scholarly journals ipmr: Flexibly implement Integral Projection Models in R

2021 ◽  
Author(s):  
Sam C. Levin ◽  
Dylan Z. Childs ◽  
Aldo Compagnoni ◽  
Sanne Evers ◽  
Tiffany Knight ◽  
...  
Keyword(s):  
Management Strategies ◽  
Natural Populations ◽  
R Package ◽  
Life Cycles ◽  
Plant Population Dynamics ◽  
Integral Projection Models ◽  
Integral Projection ◽  
Structured Population Models ◽  
Model Complex ◽  
Time Required

Integral projection models (IPMs) are an important tool for studying the dynamics of populations structured by one or more continuous traits (e.g. size, height, color). Researchers use IPMs to investigate questions ranging from linking drivers to plant population dynamics, planning conservation and management strategies, and quantifying selective pressures in natural populations. The popularity of stage-structured population models has been supported by R scripts and packages (e.g. IPMpack, popbio, popdemo, lefko3) aimed at ecologists, which have introduced a broad repertoire of functionality and outputs. However, pressing ecological, evolutionary, and conservation biology topics require developing more complex IPMs, and considerably more expertise to implement them. Here, we introduce ipmr, a flexible R package for building, analyzing, and interpreting IPMs. The ipmr framework relies on the mathematical notation of the models to express them in code format. Additionally, this package decouples the model parameterization step from the model implementation step. The latter point substantially increases ipmr's flexibility to model complex life cycles and demographic processes. ipmr can handle a wide variety of models, including density dependence, discretely and continuously varying stochastic environments, and multiple continuous and/or discrete traits. ipmr can accommodate models with individuals cross-classified by age and size. Furthermore, the package provides methods for demographic analyses (e.g. asymptotic and stochastic growth rates) and visualization (e.g. kernel plotting). ipmr is a flexible R package for integral projection models. The package substantially reduces the amount of time required to implement general IPMs. We also provide extensive documentation with six vignettes and help files, accessible from an R session and online.

scholarly journals IPMpack: an R package for integral projection models

2012 ◽  
Vol 4 (2) ◽  
pp. 195-200 ◽  
Author(s):  
C. Jessica E. Metcalf ◽  
Sean M. McMahon ◽  
Roberto Salguero-Gómez ◽  
Eelke Jongejans
Keyword(s):  
R Package ◽  
Integral Projection Models ◽  
Integral Projection

scholarly journals Advancing population ecology with integral projection models: a practical guide

2014 ◽  
Vol 5 (2) ◽  
pp. 99-110 ◽  
Author(s):  
Cory Merow ◽  
Johan P. Dahlgren ◽  
C. Jessica E. Metcalf ◽  
Dylan Z. Childs ◽  
Margaret E.K. Evans ◽  
...  
Keyword(s):  
Population Ecology ◽  
Integral Projection Models ◽  
Integral Projection ◽  
Practical Guide

Grantmaking Foundations’ Asset Management, Payout Rates, and Longevity Under Changing Market Conditions: Results From a Monte Carlo Simulation Study

2019 ◽  
Vol 49 (2) ◽  
pp. 424-447
Author(s):  
Zvika Afik ◽  
Simon Benninga ◽  
Hagai Katz
Keyword(s):  
Monte Carlo ◽  
Asset Management ◽  
Management Strategies ◽  
Problem Area ◽  
Life Cycles ◽  
Investment Strategies ◽  
Monte Carlo Simulation Study ◽  
Success Stories ◽  
Investment Returns ◽  
Grantmaking Foundations

Today’s uncertain financial markets could affect foundations’ future grantmaking capacities. We review foundations’ financial decision-making patterns and their effect on foundations’ assets, longevity goals, and payouts. Using three fictional foundations with different longevity goals and grantmaking preferences, we demonstrate the delicate balance and tight nexus between asset management strategies, payout rates, and longevity. To do so, we perform stochastic Monte Carlo simulations of multiple foundation life cycles, conducted under diverse capital market scenarios. The findings suggest that foundations should (a) readjust their return expectations to today’s less favorable markets; (b) reduce their reliance on past portfolios’ investment returns or unique “success stories” in making decisions; (c) appreciate the strong interdependence between portfolio-mix, payout rates, and longevity; (d) consider effects of their particular mission/problem area on these parameters; and (e) use tailored projection analyses that simulate various investment strategies, payouts rates, and longevity to meet their grantmaking goals.

