Name: ensembles
Owner: Ocean Health Index - Science
Description: Improving estimates of population status and trend with superensemble models
Forked from: datalimited/ensembles
Created: 2017-01-03 20:54:49.0
Updated: 2017-01-03 20:55:46.0
Pushed: 2017-02-28 22:58:18.0
Size: 66101
Language: R
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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:
ages <- c("mblm", "randomForest", "plyr", "dplyr", "ggplot2",
eshape2", "gbm", "devtools", "doParallel", "hexbin", "pROC",
ColorBrewer", "Rcpp", "R2jags", "arm", "bbmle")
r
all.packages(packages)
ools::install_github("datalimited/datalimited")
art in the root "ensembles" folder, then:
d("analysis")
ce("0-ensemble-functions.R")
ce("1-read-old-ram-fits.R")
ce("2-merge-ram-fits.R")
ce("3-load-sim-data.R")
ce("4-add-spectral.R")
ce("5-simulation-ensembles.R")
ce("6-sim-to-ram.R")
ce("7-plot-sims.R")
ce("8-main-figs.R")
ce("8-motivate-fig.R")
ce("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 | 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 |