsims.R - Simulate competition between all
combinations of a gleaner, opportunist and dormancy strategist under
different patterns of resource supply.
dormancy-tradeoff-3sppsims-chemo.R - Simulate competition between all
combinations of a gleaner, opportunist and dormancy strategist under
continuous/chemostat resource supply.
dormancy-tradeoff-fig3.R - Summarize and plot simulation output from
dormancy-tradeoff-3sppsims.R and dormancy-tradeoff-3sppsims-chemo.R
(Fig 3 in ms).
dormancy-tradeoff-spp-params.R - Parameters for core analyses.
dormancy-tradeoff-functions.R - Functions for defining ODE, extracting
and wrangling saved sims, plotting etc.
The runtime for the core simulations in dormancy-tradeoff-3sppsims.R
(Fig 3 in ms) is likely to be on the order of days (or at least many
hours). To save having to rerun all simulations, all outputs from
dormancy-tradeoff-3sppsims.R and dormancy-tradeoff-3sppsims-chemo.R
are provided as individual zipped csv files in the latest
release
associated with this repo. As described below, these can be downloaded
using the piggyback package, and distributed into the appropriate
directory structure for importing into dormancy-tradeoff-fig3.R. Note,
the download time for each of the four batches of sim files (all 3 spp
and the three pairwise dynamics) is likely to be on the order of hours
(or at least many mins, but not days!). Note also that the code in
dormancy-tradeoff-fig3.R can tested on one batch of data at a time
(i.e. there is no need to download all four batches at the same time).
Finally, please note there are 960 zipped csv files in the release with
a combined size of ~15GB.
library(piggyback)
simnames <- pb_list(repo = "andrewletten/dormancy-tradeoff-code", tag = "latest")
# Make a new directory in the data directory in the cloned repo
dir.create("data/N1N2N3_gz", recursive = TRUE) # all 3 spp
dir.create("data/N1N2_gz", recursive = TRUE) # gleaner and dormancy strategist
dir.create("data/N1N3_gz", recursive = TRUE) # opportunist and dormancy strategist
dir.create("data/N2N3_gz", recursive = TRUE) # gleaner and opportunist
N1N2N3_files <- simnames$file_name[grep("^N1N2N3_", simnames$file_name)]
pb_download(
file = N1N2N3_files,
dest = "data/N1N2N3_gz",
repo = "andrewletten/dormancy-tradeoff-code",
tag = "latest"
)
N1N2_files <- simnames$file_name[grep("^N1N2_", simnames$file_name)]
pb_download(
file = N1N2_files,
dest = "data/N1N2_gz",
repo = "andrewletten/dormancy-tradeoff-code",
tag = "latest"
)
N1N3_files <- simnames$file_name[grep("^N1N3_", simnames$file_name)]
pb_download(
file = N1N3_files,
dest = "data/N1N3_gz",
repo = "andrewletten/dormancy-tradeoff-code",
tag = "latest"
)
N2N3_files <- simnames$file_name[grep("^N2N3_", simnames$file_name)]
pb_download(
file = N2N3_files,
dest = "data/N2N3_gz",
repo = "andrewletten/dormancy-tradeoff-code",
tag = "latest"
)Once the sim files are downloaded, run dormancy-tradeoff-fig3.R to
reproduce the different iterations (species combinations) in the panels
of Fig 3.