scholarly journals Aspects of the ecology of Penelope superciliaris temminck, 1815 (Aves: Cracidae) in the Araripe National Forest, Ceará, Brazil

2015 ◽  
Vol 75 (4 suppl 1) ◽  
pp. 126-135 ◽  
Author(s):  
T. N. Thel ◽  
P. H. R. Teixeira ◽  
R. M. Lyra-Neves ◽  
W. R. Telino-Júnior ◽  
J. M. R. Ferreira ◽  
...  
Keyword(s):  
Direct Observation ◽  
Feeding Ecology ◽  
Management Strategies ◽  
Natural Populations ◽  
Line Transect ◽  
National Forest ◽  
Population Parameters ◽  
Neotropical Forests ◽  
Frugivorous Birds ◽  
Fecal Samples

Abstract Guans are large frugivorous birds that inhabit Neotropical forests and play a fundamental role in seed dispersal and forest regeneration. Despite their ecological importance, the natural populations of these birds are increasingly threatened by deforestation and hunting pressure. The present study was conducted in the Araripe National Forest, Ceará (Brazil), with the objective of estimating population parameters (density and total population size) in the Rusty-margined Guan (Penelope superciliaris) and the White-browed Guan (Penelope jacucaca), as well as providing data on their feeding ecology, including seasonal variation and fruit morphology. The study was based on the monthly collection of data between November, 2011, and October, 2012. Population parameters were estimated using line transect surveys, while feeding ecology was studied by direct observation, and the collection of plant and fecal samples. The estimated population density of P. superciliaris was 19.17 individuals/km2 (CV=13.98%), with a mean of 0.13 sightings per 10 km walked. Penelope jacucaca was not encountered during the surveys. A total of 14 plant species were recorded in the diet of P. superciliaris, 12 by direct observation, and two from fecal samples. Fruit diameter varied from 6.3±1.35 mm (Miconia albicans) to 29.9±1.7 mm (Psidium sp.). Yellow was the most frequent fruit color (41.6%, n=5), with two species each (16.6%) providing black, green, and red fruits. Fleshy fruits of the baccate (50.0%, n=6) and drupe (33.3%, n=4) types were the most consumed. The data on population parameters and feeding ecology collected in the present study provide an important database for the development of effective management strategies by environmental agencies for the conservation of the populations of the two guan species.

scholarly journals Perspectives from animal demography on incorporating evolutionary mechanism into plant population dynamics

2018 ◽  
Author(s):  
Maria Paniw
Keyword(s):  
Environmental Change ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Population Level ◽  
Plant Population ◽  
Future Research ◽  
Phenotypic Traits ◽  
Plant Population Dynamics ◽  
Future Research Agenda ◽  
Powerful Approach

AbstractWith a growing number of long-term, individual-based data on natural populations available, it has become increasingly evident that environmental change affects populations through complex, simultaneously occurring demographic and evolutionary processes. Analyses of population-level responses to environmental change must therefore integrate demography and evolution into one coherent framework. Integral projection models (IPMs), which can relate genetic and phenotypic traits to demographic and population-level processes, offer a powerful approach for such integration. However, a rather artificial divide exists in how plant and animal population ecologists use IPMs. Here, I argue for the integration of the two sub-disciplines, particularly focusing on how plant ecologists can diversify their toolset to investigate selection pressures and eco-evolutionary dynamics in plant population models. I provide an overview of approaches that have applied IPMs for eco-evolutionary studies and discuss a potential future research agenda for plant population ecologists. Given an impending extinction crisis, a holistic look at the interacting processes mediating population persistence under environmental change is urgently needed.

Hybridization in leopard frogs (Rana pipiens complex): terrestrial performance of newly metamorphosed hybrid and parental genotypes in field enclosures

2001 ◽  
Vol 79 (9) ◽  
pp. 1552-1558 ◽  
Author(s):  
Matthew J Parris
Keyword(s):  
Growth Rates ◽  
Life Histories ◽  
Parental Species ◽  
Natural Populations ◽  
Life Cycles ◽  
Natural Hybridization ◽  
Evolutionary Potential ◽  
Leopard Frogs ◽  
Rana Blairi ◽  
Advanced Generation

