IPM Construction and Reporting

Functions for initializing an IPM, constructing sub-kernels, defining numerical integration, defining initial conditions, defining the environmental state, handling eviction, and generating automated reports describing the IPM.

init_ipm()

Initialize an IPM

define_impl() make_impl_args_list() define_domains() define_pop_state() define_env_state() discretize_pop_vector()

Helpers for IPM construction

define_kernel()

Functions to initialize and define IPM kernels

truncated_distributions() discrete_extrema()

Eviction correction

use_vr_model()

Predict methods in ipmr

make_ipm_report() make_ipm_report_body()

Generate an RMarkdown file with IPM metadata

make_ipm()

Methods to implement an IPM

Projection Diagnostics

Evaluate the behavior of the population projection.

is_conv_to_asymptotic() conv_plot()

Check for model convergence to asymptotic dynamics

Access parts of a proto_ipm and IPM objects

Extract and set various pieces of information from proto_ipm and IPM objects.

domains() vital_rate_exprs() vital_rate_funs() `vital_rate_exprs<-`() new_fun_form() kernel_formulae() `kernel_formulae<-`() parameters() `parameters<-`() int_mesh() pop_state()

Accessor functions for (proto_)ipm objects

collapse_pop_state()

Extract threshold based population size information

Further Analyses

Functions to for analysis of asymptotic dynamics, and helpers to extract information needed for analysis of stochastic dynamcis.

lambda()

Compute the per-capita growth rate for an IPM object

right_ev() left_ev()

Compute the standardized left and right eigenvectors via iteration

format_mega_kernel() make_iter_kernel()

Create iteration kernels from an IPM object

mean_kernel()

Mean kernels for stochastic models

`%^%` mat_power()

Raise a matrix to a power

right_mult() left_mult()

Right/left multiplication

Printing and Plotting

Functions to print and plot proto_ipm and IPM objects.

ipm_to_df()

Convert ipmr matrix to long data frame

print(<proto_ipm>) print(<simple_di_det_ipm>) print(<simple_dd_det_ipm>) print(<simple_di_stoch_kern_ipm>) print(<simple_dd_stoch_kern_ipm>) print(<simple_di_stoch_param_ipm>) print(<simple_dd_stoch_param_ipm>) print(<general_di_det_ipm>) print(<general_dd_det_ipm>) print(<general_di_stoch_kern_ipm>) print(<general_dd_stoch_kern_ipm>) print(<general_di_stoch_param_ipm>) print(<general_dd_stoch_param_ipm>)

Print proto_ipms or *_ipm objects

plot(<ipmr_matrix>) plot(<simple_di_det_ipm>) plot(<simple_di_stoch_param_ipm>) plot(<simple_di_stoch_kern_ipm>) plot(<general_di_det_ipm>)

Plot a matrix or an *_ipm object

Exported Data

Pre-built proto_ipms and a set of raw demographic data for an Israeli Carpobrotus population.

sim_di_det_ex

Simple deterministic IPM example

gen_di_det_ex

A general deterministic IPM example

iceplant_ex

Raw demographic data to construct an example IPM

monocarp_proto

A proto_ipm for a monocarpic perennial