Package: lefko3 6.7.3

lefko3: Historical and Ahistorical Population Projection Matrix Analysis

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.

Authors:Richard P. Shefferson [aut, cre], Johan Ehrlen [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lefko3/json (API)

# Install 'lefko3' in R:
install.packages('lefko3', repos = c('https://dormancy1.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dormancy1/lefko3/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • anthyllis - Matrix Set of _Anthyllis vulneraria_ Populations in Belgium
  • cypdata - Demographic Dataset of _Cypripedium candidum_ Population, in Horizontal Format
  • cypvert - Demographic Dataset of _Cypripedium candidum_ Population, in Vertical Format
  • lathyrus - Demographic Dataset of _Lathyrus vernus_ Population
  • pyrola - Demographic Dataset of _Pyrola japonica_ and _Pyrola subaphylla_ Populations, in Horizontal Format

On CRAN:

Conda:

openblascpp

7.03 score 1 packages 50 scripts 842 downloads 58 exports 69 dependencies

Last updated from:1ddb6092e5. Checks:13 OK. Indexed: yes.

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linux-devel-arm64OK539
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linux-release-arm64OK528
linux-release-x86_64OK572
macos-release-arm64OK382
macos-release-x86_64OK782
macos-oldrel-arm64OK453
macos-oldrel-x86_64OK602
windows-develOK603
windows-releaseOK600
windows-oldrelOK579
wasm-releaseOK253

Exports:actualstage3add_lMadd_stageaflefko2append_lParlefko2beverton3bootstrap3cond_diffcond_hmpmcreate_lMcreate_pmcycle_checkdelete_lMdensity_inputdensity_vrdiff_lMedit_lMelasticity3f_projection3flefko2flefko3flesliehfv_qchist_nullhistoricalize3image3lambda3lmeanlogistic3ltre3markov_runmatrix_interpminiModmodelsearchmpm_createoverwriteprojection3repvalue3ricker3rlefko2rlefko3rlesliesensitivity3sf_createsf_distribsf_skeletonslambda3stablestage3stage_weightstart_inputsubset_lMsummary_hfvsup_skeletonsupplementalusher3verticalize3vrm_import

Dependencies:backportsBHbootbroomclicolorspacecowplotcpp11DerivdoBydplyrfarverforecastfracdiffgenericsggplot2glmmTMBgluegtableinsightisobandlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixmgcvmicrobenchmarkminqamodelrMuMInnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpsclpurrrR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangS7sandwichscalesstringistringrtibbletidyrtidyselecttimeDateTMBurcautf8vctrsVGAMviridisLitewithrzoo

Basic theory and concepts
INTRODUCTION TO PACKAGE LEFKO3 | BASIC CONCEPTS | Life history models and projection matrices | Ahistorical vs. historical matrix models | Raw vs. function-based matrix models, including integral projection models | Different parameterizations of the historical MPM | Leslie (age-classified) MPMs | Age-by-stage MPMs | WORKFLOW | Step 1: Life history model development | Step 2a: Dataset organization | Step 2b: Provide supplemental information for matrix estimation | Step 3: Assess whether historical MPM is justified, and develop models of demographic parameters | Step 4: Estimate matrices | Step 4a. Importing matrices and IPMs | Step 4b. Edit matrices | Step 5. MPM analyses | Deterministic vs. stochastic analysis | Density independent vs. density dependent analysis | Population growth rate | Stable stage distribution and reproductive value | Sensitivity and elasticity | Life table response experiments (LTREs) | Custom projections | Further analyses | Acknowledgements | Literature cited
Rendered fromChapter1.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2026-02-17

Cypripedium candidum function-based MPMs
ORGANISM AND POPULATION | BASIC WORKFLOW | Step 1. Life history model development | Step 2a. Data standardization | Step 2b. Vertical dataset standardization | Step 2c. Provide supplemental information for matrix estimation | Step 3. Tests of history, and vital rate modeling | Step 3a. General modeling strategy | Step 3b. Size and fecundity distributions | Step 3c. Model building and selection | Step 4. MPM estimation | Step 5. MPM analysis | Acknowledgements | Literature cited
Rendered fromChapter5.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2026-02-17

Lathyrus vernus function-based age-by-stage MPMs, LTRE and sLTRE analysis
ORGANISM AND POPULATION | BASIC WORKFLOW | Step 1. Life history model development | Step 2a. Data standardization | Step 2b. Provide supplemental information for matrix estimation | Step 3. Tests of history, and vital rate modeling | Step 4. MPM estimation | Step 5. MPM analysis | Acknowledgements | Literature cited
Rendered fromChapter8.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2026-02-17

