# Metapopulation simulations for conserving salmon through portfolio optimization

## Documentation for package ‘metafolio’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

metafolio-package | metafolio: An R package to simulate metapopulations for portfolio optimization
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 metapopulation
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 portfolio optimization
metasim_base | Base-level metapopulation simulation function
meta_sim | Run a single metapopulation simulation.
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) across stocks.
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 variance values
thermal_area | Return desired squared deviation between desired area and actual area under a curve
thermal_curve_a | Create thermal tolerance curves.
thermal_integration | Integrate thermal tolerance curves to get maximum Ricker a values
VaR | Value at Risk