課程資訊
課程名稱
R語言漁業分析
Fisheries Analyses with R 
開課學期
110-2 
授課對象
理學院  海洋生物及漁業組  
授課教師
張以杰 
課號
Ocean5138 
課程識別碼
241 U6350 
班次
 
學分
3.0 
全/半年
半年 
必/選修
選修 
上課時間
星期二6,7,8(13:20~16:20) 
上課地點
共207 
備註
總人數上限:9人 
Ceiba 課程網頁
http://ceiba.ntu.edu.tw/1102Ocean5138_ 
課程簡介影片
 
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課程概述

本課程教導學生如何在R統計語言中操作常用的漁業分析。對於每種分析方法亦提供了足夠的背景知識,以便使學生在應用方法時也瞭解其具體理論基礎。

課程中包含了不同漁業分析方法的源由和假設,並演示如何在R中進行實作。該課程包含漁業科學家常用的分析,亦包含漁業或生態領域研究生論文常用的分析。大多數的主題為入門級或中高級。

前三週對R統計語言進行介紹,為後續的漁業分析課程先建立基礎。第4周和第5週(Age Comparisons and Age Length Key)所介紹的方法將提供作為續課程所需的資料。線性迴歸是許多漁業分析中的基礎統計方法,它會在第7週的體長體重關係課程來介紹。在第7週的線性迴歸熟練後,將後續應用在第9(Condition)、11(Abundance from Depletion Data)和12(Mortality Rate)週。非線性迴歸將在第13週的魚類成長分析中來介紹,之後將應用在第14週的魚類加入量與產卵親魚量關係。剩餘生產模型將在第15周來介紹。課程的最後一週(第16週)為群組討論。

This course is a “how-to” guide for conducting common fisheries-related analyses in R. For each method, enough background information is provided so that the students are assured of the specific details of the implementation of the method.

Specific formulae and the assumptions of the method are described, along with a demonstration of how to perform the analysis in R. The analyses included in this course are commonly performed by practicing fisheries scientists and are also present in many graduate fisheries science or ecology courses. Most topics are covered at the introductory or intermediate level.

The first three weeks provide a minimal introduction to the R environment that builds a foundation for the remaining weeks on fisheries-specific analyses. Weeks 4 and 5 (Age Comparisons and Age Length Key) describe methods commonly used to provide data for topics in later weeks. Linear regression, a foundational statistical method in many fisheries-specific analyses, is introduced within the context of the Weight-Length Relationship in week 7. The linear regression material in week 7 should be mastered before weeks 9 (Condition), 11 (Abundance from Depletion Data), and 12 (Mortality Rates), which all utilize linear regression. Similarly, nonlinear regression is introduced within the context of analyzing Individual Growth in week 13 and is then used to examine the Stock-Recruit Relationship in week 14. The Surplus Production Model will be introduced in week 15. The course will be ended by a group discussion in week 16.
 

課程目標
本課程的主要目為讓學生能夠熟練地用R語言來進行漁業分析。學生將培養資料分析,建立量化魚類族群動態模式的專業技能等。 在課程中,學生將定期地進行漁業數據分析,建模和結果解釋。課程期望學生學習如何編寫自己論文分析中的R語言程式碼。

The main objective of the course was to become skillful to conduct fisheries analyses with R. Students will develop professional skills in data analysis, quantitative fish population modeling. Students will carry out fisheries data analysis, modelling, and interpretation on a regular basis throughout the course. The course expects students to learn how to write the R code for their own research. 
課程要求
 
預期每週課後學習時數
 
Office Hours
 
參考書目
Ogle D.H. (2016). Introductory fisheries analyses with R. Boca Raton: CRC Press. 
指定閱讀
Ogle D.H. (2016). Introductory fisheries analyses with R. Boca Raton: CRC Press.
Book’s website: https://derekogle.com/IFAR/  
評量方式
(僅供參考)
   
課程進度
週次
日期
單元主題
第1週
02/15  Very Brief Introduction to R Basics 
第2週
02/22  Loading Data and Basic Manipulations 
第3週
03/01  Plotting Fundamentals 
第4週
03/08  Age Comparisons 
第5週
03/15  Age Length Key 
第6週
03/22  Size Structure (學生分組報告) 
第7週
03/29  Weight Length Relationships  
第8週
04/05  Holiday(清明節) 
第9週
04/12  Condition (學生分組報告) 
第10週
04/19  Abundance from Capture Recapture Data 
第11週
04/26  Abundance from Depletion Data 
第12週
05/03  Mortality Rates 
第13週
05/10  Individual Growth (學生分組報告) 
第14週
05/17  Recruitment 
第15週
05/24  Surplus Production Model 
第16週
05/31  Final discussion