Lathyrus vernus IPMs
ORGANISM AND POPULATION | BASIC WORKFLOW | Step 1. Life history model development | Step 2a. Dataset standardization | Step 2b: Develop supplemental information for matrix estimation | Step 3. Tests of history, and vital rate modeling | Step 4. IPM estimation | Step 5. MPM analysis | Acknowledgements | Literature cited
Rendered fromChapter6.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2026-02-17

Lathyrus vernus raw MPMs
ORGANISM AND POPULATION | BASIC WORKFLOW | Step 1. Life history model development | Step 2a. Data standardization | Step 2b. Provide supplemental information for matrix estimation | Step 3. Tests of history | Step 4. MPM estimation | Step 5. MPM analysis | Acknowledgements | Literature cited
Rendered fromChapter2.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2026-02-17

LTREs, sLTREs, and MPM import with Anthyllis vulneraria
ORGANISM AND POPULATIONS | BASIC WORKFLOW | Step 1. Life history model development | Step 3. MPM analysis | Highest stochastic mean LTRE contribution: | Highest stochastic mean LTRE contribution is associated with element: | Lowest stochastic mean LTRE contribution: | Lowest stochastic mean LTRE contribution is associated with element: | Highest stochastic SD LTRE contribution: | Highest stochastic SD LTRE contribution is associated with element: | Lowest stochastic SD LTRE contribution: | Lowest stochastic SD LTRE contribution is associated with element: | Total positive deterministic LTRE contributions: | Total negative deterministic LTRE contributions: | Total positive stochastic mean LTRE contributions: | Total negative stochastic mean LTRE contributions: | Total positive stochastic SD LTRE contributions: | Total negative stochastic SD LTRE contributions:
Rendered fromChapter9.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2026-02-17

