# My R learning notes 3: how to calculate the shortest distance to coast?

Recently, I have been working on processing data from multiple sites, which involved calculating the distance to the nearest coastline for the study sites. After exploring various methods in R and ArcGIS to compute the shortest distances, I found that many were complex and tedious. However, by integrating ideas from different sources, I’ve developed a simplest and fastest approach for calculating the shortest distance for each site by using R. This method is capable of processing multiple sites at the same time. I’d happy to share my codes below. Please feel free to let me know if you have any questions 🙂

library(ggOceanMaps) # in order to use its function dis2land, the output are in kilometers.
library(rnaturalearth)
library(sf)

coast <- ne_coastline(scale=10, returnclass = “sf”)

```# For example, I have a csv file called "Global sites", with three columns: sites_codes, Longitude (LON), and latitude (LAT):
```

# Calculate the shortest distance
ggOceanMaps::dist2land(Your_sites,shapefile =coast)

```# The results will look like:
ldist is the shortest distance (kilometers).```

The usage of ggOceanMaps library: We will use its function called “dis2land” to calculate the shortest distance. The function was originally designed for calculating the distance from a point in the ocean to the land (reference: R/dist2land.R ). But we  can replace the shapefile of the ocean by the shapefile of the coastline, so that we can calculate distance to the closest shoreline. The output is “ldist” and it is in kilometers.

The usage of rnaturalearth library: we can get the global coastline shapefile with the available finest resolution (scale =10) directly from this library.

The method presents here is inspired by Mikko’s answer at https://stackoverflow.com/questions/51837454/r-measuring-distance-from-a-coastline.

# 寻绎 （读后感杂思）不定时更新 Reflections and Miscellaneous Thoughts After Reading

After discontinuing the use of a particular bookmarked platform for books, I have decided to dedicate a standalone article on my personal website to document various reflections after reading. I’ve chosen to title this piece ‘Seeking Threads,’ inspired by the definition in ‘Shuowen Jiezi’ (an ancient Chinese dictionary completed around the year 100 AD). My hope is to follow the threads of these scattered thoughts and uncover life’s ultimate answers. Reading is purely for my personal enjoyment, and my perspectives are entirely subjective. Feel free to share your comments and engage in discussions. Your ideas and perspectives are welcomed and valued.

2022.05.08 穆勒《论自由》John Stuart Mill’s “On Liberty And Utilitarianism”：读到个性自由的一章，书里写道：“但是有些人，尤其是女人，却会因为做了‘众莫肯为’之事，或竟而不肯去做‘众皆争从’之事而遭到谴责，简直就像犯了某种严重的道德罪行一样，成为讥评的主题。” 穆勒写这段话在19世纪…如今社会进步了吗？！！In the chapter on individual freedom, Mill articulates that certain individuals, particularly women, might attract censure for engaging in actions deemed unconventional, or even more so for abstaining from actions considered customary, as if they had committed a grave moral transgression, becoming the target of criticism. Mill penned these words in the 19th century. Has societal progress been achieved since then?

2022.06.04 穆勒《论自由》John Stuart Mill’s “On Liberty And Utilitarianism”：读完了一整本书，明白了穆勒想阐述的自由的界限。遗憾的是，如今的我们在虚拟的世界里都已经没法自由地标记自己读过的书了。Having completed an entire book, I’ve gained a nuanced understanding of the boundaries of freedom that Mill sought to elucidate. Unfortunately, we no longer have the freedom to freely mark the books we’ve read in certain countries.

