R: Integral Projection Models

# Integral Projection Models

## Documentation for package ‘ipmr’ version 0.0.7

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

## Help Pages

A C D F G I K L M N P R S T U V misc

## -- A --

as.matrix.ipmr_ipm | Convert to bare matrices
as.matrix.ipmr_matrix | Convert to bare matrices

## -- C --

collapse_pop_state | Extract threshold based population size information
conv_plot | Check for model convergence to asymptotic dynamics
conv_plot.ipmr_ipm | Check for model convergence to asymptotic dynamics

## -- D --

define_domains | Helpers for IPM construction
define_env_state | Helpers for IPM construction
define_impl | Helpers for IPM construction
define_kernel | Functions to initialize and define IPM kernels
define_pop_state | Helpers for IPM construction
discrete_extrema | Eviction correction
discretize_pop_vector | Helpers for IPM construction
domains | Accessor functions for (proto_)ipm objects
domains.default | Accessor functions for (proto_)ipm objects
domains.proto_ipm | Accessor functions for (proto_)ipm objects

## -- F --

format_mega_kernel | Create iteration kernels from an IPM object
format_mega_kernel.age_x_size_ipm | Create iteration kernels from an IPM object
format_mega_kernel.default | Create iteration kernels from an IPM object

## -- G --

gen_di_det_ex | A general deterministic IPM example

## -- I --

iceplant_ex | Raw demographic data to construct an example IPM
init_ipm | Initialize an IPM
int_mesh | Accessor functions for (proto_)ipm objects
int_mesh.ipmr_ipm | Accessor functions for (proto_)ipm objects
ipm_to_df | Convert ipmr matrix to long data frame
ipm_to_df.array | Convert ipmr matrix to long data frame
ipm_to_df.default | Convert ipmr matrix to long data frame
is_conv_to_asymptotic | Check for model convergence to asymptotic dynamics
is_conv_to_asymptotic.ipmr_ipm | Check for model convergence to asymptotic dynamics

## -- K --

kernel_formulae | Accessor functions for (proto_)ipm objects
kernel_formulae.default | Accessor functions for (proto_)ipm objects
kernel_formulae.proto_ipm | Accessor functions for (proto_)ipm objects
kernel_formulae<- | Accessor functions for (proto_)ipm objects
kernel_formulae<-.proto_ipm | Accessor functions for (proto_)ipm objects

## -- L --

lambda | Compute the per-capita growth rate for an IPM object
lambda.general_dd_det_ipm | Compute the per-capita growth rate for an IPM object
lambda.general_dd_stoch_kern_ipm | Compute the per-capita growth rate for an IPM object
lambda.general_dd_stoch_param_ipm | Compute the per-capita growth rate for an IPM object
lambda.general_di_det_ipm | Compute the per-capita growth rate for an IPM object
lambda.general_di_stoch_kern_ipm | Compute the per-capita growth rate for an IPM object
lambda.general_di_stoch_param_ipm | Compute the per-capita growth rate for an IPM object
lambda.simple_dd_det_ipm | Compute the per-capita growth rate for an IPM object
lambda.simple_dd_stoch_kern_ipm | Compute the per-capita growth rate for an IPM object
lambda.simple_dd_stoch_param_ipm | Compute the per-capita growth rate for an IPM object
lambda.simple_di_det_ipm | Compute the per-capita growth rate for an IPM object
lambda.simple_di_stoch_kern_ipm | Compute the per-capita growth rate for an IPM object
lambda.simple_di_stoch_param_ipm | Compute the per-capita growth rate for an IPM object
left_ev | Compute the standardized left and right eigenvectors via iteration
left_ev.general_di_det_ipm | Compute the standardized left and right eigenvectors via iteration
left_ev.general_di_stoch_kern_ipm | Compute the standardized left and right eigenvectors via iteration
left_ev.general_di_stoch_param_ipm | Compute the standardized left and right eigenvectors via iteration
left_ev.simple_di_det_ipm | Compute the standardized left and right eigenvectors via iteration
left_ev.simple_di_stoch_kern_ipm | Compute the standardized left and right eigenvectors via iteration
left_ev.simple_di_stoch_param_ipm | Compute the standardized left and right eigenvectors via iteration
left_mult | Right/left multiplication

