Data from: Ebola cases and health system demand in Liberia

This zip directory contains the data, R code, and simulation results required to reproduce analyses reported in the associated paper

Appendix A. The statistical analysis of extinction times of 1074 experimental populations of Daphnia pulicaria.

The statistical analysis of extinction times of 1074 experimental populations of Daphnia pulicaria

Supplement 1. R functions for fitting the LOBAG and LOBAG-OC models.

<h2>File List</h2><div> <p><a href="lobag.R">lobag.R</a> (MD5: 297094eda0d98965c144121e7849ea6b)</p> </div><h2>Description</h2><div> <p>The file lobag.R contains code for four functions used to fit and predict species' ecological niches using the LOBAG and LOBAG-OC models. Functions depend on the kernlab package. Function arguments include covariate data at presence points (LOBAG and LOBAG-OC) and background points (LOBAG only) and various tuning parameters, as described in the main text.</p> </div

Supplement 1. Data and R code for analyzing extinction times of experimental Daphnia populations.

<h2>File List</h2><blockquote> <p><a href="data.csv">data.csv</a> - Table of raw data<br> <a href="DaphExt.r">DaphExt.r</a> - R code for performing analysis</p> <p> </p> </blockquote><h2>Description</h2><blockquote> <p>The file data.csv is a comma separated ASCII file containing extinction times for 281 populations of <i>Daphnia magna</i> under three levels of environmental variation. The first line is a header containing variable names. The variable treatment takes values "low", "medium", or "high" referring to the experimental treatment. The variables treatment2 and treatment3 are re-coded versions of treatment provided for convenience. The variable treatment2 assigns the level "A" to subjects in the "low" experimental treatment, assigns "B" to subjects in the "medium" experimental treatment, and assigns "C" to subjects in the "high" experimental treatment. The variable treatment3 pools subjects in the "low" and "medium" treatments, assigning them the level "A", while subjects in the "high" experimental treatment are assigned "C", as before. The variable id is a unique identifier for each population. The variable ext is a censoring variable, taking the value "1" if the population went extinct during the course of the experiment and "0" otherwise. The variable dur reports the duration of population observation, the time-to-extinction in the case of populations going extinct and the duration of the experiment otherwise.</p> <p>The file DaphExt.r contains R code for performing the Cox proportional hazards regression, estimating the survival distribution using the Kaplan-Meier estimator, and reproducing figures from the text. In addition to the basic R environment, this code depends on functions in the package survival which can be obtained along with the basic R environment from the Comprehensive R Archive Network (CRAN) found at <a href="www.r-project.org">www.r-project.org</a>.</p> </blockquote

Supplement 1. Raw data in comma-separated format.

<h2>File List</h2><div> <p><a href="data.csv">data.csv</a> (MD5: eac4699fe882465f09cc1d7465164e7a)</p> </div><h2>Description</h2><div> <p>The file data.csv contains data on extinction time of 1,080 experimental populations. Six populations were accidentally destroyed (indicated by Days = −9999). Data columns include:</p> <p>1. Tube.ID – A unique identifier for each population</p> <p>2. Block – Block number</p> <p>3. Startno – The initial population size, either x0 = 3 or x0 = 18</p> <p>4. Start – Date population was initialized</p> <p>5. End – Date population was scored extinct</p> <p>6. Days – Duration of population persistence (extinction time) in days, i.e., End − Start</p> <p>7. Tetracycline – Indicator for tetracycline addition (0: No, 1: Yes)</p> </div

Data

Trajectories of Ebola infection probability in West Africa

Supplement 2. R code for data summary models, estimating experimental effects with mixed effects models, and fitting alternative distributions for the tail probabilities of extinction time.

<h2>File List</h2><div> <p><a href="pulicaria-code.R">pulicaria-code.R</a> (MD5: 907cfa2626421dc29c58eebfb0c38329)</p> </div><h2>Description</h2><div> <p>The file pulicaria-code.R (298 lines) contains R code for all analyses included in the main text and supplement. Requires data.csv and depends on R packages moments, xtable, MIfuns, lme4, and external R code for fitting power law distributions written by Cosma Shalizi and hosted by the Santa Fe Institute at <a href="http://tuvalu.santafe.edu/~aaronc/powerlaws/">http://tuvalu.santafe.edu/~aaronc/powerlaws/</a>.<br> </p> </div

Mesocosm_water_conditions

contains water condition data from each mesocosm collected at every sampling dat

Mesocosm_treatments

identifies the experimental treatments imposed on each mesocos

Mesocosm_sample_data

contains the abundance and identity of each taxon collecte