metafolio: Metapopulation simulations for conserving salmon through portfolio optimization

The metafolio R package is a tool to simulate salmon metapopulations and apply financial portfolio optimization concepts. The package accompanies the paper 'Portfolio conservation of metapopulations under climate change'. See citation("metafolio").

Install the latest version of this package by entering the following in R:
install.packages("metafolio")
AuthorSean C. Anderson [aut, cre], Jonathan W. Moore [ctb], Michelle M. McClure [ctb], Nicholas K. Dulvy [ctb], Andrew B. Cooper [ctb]
Date of publication2014-07-10 08:45:42
MaintainerSean C. Anderson <sean@seananderson.ca>
LicenseGPL-2
Version0.1.0
http://github.com/seananderson/metafolio

View on CRAN

Man pages

add_dens_polygon: Add a kernel density polygon

annotate: Add annotations to panel

count_quasi_exts: Take 'meta_sim' output objects and count quasi extinctions

create_asset_weights: Create an asset weights matrix

custom_bw: Custom bandwidth

CVaR: Conditional Value at Risk

est_beta_params: Get beta parameters from mean and variance

fastlm: Super fast linear regression

fit_ricker: Fit Ricker linear regression

generate_env_ts: Create an environmental time series.

generate_straying_matrix: Generate a matrix of straying proportions within a...

get_conserv_plans_mv: Run simulation for conservation schemes

get_efficient_frontier: Get the efficient frontier from mean and variance values

get_port_vals: Get portfolio mean and variance values

get_quantile_contour: Get quantile contour

gg_color_hue: ggplot2-like colour scale in HCL space

impl_error: Add implementation error

is_element: Check if x is an element of y.

is_quasi_ext: Return whether there was an instance of quasi extinction

metafolio: metafolio: An R package to simulate metapopulations for...

meta_sim: Run a single metapopulation simulation.

metasim_base: Base-level metapopulation simulation function

monte_carlo_portfolios: Monte Carlo asset weights into portfolios

my.axis: Add a pretty axis

optim_thermal: Optimize to find optimal max productivity Ricker a

plot_cons_plans: Plot conservation plans in mean-variance space

plot_correlation_between_returns: Plot correlation of returns (i.e. metapopulation abundance)...

plot_efficient_portfolios: Basic plot of efficient portfolio and asset contributions

plot_panel_lines: Standard matrix plot of values by stream for one panel:

plot_rickers: Plot sample Ricker curves for each stock

plot_sim_ts: Plot various time series from a simulation run

plot_sp_A_ts: Plot sample time series from a portfolio simulation

ricker: A simple Ricker model

ricker_escapement: Assign a salmon escapement target based on a Ricker curve

ricker_v_t: Ricker stock-recruit function with specified error

run_cons_plans: Run conservation plans and return the portfolio mean and...

thermal_area: Return desired squared deviation between desired area and...

thermal_curve_a: Create thermal tolerance curves.

thermal_integration: Integrate thermal tolerance curves to get maximum Ricker a...

VaR: Value at Risk

Functions

add_dens_polygon Man page
annotate Man page
count_quasi_exts Man page
create_asset_weights Man page
custom_bw Man page
CVaR Man page
est_beta_params Man page
fastlm Man page
fit_ricker Man page
generate_env_ts Man page
generate_straying_matrix Man page
get_conserv_plans_mv Man page
get_efficient_frontier Man page
get_port_vals Man page
get_quantile_contour Man page
gg_color_hue Man page
impl_error Man page
is_element Man page
is_quasi_ext Man page
metafolio Man page
metafolio-package Man page
meta_sim Man page
metasim_base Man page
monte_carlo_portfolios Man page
my.axis Man page
optim_thermal Man page
plot_cons_plans Man page
plot_correlation_between_returns Man page
plot_efficient_portfolios Man page
plot_panel_lines Man page
plot_rickers Man page
plot_sim_ts Man page
plot_sp_A_ts Man page
ricker Man page
ricker_escapement Man page
ricker_v_t Man page
run_cons_plans Man page
thermal_area Man page
thermal_curve_a Man page
thermal_integration Man page
VaR Man page

Files

inst
inst/examples
inst/examples/plot_thermal_curves.R inst/examples/cons_plans_n_random_resp_div.R inst/examples/README.R inst/examples/cons_plans2.R inst/examples/plot_thermal_curves_scenarios.R inst/examples/figs2eps.R inst/examples/plot_sim_ts_simple.R inst/examples/plot_straying_matrix.R inst/examples/pdf_eps.R inst/examples/example_returns_3.R inst/examples/cons_squeeze.R
inst/CITATION
inst/doc
inst/doc/metafolio.pdf
inst/doc/metafolio.R
inst/doc/metafolio.Rnw
src
src/metasim_base.cpp
src/Makevars
src/Makevars.win
src/RcppExports.cpp
NAMESPACE
R
R/metafolio.R R/is_quasi_ext.R R/generate_straying_matrix.R R/plot_rickers.R R/ricker.R R/get_conserv_plans_mv.R R/meta_sim.R R/create_asset_weights.R R/plot_sp_A_ts.R R/monte_carlo_portfolios.R R/RcppExports.R R/gg_color_hue.R R/thermal_integration.R R/plot_efficient_portfolios.R R/run_cons_plans.R R/get_port_vals.R R/plot_sim_ts.R R/thermal_curve_a.R R/plot_correlation_between_returns.R R/count_quasi_exts.R R/plot_cons_plans.R R/generate_env_ts.R
vignettes
vignettes/port_vals.rda
vignettes/metafolio.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/is_element.Rd man/get_conserv_plans_mv.Rd man/create_asset_weights.Rd man/monte_carlo_portfolios.Rd man/annotate.Rd man/plot_panel_lines.Rd man/ricker_v_t.Rd man/thermal_area.Rd man/ricker.Rd man/plot_sp_A_ts.Rd man/impl_error.Rd man/count_quasi_exts.Rd man/get_efficient_frontier.Rd man/plot_sim_ts.Rd man/VaR.Rd man/thermal_integration.Rd man/plot_efficient_portfolios.Rd man/metasim_base.Rd man/est_beta_params.Rd man/generate_env_ts.Rd man/ricker_escapement.Rd man/fastlm.Rd man/my.axis.Rd man/get_quantile_contour.Rd man/fit_ricker.Rd man/CVaR.Rd man/run_cons_plans.Rd man/thermal_curve_a.Rd man/plot_cons_plans.Rd man/plot_correlation_between_returns.Rd man/meta_sim.Rd man/gg_color_hue.Rd man/plot_rickers.Rd man/optim_thermal.Rd man/generate_straying_matrix.Rd man/is_quasi_ext.Rd man/get_port_vals.Rd man/add_dens_polygon.Rd man/metafolio.Rd man/custom_bw.Rd

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