Terrestrial ecology has been largely neglected in the study of amphibian life histories because it is difficult to manipulate most species during the terrestrial stage. I examined the terrestrial performance of Rana blairi, Rana sphenocephala, and four hybrid (two F1 and two advanced generation) genotypes in replicated experimental enclosures to test for differences in traits related to juvenile terrestrial fitness. I produced all genotypes by means of artificial fertilizations using frogs collected from natural populations in central Missouri, and juvenile frogs were obtained from larvae reared in experimental ponds. Following metamorphosis, froglets were raised in single-genotype groups in terrestrial enclosures through the first overwintering. The proportion surviving did not vary among genotypes, but the power to detect significant differences was low. F1 hybrid genotypes BS and SB demonstrated significantly higher growth rates than either parental species or advanced-generation hybrid genotypes. Observation of growth rates of advanced-generation hybrids equal to those of the parental species, and heterosis in F1 hybrids for growth rate, suggests that natural hybridization between R. blairi and R. sphenocephala can produce novel and relatively fit hybrid genotypes. Direct measurement of multiple fitness components for hybrid and parental genotypes is critical for assessing the evolutionary potential of natural hybridization in organisms with complex life cycles.

Integral projection models

2021 ◽  
pp. 181-196
Author(s):  
Edgar J. González ◽  
Dylan Z. Childs ◽  
Pedro F. Quintana-Ascencio ◽  
Roberto Salguero-Gómez
Keyword(s):  
Population Dynamics ◽  
Environmental Variables ◽  
Linear Models ◽  
Vital Rates ◽  
Matrix Population Models ◽  
Generalised Linear Models ◽  
Integral Projection Models ◽  
Integral Projection ◽  
Over Time

Integral projection models (IPMs) allow projecting the behaviour of a population over time using information on the vital processes of individuals, their state, and that of the environment they inhabit. As with matrix population models (MPMs), time is treated as a discrete variable, but in IPMs, state and environmental variables are continuous and are related to the vital rates via generalised linear models. Vital rates in turn integrate into the population dynamics in a mechanistic way. This chapter provides a brief description of the logic behind IPMs and their construction, and, because they share many of the analyses developed for MPMs, it only emphasises how perturbation analyses can be performed with respect to different model elements. The chapter exemplifies the construction of a simple and a more complex IPM structure with an animal and a plant case study, respectively. Finally, inverse modelling in IPMs is presented, a method that allows population projection when some vital rates are not observed.

Comparison of Conventional and Alternative Nursery Weed Management Strategies

1995 ◽  
Vol 9 (4) ◽  
pp. 761-767 ◽  
Author(s):  
James B. Calkins ◽  
Bert T. Swanson
Keyword(s):  
Weed Management ◽  
Cover Crop ◽  
Production Systems ◽  
Management Strategies ◽  
Life Cycles ◽  
Weed Suppression ◽  
Winter Rye ◽  
Field Management ◽  
Companion Crop ◽  
Herbicide Management

Soil cultivation (3 to 5 times/yr) and herbicide management (oxadiazon, 3.92 kg ai/ha), agricultural standards for reducing weed competition, were compared to three alternative nursery field management systems regarding weed suppression: ‘Norcen’ bird's-foot trefoil companion crop, ‘Wheeler’ winter rye cover crop/mulch, and grass sod (80% ‘Eton’ perennial ryegrass and 20% ‘Ruby’ red fescue). Field management treatment had a significant effect on observed weed populations. Weed densities were also subject to yearly variations caused by climate and endogenous weed life cycles. Herbicide management (oxadiazon) consistently provided the best control of undesired vegetation (0.3 weeds/m2) followed by the grass sod (0.7 weeds/m2), Wheeler rye cover crop/mulch (1.7 weeds/m2), Norcen bird's-foot trefoil companion crop (8.6 weeds/m2), and cultivated (55.7 weeds/m2) treatments, respectively. Although the grass sod treatment provided excellent control of undesired vegetation, as an alternative to cultivation and herbicide use, it proved to be excessively competitive with the nursery crop. The bird's-foot trefoil treatment quickly became infested with broadleaf weeds the eradication of which proved difficult. The Wheeler winter rye cover crop/mulch field management system provided acceptable weed control combined with other beneficial effects on the plant/soil environment. Results support the effectiveness of Wheeler winter rye and perhaps other allelopathic cover crop/mulch systems in controlling undesired vegetation in horticultural field production systems.

Sign in / Sign up

Export Citation Format

Share Document