## -- M --

make_impl_args_list | Helpers for IPM construction
make_ipm | Methods to implement an IPM
make_ipm.general_dd_det | Methods to implement an IPM
make_ipm.general_dd_stoch_kern | Methods to implement an IPM
make_ipm.general_dd_stoch_param | Methods to implement an IPM
make_ipm.general_di_det | Methods to implement an IPM
make_ipm.general_di_stoch_kern | Methods to implement an IPM
make_ipm.general_di_stoch_param | Methods to implement an IPM
make_ipm.simple_dd_det | Methods to implement an IPM
make_ipm.simple_dd_stoch_kern | Methods to implement an IPM
make_ipm.simple_dd_stoch_param | Methods to implement an IPM
make_ipm.simple_di_det | Methods to implement an IPM
make_ipm.simple_di_stoch_kern | Methods to implement an IPM
make_ipm.simple_di_stoch_param | Methods to implement an IPM
make_ipm_report | Generate an RMarkdown file with IPM metadata
make_ipm_report.default | Generate an RMarkdown file with IPM metadata
make_ipm_report.ipmr_ipm | Generate an RMarkdown file with IPM metadata
make_ipm_report_body | Generate an RMarkdown file with IPM metadata
make_iter_kernel | Create iteration kernels from an IPM object
mat_power | Raise a matrix to a power
mean_kernel | Mean kernels for stochastic models
monocarp_proto | A 'proto_ipm' for a monocarpic perennial

## -- N --

new_fun_form | Accessor functions for (proto_)ipm objects

## -- P --

parameters | Accessor functions for (proto_)ipm objects
parameters.default | Accessor functions for (proto_)ipm objects
parameters.proto_ipm | Accessor functions for (proto_)ipm objects
parameters<- | Accessor functions for (proto_)ipm objects
parameters<-.proto_ipm | Accessor functions for (proto_)ipm objects
plot.general_di_det_ipm | Plot a matrix or an *_ipm object
plot.ipmr_matrix | Plot a matrix or an *_ipm object
plot.simple_di_det_ipm | Plot a matrix or an *_ipm object
plot.simple_di_stoch_kern_ipm | Plot a matrix or an *_ipm object
plot.simple_di_stoch_param_ipm | Plot a matrix or an *_ipm object
pop_state | Accessor functions for (proto_)ipm objects
pop_state.default | Accessor functions for (proto_)ipm objects
pop_state.proto_ipm | Accessor functions for (proto_)ipm objects
print.general_dd_det_ipm | Print proto_ipms or *_ipm objects
print.general_dd_stoch_kern_ipm | Print proto_ipms or *_ipm objects
print.general_dd_stoch_param_ipm | Print proto_ipms or *_ipm objects
print.general_di_det_ipm | Print proto_ipms or *_ipm objects
print.general_di_stoch_kern_ipm | Print proto_ipms or *_ipm objects
print.general_di_stoch_param_ipm | Print proto_ipms or *_ipm objects
print.proto_ipm | Print proto_ipms or *_ipm objects
print.simple_dd_det_ipm | Print proto_ipms or *_ipm objects
print.simple_dd_stoch_kern_ipm | Print proto_ipms or *_ipm objects
print.simple_dd_stoch_param_ipm | Print proto_ipms or *_ipm objects
print.simple_di_det_ipm | Print proto_ipms or *_ipm objects
print.simple_di_stoch_kern_ipm | Print proto_ipms or *_ipm objects
print.simple_di_stoch_param_ipm | Print proto_ipms or *_ipm objects

## -- R --

right_ev | Compute the standardized left and right eigenvectors via iteration
right_ev.general_di_det_ipm | Compute the standardized left and right eigenvectors via iteration
right_ev.general_di_stoch_kern_ipm | Compute the standardized left and right eigenvectors via iteration
right_ev.general_di_stoch_param_ipm | Compute the standardized left and right eigenvectors via iteration
right_ev.simple_di_det_ipm | Compute the standardized left and right eigenvectors via iteration
right_ev.simple_di_stoch_kern_ipm | Compute the standardized left and right eigenvectors via iteration
right_ev.simple_di_stoch_param_ipm | Compute the standardized left and right eigenvectors via iteration
right_mult | Right/left multiplication

## -- S --

sim_di_det_ex | Simple deterministic IPM example

## -- T --

truncated_distributions | Eviction correction

## -- U --

use_vr_model | Predict methods in ipmr

## -- V --

vital_rate_exprs | Accessor functions for (proto_)ipm objects
vital_rate_exprs.default | Accessor functions for (proto_)ipm objects
vital_rate_exprs.proto_ipm | Accessor functions for (proto_)ipm objects
vital_rate_exprs<- | Accessor functions for (proto_)ipm objects
vital_rate_exprs<-.proto_ipm | Accessor functions for (proto_)ipm objects
vital_rate_funs | Accessor functions for (proto_)ipm objects
vital_rate_funs.ipmr_ipm | Accessor functions for (proto_)ipm objects

## -- misc --

%^% | Raise a matrix to a power