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1 change: 1 addition & 0 deletions README.Rmd
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---
output: github_document
bibliography: references.bib
csl: ecology.csl
---

<!-- README.md is generated from README.Rmd. Please edit that file -->
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76 changes: 37 additions & 39 deletions README.md
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Expand Up @@ -74,15 +74,13 @@ and [Lora Murphy](https://www.caryinstitute.org/lora-murphy) from the
(Milbrook, NY, US). The package was designed to facilitate the use of
maximum likelihood estimation in R, using simulated annealing as the
optimization routine. The implementation of simulated annealing was
adapted from Goffe, Ferrier, and Rogers (1994), and allows bounded
searches.
adapted from Goffe et al. (1994), and allows bounded searches.

The likelihood package has been used in multiple scientific studies to
explore various aspects of tree forest ecology worldwide (*e.g*. Canham
and Uriarte 2006; Gómez-Aparicio et al. 2009, 2011; Gea-Izquierdo,
Fernández-de-Uña, and Cañellas 2013; Canham et al. 2006;
Fernández-de-Uña, Cañellas, and Gea-Izquierdo 2015). Despite its broad
use, it has lacked user-friendly tools for managing and exploring
and Uriarte 2006, Canham et al. 2006, Gómez-Aparicio et al. 2009, 2011,
Gea-Izquierdo et al. 2013, Fernández-de-Uña et al. 2015). Despite its
broad use, it has lacked user-friendly tools for managing and exploring
parameter estimation results. This gap inspired the development of the
likelihoodTools package

Expand All @@ -100,73 +98,73 @@ fellowship program. Grant JDC2022-050056-I funded by MCIN/AEI/
## References

<div id="refs" class="references csl-bib-body hanging-indent"
entry-spacing="0">
entry-spacing="0" line-spacing="2">

<div id="ref-Canhametal2006NeighborhoodAnalyses" class="csl-entry">

Canham, Charles D., Michael J. Papaik, María Uriarte, William H.
McWilliams, Jennifer C. Jenkins, and Mark J. Twery. 2006. Neighborhood
Analyses of Canopy Tree Competition Along Environmental Gradients in New
England Forests.” *Ecological Applications* 16 (2): 540–54.
[https://doi.org/10.1890/1051-0761(2006)016\[0540:NAOCTC\]2.0.CO;2](https://doi.org/10.1890/1051-0761(2006)016[0540:NAOCTC]2.0.CO;2).
Canham, C. D., M. J. Papaik, M. Uriarte, W. H. McWilliams, J. C.
Jenkins, and M. J. Twery. 2006. [Neighborhood analyses of canopy tree
competition along environmental gradients in new england
forests](https://doi.org/10.1890/1051-0761(2006)016[0540:NAOCTC]2.0.CO;2).
Ecological Applications 16:540–554.

</div>

<div id="ref-CanhamUriarte2006AnalysisNeighborhood" class="csl-entry">

Canham, Charles D., and María Uriarte. 2006. Analysis of Neighborhood
Dynamics of Forest Ecosystems Using Likelihood Methods and Modeling.”
*Ecological Applications* 16 (1): 62–73.
<https://doi.org/10.1890/04-0657>.
Canham, C. D., and M. Uriarte. 2006. [Analysis of neighborhood dynamics
of forest ecosystems using likelihood methods and
modeling](https://doi.org/10.1890/04-0657). Ecological Applications
16:62–73.

</div>

<div id="ref-FernandezdeUnaetal2015StandCompetition" class="csl-entry">

Fernández-de-Uña, Laura, Isabel Cañellas, and Guillermo Gea-Izquierdo.
2015. “Stand Competition Determines How Different Tree Species Will Cope
with a Warming Climate.” *PLOS ONE* 10 (3, 3): e0122255.
<https://doi.org/10.1371/journal.pone.0122255>.
Fernández-de-Uña, L., I. Cañellas, and G. Gea-Izquierdo. 2015. [Stand
competition determines how different tree species will cope with a
warming climate](https://doi.org/10.1371/journal.pone.0122255). PLOS ONE
10:e0122255.

</div>

<div id="ref-GeaIzquierdoetal2013GrowthProjections" class="csl-entry">

Gea-Izquierdo, Guillermo, Laura Fernández-de-Uña, and Isabel Cañellas.
2013. “Growth Projections Reveal Local Vulnerability of Mediterranean
Oaks with Rising Temperatures.” *Forest Ecology and Management* 305:
282–93. <https://doi.org/10.1016/j.foreco.2013.05.058>.
Gea-Izquierdo, G., L. Fernández-de-Uña, and I. Cañellas. 2013. [Growth
projections reveal local vulnerability of Mediterranean oaks with rising
temperatures](https://doi.org/10.1016/j.foreco.2013.05.058). Forest
Ecology and Management 305:282–293.

</div>

<div id="ref-Goffeetal1994GlobalOptimization" class="csl-entry">

Goffe, William L., Gary D. Ferrier, and John Rogers. 1994. Global
Optimization of Statistical Functions with Simulated Annealing.”
*Journal of Econometrics* 60 (1-2): 65–99.
<https://doi.org/10.1016/0304-4076(94)90038-8>.
Goffe, W. L., G. D. Ferrier, and J. Rogers. 1994. [Global optimization
of statistical functions with simulated
annealing](https://doi.org/10.1016/0304-4076(94)90038-8). Journal of
Econometrics 60:65–99.

</div>

<div id="ref-GomezAparicioetal2011DisentanglingRelative"
class="csl-entry">

Gómez-Aparicio, Lorena, Raúl García-Valdés, Paloma Ruíz-Benito, and
Miguel A. Zavala. 2011. Disentangling the Relative Importance of
Climate, Size and Competition on Tree Growth in Iberian Forests:
Implications for Forest Management Under Global Change: Neighborhood
Models and Tree Growth Drivers.” *Global Change Biology* 17 (7):
2400–2414. <https://doi.org/10.1111/j.1365-2486.2011.02421.x>.
Gómez-Aparicio, L., R. García-Valdés, P. Ruíz-Benito, and M. A. Zavala.
2011. [Disentangling the relative importance of climate, size and
competition on tree growth in iberian forests: Implications for forest
management under global change: Neighborhood models and tree growth
drivers](https://doi.org/10.1111/j.1365-2486.2011.02421.x). Global
Change Biology 17:2400–2414.

</div>

<div id="ref-GomezAparicioetal2009ArePine" class="csl-entry">

Gómez-Aparicio, Lorena, Miguel A. Zavala, Francisco J. Bonet, and Regino
Zamora. 2009. “Are Pine Plantations Valid Tools for Restoring
Mediterranean Forests? An Assessment Along Abiotic and Biotic
Gradients.” *Ecological Applications* 19 (8): 2124–41.
<https://doi.org/10.1890/08-1656.1>.
Gómez-Aparicio, L., M. A. Zavala, F. J. Bonet, and R. Zamora. 2009. [Are
pine plantations valid tools for restoring Mediterranean forests? An
assessment along abiotic and biotic
gradients](https://doi.org/10.1890/08-1656.1). Ecological Applications
19:2124–2141.

</div>

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188 changes: 188 additions & 0 deletions ecology.csl
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