| Kategorie |
Textpublikation |
| Referenztyp |
Zeitschriften |
| DOI |
10.1111/2041-210X.13910
|
Lizenz  |
|
| Titel (primär) |
Rpadrino: An R package to access and use PADRINO, an open access database of Integral Projection Models |
| Autor |
Levin, S.C.; Evers, S.; Potter, T.; Peña Guerrero, M.; Childs, D.Z.; Compagnoni, A.; Knight, T.M.; Salguero-Gómez, R. |
| Quelle |
Methods in Ecology and Evolution |
| Erscheinungsjahr |
2022 |
| Department |
BZF; iDiv |
| Band/Volume |
13 |
| Heft |
9 |
| Seite von |
1923 |
| Seite bis |
1929 |
| Sprache |
englisch |
| Topic |
T5 Future Landscapes |
| Daten-/Softwarelinks |
https://doi.org/10.5281/zenodo.6573869 |
| Supplements |
Supplement 1
Supplement 2
Supplement 3 |
| Keywords |
database; demography; elasticity; life history; open access; population dynamics; sensitivity |
| Abstract |
- Discrete time structured population projection models
are an important tool for studying population dynamics. Within this
field, integral projection models (IPMs) have become a popular method
for studying populations structured by continuously distributed traits
(e.g. height, weight). Databases of discrete time, discrete state
structured population models, for example DATLife (life tables) and
COMPADRE & COMADRE (matrix population models), have made
quantitative syntheses straightforward to implement. These efforts allow
researchers to address questions in both basic and applied ecology and
evolutionary biology. Since their introduction in 2000, over 300 works
containing IPMs have been published, offering opportunities for
ecological synthesis too. We describe a novel framework to quickly
reconstruct these models for subsequent analyses using Rpadrino R
package, which serves as an interface to PADRINO, a new database of
IPMs.
- We introduce an R package, Rpadrino, which enables
users to download, subset, reconstruct, and extend published IPMs.
Rpadrino makes use of recently created software, ipmr, to provide an
engine to reconstruct a wide array of IPMs from their symbolic
representations and conduct subsequent analyses. Rpadrino and ipmr are
extensively documented to help users learn their usage.
- Rpadrino currently enables users to reconstruct 280
IPMs from 40 publications that describe the demography of 14 animal and
26 plant species. All of these IPMs are tested to ensure they reproduce
published estimates. Rpadrino provides an interface to augment PADRINO
with external data and modify parameter values, creating a platform to
extend models beyond their original purpose while retaining full
reproducibility.
- PADRINO and Rpadrino provide a toolbox for asking new
questions and conducting syntheses with peer-reviewed published IPMs.
Rpadrino provides a user-friendly interface so researchers do not need
to worry about the database structure or syntax, and can focus on their
research questions and analyses. Additionally, Rpadrino is thoroughly
documented and provides numerous examples of how to perform analyses
which are not included in the package's functionality.
|
| dauerhafte UFZ-Verlinkung |
https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=26290 |
Levin, S.C., Evers, S., Potter, T., Peña Guerrero, M., Childs, D.Z., Compagnoni, A., Knight, T.M., Salguero-Gómez, R. (2022):
Rpadrino: An R package to access and use PADRINO, an open access database of Integral Projection Models
Methods Ecol. Evol. 13 (9), 1923 - 1929 10.1111/2041-210X.13910 |
