Rcompadre and Rage - two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life history traits from matrix population models

Jones, Owen R.; Barks, Patrick; Stott, Iain; James, Tamora D.; Levin, Sam; Petry, William K.; Capdevila, Pol; Che‐Castaldo, Judy; Jackson, John; Römer, Gesa; Schuette, Caroline; Thomas, Chelsea C.; Salguero‐Gómez, Roberto

doi:10.1101/2021.04.26.441330

Cited by 10 publications

(7 citation statements)

References 37 publications

(51 reference statements)

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“…These traits were calculated using the Markov Chain Decomposition method where the time spent in each stage (

N

matrix) can be estimated from the

T

matrix, which also allows calculation of the life‐table elements, survivorship (

{l}_{x})

and fertility (

{m}_{x})

(Caswell, 2001). For this, we used the R package Rage (Jones & Salguero‐Gómez, 2020) that applies Caswell's methods to calculate age‐specific traits from stage‐specific models. Specifically, with the survivorship schedule,

{L}_{{\rm{\max }}}

, the age at which survivorship drops to a critical point (0.01 default value) and

{{L}}_{\text{mean}}

were calculated.…”

Section: Methodsmentioning

confidence: 99%

Using life‐history trait variation to inform ecological risk assessments for threatened and endangered plant species

Rueda‐Cediel

Galić

Brain

et al. 2022

Integr Envir Assess & Manag

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Developing population models for assessing risks to terrestrial plant species listed as threatened or endangered under the Endangered Species Act (ESA) is challenging given a paucity of data on their life histories. The purpose of this study was to develop a novel approach for identifying relatively data-rich nonlisted species that could serve as representatives for species listed under the ESA in the development of population models to inform risk assessments. We used the USDA PLANTS Database, which provides data on plants present in the US territories, to create a list of herbaceous plants. A total of 8742 species was obtained, of which 344 were listed under the ESA. Using the most up-to-date phylogeny for vascular plants in combination with a database of matrix population models for plants (COMPADRE) and cluster analyses, we investigated how listed species were distributed across the plant phylogeny, grouped listed and nonlisted species according to their life history, and identified the traits distinguishing the clusters. We performed elasticity analyses to determine the relative sensitivity of population growth rate to perturbations of species' survival, growth, and reproduction and compared these across clusters and between listed and nonlisted species. We found that listed species were distributed widely across the plant phylogeny as well as clusters, suggesting that listed species do not share a common evolution or life-history characteristics that would make them uniquely vulnerable. Lifespan and age at maturity were more important for distinguishing clusters than were reproductive traits. For clusters that were intermediate in their lifespan, listed and nonlisted species responded similarly to perturbations of their life histories. However, for clusters at either extreme of lifespan, the response to survival perturbations varied depending on conservation status. These results can be used to guide the choice of representative species for population model development in the context of ecological risk assessment.

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“…These traits were calculated using the Markov Chain Decomposition method where the time spent in each stage (

N

matrix) can be estimated from the

T

matrix, which also allows calculation of the life‐table elements, survivorship (

{l}_{x})

and fertility (

{m}_{x})

{L}_{{\rm{\max }}}

, the age at which survivorship drops to a critical point (0.01 default value) and

{{L}}_{\text{mean}}

were calculated.…”

Section: Methodsmentioning

confidence: 99%

Using life‐history trait variation to inform ecological risk assessments for threatened and endangered plant species

Rueda‐Cediel

Galić

Brain

et al. 2022

Integr Envir Assess & Manag

View full text Add to dashboard Cite

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“…• To match spatial bioclimatic data and climatic projections to population dynamics processes (e.g., Hoffmann, 1999;Weppler, Stoll, & Stöcklin, 2006). The mathematical derivations of key life history traits (e.g., generation time, mean life expectancy, rate of senescence, degree of iteroparity) require that these processes be clearly separated (Jones et al, 2022). This is critical for the family of analyses based on Markov chains; the matrix 𝑼 defines the transient state transitions in an absorbing Markov chain (Caswell, 2011(Caswell, , 2013.…”

Section: Gps Coordinates Of Studied Populationsmentioning

confidence: 99%

“…The database is now accessible via a queryable website (https://compadre-db.org/QueryDatabase) that allows users to find and download individual matrices. We also strive to empower researchers and educators with teaching materials (https://compadre-db.org/Education) and the production of new R-packages (Jones et al, 2022) for ease and scalability of MPM-related research. Along with these materials, all details of the database structure and workflow are open-access (https://jonesor.github.io/CompadreGuides/user-guide.html).…”

Section: Archival Of Information In Compadre and Comadrementioning

confidence: 99%

A standard protocol to report discrete stage-structured demographic information

Gascoigne

Rolph

Sankey

et al. 2023

Preprint

Self Cite

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Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology, and conservation science. Accordingly, MPMs now exist for over 3,000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n=60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility, and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardized protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare, and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology, and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility.

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“…Other life history traits that can be calculated from this matrix are stable stage distribution, reproductive value of each stage, and per-stage survivability. We will also use the R package Rage (Jones et al 2021) to calculate the age in each stage, life expectancy and longevity, the age and probability of reaching maturity, and generation time of this population. We then used the rage package in R to analyze various life history traits of this matrix, the output of which is included in the supplementary material.…”

Section: Model Analysismentioning

confidence: 99%

Assessing the need for temporary fishing closures to support sustainability for a small-scale octopus fishery

Wulfing

Kadba

Baker-Médard

et al. 2023

Preprint

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Mechanistic models are particularly useful for understanding and predicting population dynamics in data deficient species. Data deficiency is a relevant issue in small scale fisheries as they are generally under studied and underrepresented in global fishing datasets. As overfishing remains a global issue, especially in small-scale fisheries, one commonly utilized conservation method is temporary closures. The blue octopus (Octopus cyanea) fishery off the southwest coast of Madagascar is one such system that uses temporary closures, yet lacks sufficient data collection to assess the viability of the population. This fishery is a key economic resource for the local community as blue octopus catch is sold by local fishers to international and local export markets and is a major component of fisher income. To assess the sustainability of blue octopus, we parameterize a Levkovitch population matrix model using existing catch data. In this study, we show that this population was in a decline of 1.8% per month at the time of data collection. To sustain the existing population of blue octopus, our model indicates that the fishery would need to close for at least three months annually. Increasing the length of closure is predicted to significantly increase the octopus population at these sites. We show that if implemented correctly, temporary closures could be used to restore this population. The local communities of Madagascar have implemented various fishing restrictions to ensure sustainable fishing, indicating a need for further research into the effectiveness of these fishing closures. Therefore, our study provides insight into the underlying population dynamics of this fishery and provides survivability estimates of this species.

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Rcompadre and Rage - two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life history traits from matrix population models

Cited by 10 publications

References 37 publications

Using life‐history trait variation to inform ecological risk assessments for threatened and endangered plant species

Using life‐history trait variation to inform ecological risk assessments for threatened and endangered plant species

A standard protocol to report discrete stage-structured demographic information

Assessing the need for temporary fishing closures to support sustainability for a small-scale octopus fishery

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