2022.08.17 伍尔夫《一间只属于自己的房间》Virginia Woolf’s “A Room of One’s Own”：惊叹于伍尔夫敏锐的文学鉴赏力、观察力和深厚的文学功底。读这本书，就像跟着这位19世纪的女子，行走在城市、公园、学校和图书馆，经历和思考女性与小说的联系，以及两种性别的关系；又像看着她不急不慢地建造一座只为女性建立的文学殿堂，看着论点的地基深深插入地下，论证向四周缓缓铺陈开来，又随着论据的叠加越积越高，越来越快，最后汇集在穹顶上，倾泻出智慧的光芒。希望未来这样的殿堂越来越多，希望每个女孩都有一间属于自己的房间，一笔让自己的心智和才华无拘无束发展的收入，享受着世界最美好的自由和爱。I am deeply impressed by Woolf’s acute literary appreciation, powers of observation, and profound literary prowess. Reading this book is akin to journeying alongside this 19th-century woman, traversing cities, parks, schools, and libraries, experiencing and contemplating the intricate relationship between women and novels, as well as the dynamics between the two genders. It’s reminiscent of watching her methodically construct a literary haven exclusively for women, witnessing the foundations of her arguments deeply embedded in the ground, the exposition of her reasoning spreading methodically in all directions. It unfolds with the gradual accumulation of evidence, growing higher and faster, eventually converging at the summit and pouring forth the radiant light of wisdom. I am hoping that there will be an increasing number of such havens in the future, desiring that every girl possesses a room of her own, an income that liberates her intellect and talents boundlessly, allowing her to bask in the world’s most beautiful freedom and love.

2022.08.27 萨拉马戈《失明症漫记》 José Saramago’s “Blindness”：几点思考： 1. 对比2022年发生的一些事情，我觉得萨拉马戈是一位预言家。遗憾的是，也许是由于书里失明症蔓延得太快，没有给哄抬物价的人表现的空间 LOL. 2. 故事还可以再黑色幽默一些。按照现在的潮流，医生的妻子应该拿大女主剧本：和出轨的医生决裂；反杀欺辱她和隔离所女人们的恶人帮；再带领所有的女性突破压迫；建立互帮互助自给自足的组织… 3. 萨拉马戈还是太温情了，不够愤怒。尽管书里是糟糕混乱的世界，里面依然有不离不弃的守护（比如医生的妻子对所有人，亦或者戴墨镜的女孩对斜视小男孩），跨越鸿沟的爱情（戴眼罩的老人和戴墨镜的女孩），以及皆大欢喜的结局（所有人恢复视力）。My reflections: 1. Comparing with some events in 2022, I feel that Saramago is like a prophet. Perhaps due to the swift spread of blindness, there was no room for those inflating prices to make their mark in the book 😉   2. The narrative could have delved even deeper into dark humor. For example, aligning with the prevailing trend of net literature , the doctor’s wife could have embraced a more prominent heroine character who could have broken up with the unfaithful doctor; retaliated against the villain group who isolated and insulted women in quarantine zone, and then lead all women to liberate themselves from oppression, establishing a self-sufficient mutual aid society… 3. Although this book satirizes societal realities and human nature, it remains very heartwarming, concluding with a universally happy ending.

2022.10.24 丹 西蒙斯 《海伯利安》Dan Simmons’s “Hyperion”
：神作，第一次体会到了太空歌剧的魅力。最喜欢十字形和领事的故事。有空要去读济慈的关于海伯利安的诗。It is a masterpiece! I was my first time to experience the charm of space opera. I especially love the stories of the Priest and the Consul. I plan to read Keats’ poems about Hyperion when I have time.

2022.10.26 威廉 吉布森《神经漫游者》William Gibson’s “Neuromancer”
：朋友推荐好多年了，趁着刚读完《海伯利安》，赶紧把这本也读完了，正好可以对比一下两个开山之作。《神经漫游者》无拘无束的想象力令人惊叹。文笔有点天马行空，有些地方可能是翻译的问题，觉得有些不清不楚。比如最后的密码…是蜂巢吗？相比之下，我更喜欢《海伯利安》的文学底蕴和包容万象。It is the book that one of my friend recommended to me for many years. Since I just finished reading “Hyperion”, I think it is a good opportunity to compare these two pioneering works. “Neuromancer” showcases an unfettered imagination that is truly astonishing. The writing style is a bit fantastical, and in some places, it is unclear probably due to translation. For example, the final code… is it “hive”? Anyway, I prefer the literary depth and all-encompassing nature of “Hyperion”.

