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").

Author
Sean C. Anderson [aut, cre], Jonathan W. Moore [ctb], Michelle M. McClure [ctb], Nicholas K. Dulvy [ctb], Andrew B. Cooper [ctb]
Date of publication
2014-07-10 08:45:42
Maintainer
Sean C. Anderson <sean@seananderson.ca>
License
GPL-2
Version
0.1.0
URLs

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

Files in this package

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