Software
This population software consists of two programs:
- Population Management Library (PML): demographic and genetic analyses of studbook data which include basic statistics. A wide variety of data filters can be applied. Currently SPARKS studbook data are supported.
- studbookR: R statistics add-on package with extensive statistical analyses and graphics that can be applied to results of PML analyses
- Natural history features
- longevity and median lifespan, reproductive lifespan, clutch/litter size, seasonality in births/deaths, moonphase and birth, interbirth interval
- Census-style analyses
- census and growth rates, birth rates, sex-ratio and sex allocation, death rates, migration rates, exponential and logistic growth models
- Life tables
- age pyramid, age-specific mortality rates, age-specific fecundity rates, reproductive values, stable age distribution, population projections, Kaplan-Meier and Cox survival analyses
- Inbreeding
- neonatal and juvenile mortality, survival and fecundity curves, fitness, lethal equivalents
- Genetic variation
- founder representation, mean kinship, genedrop
- Quantitative genetics
- parent-offspring regression and animal model (MCMC and REML)
MacOS and Windows 10 software
PML-studbookRv102.dmg: Apple Mac specific disk image which contains the 64-bits version of the Population Management Library compiled for macOS Sierra (v10.12) with backward compatibility to macOS Mavericks (v10.9); and the package studbookR (R source).
The disk image includes documents to install PML and studbookR, manuals, a tutorial, an example project and a studbook data-set.
Bug fix: create the folder tmp in your home folder i.e. /Users/your-name/tmp. This folder is required by the PML fecundity and mortality analyses.
download size Disk image: 11.8 MB
md5-hash: 57c40ef7835f2e9833b40ab0fe0a7cc2
Install PMLv102b.exe: Windows installation program to install the 64 bits version of the Population Management Library for Windows 10 (with backward compatibility to version 8.1).
Note that the manuals and R package studbookR are not included and need to be downloaded separately.
Update: The installation program includes the required C++ runtime libraries.
Bug fix: create the directory tmp in your home directory i.e. C:\Users\your-name\tmp. This directory is required by the PML fecundity and mortality analyses.
download size: 3.2 MB (executable)
md5-hash: eeffb6ad185c2f9b30d03f22993a5a89
studbookR-0.4.tar.gz: This R source package contains studbookR version 0.4.
This R package provides an interface between results of studbook analyses in PML and the extensive statistical tests and graphic features that are available in R (version 3.1 or higher). This package can be installed on any computer system that supports the R software.
download size tar/gz: 3MB
md5-hash: 4d31ca49ac0e5ea6f950b9e8c10af9f6
studbookR_install.R: This R script downloads/installs dependent R packages before installing studbookR (macOS and Linux version).
download size R script: 3kB
studbookR_install_win.R: R script for Windows.
download size R script: 3kB
example.zip: An example of a PML project including studbook data (with over 2100 records). Follow the instructions in the tutorial.
download size (zip): 477 kB
md5-hash: c057c1f16c60d69eaf0904786c4930fa
Software manuals
PML Script Manual v1.0.2.pdf This manual provides an overview of the available script commands for analyses and view filters.
download size PDF: 225 kB
PML Tutorial.pdf: A short tutorial to run PML and to import SPARKS studbooks.
download size: 208 kB (PDF)
studbookR_install.pdf: Read this document before installing studbookR.
download size PDF: 204 kB