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Improving estimates of population status and trend with superensemble models
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README.md

Improving estimates of population status and trend with superensemble models

DOI

This repository holds the analysis for: Anderson, S. C., A. B. Cooper, O. P. Jensen, C. Minto, J. T. Thorson, J. C. Walsh, M. Dickey-Collas, K. M. Kleisner, C. Longo, G. C. Osio, D. Ovando, I. Mosqueira, A. A. Rosenberg, and E. R. Selig. 2017. Improving estimates of population status and trend with superensemble models. Fish and Fisheries. In press.

To recreate the analysis, source the .R files in the analysis folder in order. Or run the following in R:

packages <- c("mblm", "randomForest", "plyr", "dplyr", "ggplot2",
  "reshape2", "gbm", "devtools", "doParallel", "hexbin", "pROC",
  "RColorBrewer", "Rcpp", "R2jags", "arm", "bbmle")
install.packages(packages)
devtools::install_github("datalimited/datalimited")

# start in the root "ensembles" folder, then:
setwd("analysis")
source("0-ensemble-functions.R")
source("1-read-old-ram-fits.R")
source("2-merge-ram-fits.R")
source("3-load-sim-data.R")
source("4-add-spectral.R")
source("5-simulation-ensembles.R")
source("6-sim-to-ram.R")
source("7-plot-sims.R")
source("8-main-figs.R")
source("8-motivate-fig.R")
source("9-output-values.R")

Generated data ends up in analysis/generated-data and figures in figs. Intermediate versions of some raw data have been cached in the analysis/generated-data folder so that the scripts will run from a freshly cloned version of this repository. (Some of the raw data files are too large for Git.)

Package versions used:

package version date
arm 1.9-3 2016-11-27
bbmle 1.0.18 2016-02-11
datalimited 0.1.0 2016-12-23
devtools 1.12.0.9000 2016-12-18
doParallel 1.0.10 2015-10-14
dplyr 0.5.0 2016-06-24
gbm 2.1.1 2015-03-11
ggplot2 2.2.0 2016-11-11
hexbin 1.27.1 2015-08-19
mblm 0.12 2013-12-30
plyr 1.8.4 2016-06-08
pROC 1.8 2015-05-05
R2jags 0.5-7 2015-08-23
randomForest 4.6-12 2015-10-07
RColorBrewer 1.1-2 2014-12-07
Rcpp 0.12.8 2016-11-17
reshape2 1.4.2 2016-10-22
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