Package: lefko3 6.3.1

Richard P. Shefferson

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]

lefko3_6.3.1.tar.gz
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lefko3.pdf |lefko3.html✨
lefko3/json (API)
NEWS

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

Peer review:

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

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.42 score 11 scripts 612 downloads 54 exports 24 dependencies

Last updated 3 months agofrom:ea6193ce68. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-linux-x86_64OKNov 01 2024

Exports:actualstage3add_lMadd_stageaflefko2append_lParlefko2beverton3cond_diffcond_hmpmcreate_lMcreate_pmdelete_lMdensity_inputdensity_vrdiff_lMedit_lMelasticity3f_projection3flefko2flefko3flesliehfv_qchist_nullhistoricalize3image3lambda3lmeanlogistic3ltre3markov_runmatrix_interpminiModmodelsearchmpm_createoverwriteprojection3repvalue3ricker3rlefko2rlefko3rlesliesensitivity3sf_createsf_distribsf_skeletonslambda3stablestage3start_inputsubset_lMsummary_hfvsupplementalusher3verticalize3vrm_import

Dependencies:BHbootglmmTMBinsightlatticelme4MASSMatrixmgcvminqaMuMInnlmenloptrnumDerivpsclrbibutilsRcppRcppArmadilloRcppEigenRdpackreformulasrlangTMBVGAM

Basic theory and concepts

Richard P. Shefferson, Shun Kurokawa, and Johan Ehrlén

Rendered fromChapter1.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2024-08-21
Started: 2020-08-03

Cypripedium candidum function-based MPMs

Richard P. Shefferson, Shun Kurokawa, and Johan Ehrlén

Rendered fromChapter5.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2024-08-21
Started: 2021-01-06

Lathyrus vernus function-based age-by-stage MPMs, LTRE and sLTRE analysis

Richard P. Shefferson, Shun Kurokawa, and Johan Ehrlén

Rendered fromChapter8.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2024-08-21
Started: 2021-04-02

Lathyrus vernus IPMs

Richard P. Shefferson, Shun Kurokawa, and Johan Ehrlén

Rendered fromChapter6.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2024-08-21
Started: 2021-01-06

Lathyrus vernus raw MPMs

Richard P. Shefferson, Shun Kurokawa, and Johan Ehrlén

Rendered fromChapter2.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2024-08-21
Started: 2020-08-03

LTREs, sLTREs, and MPM import with Anthyllis vulneraria

Richard P. Shefferson and Raziel Davison

Rendered fromChapter9.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2024-08-21
Started: 2021-08-18

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 lefkoMat Objectadd_lM
Add a New Stage to an Existing LefkoMat Objectadd_stage
Create Function-based Ahistorical Age x Stage Matrix Projection Modelaflefko2
Matrix Set of _Anthyllis vulneraria_ Populations in Belgiumanthyllis
Append Projections Into New lefkoProj Objectappend_lP
Create Raw Ahistorical Age x Stage Matrix Projection Modelarlefko2
Two-parameter Beverton-Holt functionbeverton3
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
Demographic Dataset of _Cypripedium candidum_ Population, in Horizontal Formatcypdata
Demographic Dataset of _Cypripedium candidum_ Population, in Vertical Formatcypvert
Delete Matrices from lefkoMat 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 an MPM 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 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 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 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 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 a List of Projection Matricesstablestage3.list
Estimate Stable Stage Distribution of a Single Population Projection Matrixstablestage3.matrix
Create a Starting Vector for Population Projectionstart_input
Create New lefkoMat Object as Subset of Another lefkoMat Objectsubset_lM
Summary of Class "hfvdata"summary_hfv
Summary of Class "lefkoCondMat"summary.lefkoCondMat
Summarize lefkoElas Objectssummary.lefkoElas
Summarize lefkoLTRE Objectssummary.lefkoLTRE
Summary of Class "lefkoMat"summary.lefkoMat
Summary of Class "lefkoMod"summary.lefkoMod
Summarize lefkoProj Objectssummary.lefkoProj
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