Fishing and habitat condition differentially affect size spectra slopes of coral reef fishes

README for the paper: Fishing and habitat condition differentially affect size spectra slopes of coral reef fishes Paul G. Carvalho*, Fakhrizal Setiawan, Karizma Fahlevy, Beginer Subhan, Hawis Madduppa, Guangyu Zhu, Austin T. Humphries. Ecological Applications. 2021. *Corresponding author: 9 East Alumni Ave, University of Rhode Island, Kingston, RI 02881, USA; [e-mail] size_spectra_analysis.r (last updated 01/20/2021) contains code developed in R version 4.0.3 that completely replicates the analyses conducted for the paper. The file “functions.r” is loaded in this script and required for the code to run properly (see description of this file below). In addition, three GitHub packages are required for these analyses and are loaded on lines 20-22. This code quantifies size spectra slopes, runs Generalized Additive Models, and conducts multi-model inference. Code to create plots in the main paper and supplemental information are also included in this file. functions.r (last updated 01/20/2021) contains code developed in R version 4.0.3. The statistical and plotting functions defined in this file are used in “size_spectra_analysis.r”. Many of the functions were adopted from https://github.com/andrew-edwards/fitting-size-spectra. The statistical functions calculate the log-likelihood for fitting size spectrum slope and calculate 95% CI. The plotting functions trophic.plots, slope_regAndFunc, and slope_reg calculate size spectrum slopes based on trophic role (carnivore vs. herbivore) and region of Indonesia where data were collected (Raja Ampat, Wakatobi, and Lombok). The primary purpose of these functions was to condense the code in “size_spectra_analysis.r”. fish_size_spectra_data.csv contains underwater visual census data collected in Indonesia (regions: Raja Ampat, Wakatobi, and Lombok) from January 2018 to July 2018. Data include site names, transect number, species identifications, estimated size (cm), functional groups, trophic roles (i.e., carnivore, herbivore, and other), and parameter values for converting length (cm) to mass (g and kg). drivers_size_spectra_data.csv contains site and habitat data (collected from January 2018 to July 2018) that were used in the Generalized Additive Models to explain site differences in size spectra slopes. Data include site names, site coordinates, site population gravity values (a metric of human population density), hard coral cover (percentage), algae cover (percentage), and structural complexity (see methods section for details on the classification). https://github.com/andrew-edwards/fitting-size-spectra contains the original code for fitting size spectra slopes. https://github.com/m-clark/visibly contains code for color palettes and other plotting aesthetics in R.

本文档为论文《捕捞与栖息地条件对珊瑚礁鱼类体型谱斜率的差异化影响》的配套README文件。作者：Paul G. Carvalho*、Fakhrizal Setiawan、Karizma Fahlevy、Beginer Subhan、Hawis Madduppa、朱光宇（Guangyu Zhu）、Austin T. Humphries。发表期刊：*Ecological Applications*，2021年。*通讯作者：美国罗德岛大学，9 East Alumni Ave, Kingston, RI 02881；邮箱：[e-mail]

`size_spectra_analysis.r`（最后更新于2021年1月20日）包含基于R 4.0.3版本开发的代码，可完整复现论文中的所有分析流程。该脚本需加载`functions.r`文件才能正常运行（详见下述该文件的说明）。此外，本次分析需依赖3个GitHub开源包，相关加载代码位于脚本第20-22行。本代码可实现体型谱斜率量化、广义加性模型（Generalized Additive Models, GAM）构建以及多模型推断（multi-model inference）功能。此外，本文件还包含用于生成论文正文及补充材料中图表的代码。

`functions.r`（最后更新于2021年1月20日）同样基于R 4.0.3版本开发，其中定义的统计与绘图函数将被`size_spectra_analysis.r`调用。本文件中的多数函数改编自https://github.com/andrew-edwards/fitting-size-spectra。其中统计函数可计算拟合体型谱斜率的对数似然值，并求解95%置信区间；绘图函数`trophic.plots`、`slope_regAndFunc`与`slope_reg`可基于营养功能群（食肉动物与植食动物）以及数据采集的印度尼西亚海域（拉贾安帕特、瓦卡托比与龙目岛）计算体型谱斜率。本文件中函数的核心目的是精简`size_spectra_analysis.r`的代码体量。

`fish_size_spectra_data.csv`包含2018年1月至7月在印度尼西亚拉贾安帕特、瓦卡托比与龙目岛海域采集的水下视觉普查（Underwater Visual Census, UVC）数据。数据内容涵盖样点名称、样带编号、物种鉴定结果、体长估计值（单位：厘米）、功能群信息、营养功能类型（即食肉动物、植食动物及其他类群），以及将体长（厘米）转换为体重（克与千克）所需的参数值。

`drivers_size_spectra_data.csv`包含2018年1月至7月采集的样点与栖息地数据，用于广义加性模型分析以解释不同样点间体型谱斜率的差异。数据内容涵盖样点名称、样点坐标、样点人口重力值（人类人口密度的量化指标）、硬珊瑚覆盖率（百分比）、藻类覆盖率（百分比）以及生境结构复杂度（分类细节详见论文方法部分）。

https://github.com/andrew-edwards/fitting-size-spectra 包含用于拟合体型谱斜率的原始代码。
https://github.com/m-clark/visibly 包含R语言中用于配色方案与其他绘图美学设置的代码。