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lefko3 (version 5.3.0)

Historical and Ahistorical Population Projection Matrix Analysis

Description

Complete analytical environment for the construction and analysis of matrix population models and integral projection models. Includes the ability to construct historical matrices, which are 2d matrices comprising 3 consecutive times of demographic information. Estimates both raw and function-based forms of historical and standard ahistorical matrices. It also estimates function-based age-by-stage matrices and raw and function-based Leslie matrices.

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Version

Install

install.packages('lefko3')

Monthly Downloads

373

Version

5.3.0

License

GPL (>= 2)

Maintainer

Richard P. Shefferson

Last Published

June 24th, 2022

Functions in lefko3 (5.3.0)

Two-parameter Beverton-Holt function

Extract Conditional Ahistorical Difference Matrices

Creates a Skeleton Paramnames Object for Use in Function-based Modeling

Extract Conditional Ahistorical Matrices from Historical MPM

Create lefkoMat Object from Given Input Matrices

Calculate Actual Stage, Age, Stage-Pair, or Age-Stage Distributions

Create Function-based Ahistorical Age x Stage Matrix Projection Model

Add Matrices to lefkoMat Object

Demographic Dataset of Cypripedium candidum Population, in Horizontal Format

Create Raw Ahistorical Age x Stage Matrix Projection Model

Create a Data Frame of Density Dependence Relationships in Vital Rates

Create a Data Frame of Density Dependence Relationships in Matrix Elements

Delete Matrices from lefkoMat Object

Demographic Dataset of Cypripedium candidum Population, in Vertical Format

elasticity3.matrix

Estimate Elasticity of Population Growth Rate of a Single Matrix

Project Function-based Matrix Projection Model

elasticity3.lefkoMat

Estimate Elasticity of Population Growth Rate of a lefkoMat Object

elasticity3.list

Estimate Elasticity of Population Growth Rate of a List of Matrices

Calculate Difference Matrices Between lefkoMat Objects of Equal Dimensions

Estimate Elasticity of Population Growth Rate to Matrix Elements

Create Historical MPMs Assuming No Influence of Individual History

Create Historical Vertical Data Frame from Ahistorical Vertical Data Frame

image3.lefkoSens

Create Matrix Image(s) for lefkoSens Object

image3.lefkoMat

Create Matrix Image(s) for lefkoMat Object

Check Quality and Distributions of hfv Datasets

Create Function-based Age-based (Leslie) Matrix Projection Model

Create Function-based Ahistorical Matrix Projection Model

Plot Projection Simulations

Create Overwrite Table for MPM Development

summary.lefkoLTRE

Summarize lefkoLTRE Objects

summary.lefkoMat

Summary of Class "lefkoMat"

Create a Matrix Image for a Single Matrix

Create Matrix Images for Matrices in a List

Conduct a Life Table Response Experiment of a lefkoMat Object

Develop Best-fit Vital Rate Estimation Models for MPM Development

Two-parameter logistic function

Create Matrix Image

image3.lefkoElas

Create Matrix Image(s) for lefkoElas Object

sensitivity3.list

Estimate Sensitivity of Population Growth Rate of a List of Matrices

sensitivity3.matrix

Estimate Sensitivity of Population Growth Rate of a Single Matrix

stablestage3.lefkoMat

Estimate Stable Stage Distribution of Matrices in lefkoMat Object

Create Raw Historical Matrix Projection Model

Create Raw Leslie (Age-based) Matrix Projection Model

Conduct a Life Table Response Experiment

Historical and Ahistorical Population Projection Matrix Analysis

Summary of Class "hfvdata"

stablestage3.matrix

Estimate Stable Stage Distribution of a Single Population Projection Matrix

Create a Data Frame of Supplemental Data for MPM Development

Create Function-based Historical Matrix Projection Model

Estimate Mean Projection Matrices

Conduct Population Projection Simulations

Estimate Reproductive Value

summary.lefkoCondMat

Summary of Class "lefkoCondMat"

Test Overdispersion and Zero Inflation in Size and Fecundity Distributions

Create Historical Vertical Data Frame from Horizontal Data Frame

summary.lefkoElas

Summarize lefkoElas Objects

Create Stageframe for Population Matrix Projection Analysis

Two-parameter Usher function

Estimate Deterministic Population Growth Rate of Single Projection Matrix

Demographic Dataset of Lathyrus vernus Population

Estimate Dominant Eigenvalue and Deterministic Population Growth Rate

lambda3.lefkoMat

Estimate Deterministic Population Growth Rates of lefkoMat Matrices

Two-parameter Ricker function

Create Raw Ahistorical Matrix Projection Model

repvalue3.lefkoMat

Estimate Reproductive Value Vectors of Matrices in a lefkoMat Object

repvalue3.matrix

Estimate Reproductive Value Vector for a Single Population Projection Matrix

Estimate Sensitivity of Population Growth Rate to Matrix Elements

Estimate Stochastic Population Growth Rate

Create New lefkoMat Object as Subset of Another lefkoMat Object

sensitivity3.lefkoMat

Estimate Sensitivity of Population Growth Rate of a lefkoMat Object

Create a Starting Vector for Population Projection

Estimate Stable Stage Distribution

summary.lefkoProj

Summarize lefkoProj Objects

summary.lefkoMod

Summary of Class "lefkoMod"

Import Vital Rate Model Factor Values for Function-based MPM Development