From 27af7022ad97541f87d43f46bbb5ad9ad8397057 Mon Sep 17 00:00:00 2001 From: ajpelu Date: Fri, 1 Nov 2024 01:16:26 +0100 Subject: [PATCH] add csl --- README.Rmd | 1 + README.md | 76 +++++++++++---------- ecology.csl | 188 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 226 insertions(+), 39 deletions(-) create mode 100644 ecology.csl diff --git a/README.Rmd b/README.Rmd index 4b68adb..ef0acb5 100644 --- a/README.Rmd +++ b/README.Rmd @@ -1,6 +1,7 @@ --- output: github_document bibliography: references.bib +csl: ecology.csl --- diff --git a/README.md b/README.md index b38c421..355c12c 100644 --- a/README.md +++ b/README.md @@ -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 @@ -100,73 +98,73 @@ fellowship program. Grant JDC2022-050056-I funded by MCIN/AEI/ ## References
+entry-spacing="0" line-spacing="2">
-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.
-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. -. +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.
-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. -. +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.
-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. . +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.
-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. -. +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.
-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. . +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.
-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. -. +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.
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