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.


Initialize an IPM

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

Helpers for IPM construction


Functions to initialize and define IPM kernels

truncated_distributions() discrete_extrema()

Eviction correction


Predict methods in ipmr

make_ipm_report() make_ipm_report_body()

Generate an RMarkdown file with IPM metadata


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


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.


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 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.


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.


Simple deterministic IPM example


A general deterministic IPM example


Raw demographic data to construct an example IPM


A proto_ipm for a monocarpic perennial