2022.11.01 齐泽克《齐泽克的笑话》Slavoj Žižek‘s Jokes: Did You Hear the One About Hegel and Negation?”：幽默、有趣。字数很少但是信息量极大。这本书是齐泽克‘我们“感到自由”是因为我们缺乏恰当的语言来表达我们的不自由。’的出处。配合纪录片《变态者意识形态指南》，阅读体验更佳。我读的是于东兴翻译的版本，书最后有一篇莫墨斯的编后记，用一个“汉娜的洋娃娃”的笑话巧妙地串起了本书列举的所有笑话里传达的关于辩证、逻辑、意识形态的事实和荒诞，妙极了。The book is witty and entertaining. Despite its brevity, the book carries a wealth of information. This work is the origin of Slavoj Žižek’s statement ‘We feel free because we lack the very language to articulate our unfreedom.’ Reading it in conjunction with the documentary “The Pervert’s Guide to Ideology” enhances the overall experience. I read the version translated by Yu Dongxing, and the book concludes with a postscript by Momus, skillfully weaving together all the jokes mentioned in the book through a clever joke about “Hannah’s doll.” This effectively conveys the facts and absurdities surrounding dialectics, logic, and ideology, making it truly ingenious.

2022.11.12 戴蒙德 《枪炮、病菌与钢铁》Jared Diamond’s “Guns, Germs, and Steel”
：详细地阐述了地理如何影响农业生产，进而影响社会形态、制度的演化，因此形成了如今世界的强弱富穷的分布。总体阅读体验很流畅，但有些部分稍显啰嗦。作者谈及的关于先发明，再给发明的东西指定用途的说法打破了我长久以来的刻板观点。另外，作者还谈及了生物多样性对人类社会发展的影响，令我不禁想到，在物种大灭绝的现代，我们是否在为未来与外星人的竞争（如果有的话…) 自掘坟墓？最后，作者谈及日本人的起源也非常有意思，原来日韩有可能本是一家。This book meticulously explains how geography influences agricultural production, thereby affecting the evolution of social forms and systems, giving rise to the current global distribution of strength and wealth. The overall reading experience is quite smooth, though some parts may be a bit verbose. The author’s discussion of the concept of inventing first and then assigning a purpose to the invention challenges my long-standing stereotypes. Additionally, the author explores the impact of biodiversity on the development of human societies, making me ponder whether, in the modern era of mass extinctions, we are digging our own graves in the competition for the future, perhaps even with extraterrestrial beings (if they exist…). Finally, the author’s discussion of the origins of the Japanese people is also fascinating, revealing the possibility that Japan and Korea may have shared a common ancestry.

2022.11.22 上野千鹤子、铃木凉美《始于极限》Letters Between Chizuko Ueno and Ryomi Suzuki：不由感叹这是一场两代人之间绵里藏针却又不乏温暖鼓励的对谈。上野千鹤子直率犀利，铃木凉美聪明坦然。交谈里有很多令我醍醐灌顶的点，比如所谓的情色资本其实是情色商品；恋爱是我们受到伤害也互相伤害以借此摸清彼此的自我底线的过程；又比如何为表达的自由，以及”结构与主体“的关系。除此之外，她们关于”表达“的讨论使我深深获益，比如凉美谈到，如果表达能够足够准确精炼，就能避免被肆意曲解。还有上野千鹤子说不要低估读者，写文章时要想一下是写给谁看，勾勒出读者的模样。希望两位优秀的女子都务必珍重，期待她们新的作品。One can’t help but marvel at this dialogue. Chieko Ueno is candid and wise, while Ryomi Suzuki is intelligent and frank. Their conversation is filled with enlightening points, such as the realization that erotic capital is essentially erotic commodities. They delve into the notion that love is a process where we both get hurt and hurt each other to explore personal boundaries. The discussion also covers the freedom of expression and the intricate relationship between “structure and subject.” Moreover, I was greatly enlightened by their discourse on “expression”. Ryomi Suzuki notes that if expression is precise and refined enough, it can avoid arbitrary misinterpretation. Chieko Ueno emphasizes not underestimating the reader, encouraging writers to consider their audience and vividly imagine the faces of their readers. I sincerely hope these two exceptional women take good care of themselves, and I eagerly anticipate their future works.

2022.11.30 玛拉·J. 哈尔特《海洋中的爱与性》Marah J. Hardt’s “Sex in the Sea”：很好的科普文，有趣又学习了很多的知识，并且对如何保护海洋生物有了更深的理解。以后买海鲜时会关注This Fish 和Follow Fish 等生态支持型的机构。The book is entertaining and informative. I’ve gained a lot of knowledge and developed a deeper understanding of how to protect marine life. In the future, when buying seafood, I’ll pay attention to eco-friendly organizations like “This Fish” and “Follow Fish.”