Readme and manuals

Help Manual

Help pageTopics
Historical and Ahistorical Population Projection Matrix Analysislefko3-package lefko3
Calculate Actual Stage, Age, Stage-Pair, or Age-Stage Distributionsactualstage3
Add Matrices to a lefkoMat or lefkoMatList Objectadd_lM
Add a New Stage to an Existing lefkoMat or lefkoMatList Objectadd_stage
Create Function-based Ahistorical Age x Stage Matrix Projection Modelaflefko2
Matrix Set of _Anthyllis vulneraria_ Populations in Belgiumanthyllis
Append Projections To Create New lefkoProj Objectappend_lP
Create Raw Ahistorical Age x Stage Matrix Projection Modelarlefko2
Two-Parameter Beverton-Holt Functionbeverton3
Bootstrap Standardized hfv_data Datasetsbootstrap3
Extract Conditional Ahistorical Difference Matricescond_diff
Extract Conditional Ahistorical Matrices from Historical MPMcond_hmpm
Create lefkoMat Object from Given Input Matrices or an MPM Databasecreate_lM
Creates a Skeleton Paramnames Object for Use in Function-based Modelingcreate_pm
Check Continuity of Life Cycle through Matrices in lefkoMat Objectscycle_check
Demographic Dataset of _Cypripedium candidum_ Population, in Horizontal Formatcypdata
Demographic Dataset of _Cypripedium candidum_ Population, in Vertical Formatcypvert
Delete Matrices from lefkoMat or lefkoMatList Objectdelete_lM
Set Density Dependence Relationships in Matrix Elementsdensity_input
Set Density Dependence Relationships in Vital Ratesdensity_vr
Calculate Difference Matrices Between lefkoMat Objects of Equal Dimensionsdiff_lM
Edit lefkoMat or lefkoMatList Object based on Supplemental Dataedit_lM
Estimate Elasticity of Population Growth Rate to Matrix Elementselasticity3
Estimate Elasticity of Population Growth Rate of a Single Sparse Matrixelasticity3.dgCMatrix
Estimate Elasticity of Population Growth Rate of a lefkoMat Objectelasticity3.lefkoMat
Estimate Elasticity of Population Growth Rate of a lefkoMatList Objectelasticity3.lefkoMatList
Estimate Elasticity of Population Growth Rate of a List of Matriceselasticity3.list
Estimate Elasticity of Population Growth Rate of a Single Matrixelasticity3.matrix
Project Function-based Matrix Projection Modelf_projection3
Create Function-based Ahistorical Matrix Projection Modelflefko2
Create Function-based Historical Matrix Projection Modelflefko3
Create Function-based Age-based (Leslie) Matrix Projection Modelfleslie
Assess Quality of hfv Datasetshfv_qc
Create Historical MPMs Assuming No Influence of Individual Historyhist_null
Create Historical Vertical Data Frame from Ahistorical Vertical Data Framehistoricalize3
Create Matrix Imageimage3
Create a Matrix Image for a Single Sparse Matriximage3.dgCMatrix
Create Matrix Image(s) for lefkoElas Objectimage3.lefkoElas
Create Matrix Image(s) for lefkoMat Objectimage3.lefkoMat
Create Matrix Image(s) for lefkoSens Objectimage3.lefkoSens
Create Matrix Images for Matrices in a Listimage3.list
Create a Matrix Image for a Single Matriximage3.matrix
Estimate Actual or Deterministic Population Growth Ratelambda3
Demographic Dataset of _Lathyrus vernus_ Populationlathyrus
Estimate Mean Projection Matriceslmean
Two-Parameter logistic Functionlogistic3
Conduct a Life Table Response Experimentltre3
Creates Vector of Times Based on First-Order Markov Transition Matrixmarkov_run
Arranges Matrix Elements in Order of Magnitude for Interpretationmatrix_interp
Minimize lefkoMod Object by Conversion to vrm_input ObjectminiMod
Develop Best-fit Vital Rate Estimation Models for MPM Developmentmodelsearch
General Matrix Projection Model and Bootstrapped MPM Creationmpm_create
Create Overwrite Table for MPM Developmentoverwrite
Plot Projection Simulationsplot.lefkoProj
Conduct Population Projection Simulationsprojection3
Demographic Dataset of _Pyrola japonica_ and _Pyrola subaphylla_ Populations, in Horizontal Formatpyrola
Estimate Reproductive Valuerepvalue3
Estimate Reproductive Value Vector for a Single Population Projection Matrixrepvalue3.dgCMatrix
Estimate Reproductive Value Vectors of Matrices in a lefkoMat Objectrepvalue3.lefkoMat
Estimate Reproductive Value Vectors of Matrices in a lefkoMatList Objectrepvalue3.lefkoMatList
Estimate Reproductive Value Vector for a List of Projection Matricesrepvalue3.list
Estimate Reproductive Value Vector for a Single Population Projection Matrixrepvalue3.matrix
Two-Parameter Ricker Functionricker3
Create Raw Ahistorical Matrix Projection Modelrlefko2
Create Raw Historical Matrix Projection Modelrlefko3
Create Raw Leslie (Age-based) Matrix Projection Modelrleslie
Estimate Sensitivity of Population Growth Rate to Matrix Elementssensitivity3
Estimate Sensitivity of Population Growth Rate of a Single Matrixsensitivity3.dgCMatrix
Estimate Sensitivity of Population Growth Rate of a lefkoMat Objectsensitivity3.lefkoMat
Estimate Sensitivity of Population Growth Rate of a lefkoMatList Objectsensitivity3.lefkoMatList
Estimate Sensitivity of Population Growth Rate of a List of Matricessensitivity3.list
Estimate Sensitivity of Population Growth Rate of a Single Matrixsensitivity3.matrix
Create Stageframe for Population Matrix Projection Analysissf_create
Test Overdispersion and Zero Inflation in Size and Fecundity Distributionssf_distrib
Create Skeleton Stageframesf_skeleton
Estimate Stochastic Population Growth Rateslambda3
Estimate Stable Stage Distributionstablestage3
Estimate Stable Stage Distribution of a Single Population Projection Matrixstablestage3.dgCMatrix
Estimate Stable Stage Distribution of Matrices in lefkoMat Objectstablestage3.lefkoMat
Estimate Stable Stage Distribution of Matrices in lefkoMatList Objectstablestage3.lefkoMatList
Estimate Stable Stage Distribution of a List of Projection Matricesstablestage3.list
Estimate Stable Stage Distribution of a Single Population Projection Matrixstablestage3.matrix
Create a Vector of Stage Weights for Density Dependence Calculationsstage_weight
Create a Starting Vector for Population Projectionstart_input
Create New lefkoMat or lefkoMatList Object as Subset of Anothersubset_lM
Summary of Classes "hfvdata" and "hfvlistsummary_hfv
Summary of Class "lefkoCondMat"summary.lefkoCondMat
Summarize lefkoElas Objectssummary.lefkoElas
Summarize lefkoLTRE Objectssummary.lefkoLTRE
Summary of Class "lefkoMat"summary.lefkoMat
Summary of Class "lefkoMatList"summary.lefkoMatList
Summary of Class "lefkoMod"summary.lefkoMod
Summarize lefkoProj Objectssummary.lefkoProj
Create A Supplement Skeleton Data Framesup_skeleton
Create a Data Frame of Supplemental Data for MPM Developmentsupplemental
Two-Parameter Usher Functionusher3
Create Historical Vertical Data Frame from Horizontal Data Frameverticalize3
Import Vital Rate Model Factor Values for Function-based MPM Developmentvrm_import