2022.12.27 柏拉图《理想国》Plato’s “Republic”：以对话的形式，借用苏格拉底之口，循循善诱地说明为什么人以及城邦要追求正义。总的来说，柏拉图认为人要追求正义的生活，保持灵魂里理性的部分统治不理智的部分。理想的城邦亦是如此。这本书是精华和糟粕都很明显的典型。精华之处在于对真善美的颂扬以及对事物“理念”和“影子”的辨析，而糟粕之处在于对底层人、女人的贬低。很多处论证在我看来是诡辩了，然而瑕不掩瑜，是一部经典之作。This book, presented in the form of a dialogue between Socrates and other thoughtful people, to elucidate the reasons why individuals and the city-state should pursue justice. In essence, Plato argues that individuals should aspire to live justly, maintaining the dominance of reason over the irrational aspects of the soul. The ideal city-state should adhere to the same principle. This book is a quintessential example where both the essence and flaws are readily apparent. The essence lies in the celebration of truth, goodness, and beauty, as well as the analysis of the concepts of “ideas” and “shadows.” The flaws, however, manifest in the disparagement of the lower class and women. Many arguments, in my opinion, resort to sophistry; yet the flaws do not overshadow its merits.

2022.12.31 李沧东《鹿川有许多粪》 Lee Chang-dong’s “Nokcheon Has Fields of Shit”：一共有5篇短篇小说，最好看的莫过于《鹿川有许多粪》和《天灯》。个人感觉《天灯》更打动我，也许是我与信惠有一些相似的困惑，信念不够坚定，不够勇敢，时时刻刻都在挣扎。在我看来，5篇小说都在探求何为真实的生活，尤其是在所有人都无法避免地被卷入社会运动的大漩涡中，如何才能在真实和谎言中寻找一条自我和解的道路。书里的每一个人最终都走上了在旁人看来无法理解的道路，是非对错无法评价，只留一声叹息。There are a total of five short stories, and the most compelling among them are “Nokcheon Has Fields of Shit” and “Sky Lantern.” Personally, I find “Sky Lantern” more impactful, perhaps because I share some similar perplexities with Shin Hye – a lack of firm convictions and courage, a constant struggle. In my opinion, all five stories delve into the quest for what constitutes a genuine life, especially when everyone is inevitably drawn into the vortex of social movements. How does one navigate between truth and lies to find a path towards self-reconciliation? It is sad to see each character in the book eventually takes a route that where moral judgments become elusive.

2023.01.23 冯友兰《中国哲学简史》Feng Youlan’s “A Short History of Chinese Philosophy”：非常简练地阐述了先秦以来思想体系的发展，着重解释了儒家是如何与道家、佛家思想碰撞与结合，并不断发展。我最惊喜地是了解了”名家“这一思想学派，因为正好之前读了柏拉图的《理想国》，甚觉名家关于理念与事物的区别和柏拉图哲学有异曲同工之妙。可惜名家在历史长河里只昙花一现，否则我国的哲学发展很可能能走上逻辑分析的道路。另一个惊喜，是关于冯友兰对中国哲学的总结：”既是出世的，又是入世的“，令我拍案叫绝。这种既出世又入世的精妙，正是我痴迷哲学的原因。与王国维对哲学的无可奈何不同，哲学于我是立身处世的解药（入世）和精神境界的补药（出世），我从来不觉得其无用。最后，冯友兰说：”人必须先说很多话然后保持静默。”虽不知哲学将引领我去往何方，但我抵达保持静默的境界前，我希望自己能说很多很多话。This book concisely elaborates on the development of philosophical systems since the pre-Qin period, with a particular focus on how Confucianism interacts, clashes, and integrates with Daoism and Buddhism, evolving continuously. I was most pleased to learn about the “School of Names” philosophical school, especially because I had previously read Plato’s “Republic” and found parallels between the School of Names’ distinction between ideas and things and Platonic philosophy. Unfortunately, the School of Names had only a fleeting presence in the river of history; otherwise, Chinese philosophy might have embarked on the path of logical analysis. Another revelation was Feng Youlan’s summarization of Chinese philosophy: “both transcendent and immanent,” which left me in awe. This delicate balance between transcendence and immanence is precisely why I am passionate about philosophy. Unlike Wang Guowei’s sense of helplessness towards philosophy, I see philosophy as both a remedy for practical living (immanence) and an elixir for spiritual elevation (transcendence); I have never considered it useless. Lastly, Feng Youlan remarks, “One must speak a lot before maintaining silence.” Though I don’t know where philosophy will lead me, before reaching the state of silence, I hope to speak a great deal.

2023.03.28 蒂莫西·费里斯 《望向星空深处》Timothy Ferris’s “Seeing in the Dark：How Backyard Stargazers”：不负盛名的科普神作！！！不忍卒读。这本书的语言极其优美，星空的浪漫和人文的情怀交相辉映。作者旁征博引，却又不显枯燥，搭配着独特有趣的个人经历，让每一个故事都生动非凡。不仅如此，每篇章节的安排都按照一篇科普散文配上一篇人物随笔，时间上是从以前到现在，空间上是从近地球到深空，构思之精巧令人惊叹。阅读后认识了许多有趣的宇宙知识，印象最深的是奥尔特云。书后还附有详细的观星指南，真的忍不住想买英文版收藏。A renowned masterpiece in popular science!!! The language in this book is exceptionally elegant, with the romance of the stars and the human touch blending seamlessly. The author skillfully weaves in references, keeping it engaging and never dull. Accompanied by unique and amusing personal experiences, each story becomes exceptionally vivid. What’s more, the arrangement of each chapter pairs a popular science essay with a personal essay, spanning from the past to the present and from near-Earth to deep space. The ingenious design is truly impressive. After reading, I’ve acquired knowledge about many intriguing cosmic facts, with the most memorable being the Oort Cloud. The book also includes a detailed stargazing guide, making me irresistibly tempted to buy the English version for my collection.

2023.04.17 翁贝托·埃科 《玫瑰的名字》Umberto Eco’s “The Name of the Rose”：开头几章很难读，因为文中充满了天主教的历史和文化，非常晦涩。但是读到威廉和阿德索发现藏书馆有密室以及连续死亡的案件的发生符合《启示录》时，情节开始变得很精彩。故事在两个教团会面时达到高潮，尤其是修士们关于是否守贫，如何对待异教徒，以及如何对待知识的演讲读起来令人心潮澎湃。很多人说这是一部反侦探小说，我很认同。因为威廉作为深受罗杰培根影响，具有科学启蒙思想的人文主义知识分子，过分相信理性的力量，认为事件发生存在规律。然而，威廉查明真相完全是歪打正着，且最终的凶手其实只杀了自己而已，与其他的案件并不直接相关，真是印证了这本书讨论的主题：宇宙是无序的。其实再进一步想想，也正是因为博学的凶手认识到了了这一点，再加上有亚里士多德的作品加以刺激，深感若让这本书流传会撼动信仰的根基，才有了后续的悲剧。总之，整本书包容万象，还谈到了上帝之爱与肉体之爱、同性、禁欲与放纵、世俗权力与神学权柄、宝石的鉴赏等，我认为是探案版的《追忆似水年华》。The initial chapters were challenging to read as they were filled with the history and culture of Catholicism, making it quite obscure. However, as the plot unfolds with William and Adso discovering a secret room in the library and a series of deaths aligning with the Book of Revelation, the story becomes captivating. The climax occurs when the two religious orders converge, particularly the monks’ discussions on poverty, the treatment of non-believers, and the approach towards knowledge are riveting. Many describe this as an anti-detective novel, a sentiment I agree with. William, influenced by the humanistic ideals of Roger Bacon and overly reliant on the power of reason, believes that events follow a logical pattern. However, William stumbles upon the truth, and the actual murderer only ends up killing themselves, unrelated to the other deaths, affirming the theme discussed in the book: the universe is chaotic. Upon further reflection, it’s the erudite murderer’s realization of this chaos, stimulated by Aristotle’s works, coupled with the fear that the book’s dissemination would shake the foundations of faith, that leads to the tragic aftermath. In summary, the book covers a myriad of topics, delving into God’s love and physical love, homosexuality, asceticism and indulgence, secular power and theological authority, gem appreciation, and more. I see it as a detective version of “Remembrance of Things Past.”

2023.04.21 格拉宁《奇特的一生》Daniil Granin’s “Alexandrovich Lyubishchev’s better life method”：描写前苏联生物学家柳比歇夫的“传记”。作者认为柳比歇夫的一生奇特，是因为柳比歇夫对自己的时间进行规划、记录和总结，一丝不苟。我给传记加引号，是因为这本书并非严格意义的传记，全书只专注在柳比歇夫的时间统计法，而且含有作者大量的主观评论。这样的写作方法很独特，但不是我的菜。时间统计法也不适用于我。我喜欢自己的时间灵活且自由，浪费就浪费吧。This is a “biography” of the Soviet biologist Alexandrovich Lyubishchev. The author considers Alexandrovich’s life to be extraordinary because he meticulously planned, recorded, and summarized his time. I put “biography” in quotes because this book is not strictly a biography; it solely focuses on the time management method and contains a significant amount of the author’s subjective commentary. This writing approach is unique but not to my liking. The time management method is also not suitable for me. I prefer my time to be flexible and free.

2023.08.14 丹 西蒙斯 《海伯利安的陨落》Dan Simmons’s “The Fall of Hyperion”
：没有第一部写得精彩。用济慈的赛博人格串起整个故事的确构思巧妙，然而，逻辑却经不起推敲，比如为何济慈人格能梦见所有朝圣者经历的事情？又比如，人类之神“共情”据说也是溯时光而来，为何到最后是拉米亚和乔尼的孩子？看来还得继续读第三部才行。This is the second part of the entire Hyperion series. It isn’t as brilliantly written as the first part, Hyperion. While the clever idea of intertwining the entire story with Keats’ cyber-personality is well-conceived, the logic doesn’t hold up under scrutiny. For instance, why can Keats’ personality dream about everything the pilgrims experienced? Additionally, the supposed divine power of “empathy” in humans is said to come from the distant past, so why does it end up with the child of Lamiya and Johnny? I have to continue reading the third part to find answers.

2023.08.23 《图说哲学》：回家看的闲书，书名是哲学，其实里面讲的是哲学家的逸闻轶事，很浅显，有些段落七拼八凑，不知所云。对了解哲学帮助不大。唯一的亮点是很多彩图。

2023.08.26 《视读东方哲学》：还是回家看的闲书，编者是西方媒体人，书里主要介绍的是印度和中国的宗教。我对佛教之类的了解甚少，所以这本书令我收获很多。但书里关于中国哲学的介绍，参考了很多冯友兰的《中国哲学简史》的内容，因此我并没有从中了解到新的知识。但是这本书的有一个两点，是在介绍印度种姓制度时特别地让读者去思考女人属于什么种姓。这一点值得赞扬。

2023.08.28 列维特和都伯纳《魔鬼经济学》Freakonomics by Stephen J. Dubner and Steven Levitt：是一个扩展思路的小册子，有意思但是论证不够严格，可能是与其作为科普读物有关，无法给予严格的科学论证。It is interesting but lacking rigorous proofs.

2023.11.10 陀思妥耶夫斯基《群魔》Fyodor Dostoevsky’s “Demons”: 目前只看了一半左右，书里的恶魔们还没露出马脚。个人感觉这本书比《白痴》好看，但比不上《罪与罚》。I’ve only read about half of it so far, and the demons in the book haven’t revealed their true colors yet. Personally, I find this book more enjoyable than “The Idiot” but not quite up to the level of “Crime and Punishment.”

2023.12.24 陀思妥耶夫斯基《群魔》Fyodor Dostoevsky’s “Demons”: 终于读完了！后半部分的剧情比前半句精彩得多，尤其是临近结尾的连续死亡事件，让我觉得这个五人小组真是阴险得令人遍体生寒。总的来说，阅读体验并不是很好，因为小说的主要人物都不讨喜。韦尔霍文斯基父子是迄今为止令我最讨厌的小说人物了。一个又装又油，一个阴险恶毒，另一个主要人物，斯塔夫罗金，则是阴晴不定，莫名其妙。 但是他们都不是好人，是陀老所说得“群魔”。这些“恶魔”们举着自由的旗号，扰乱社会，害人害己，是影响社会正常运行的毒瘤。此外，延续陀老一贯的风格，这部小说也着眼于上帝是否应该存在的争论。基里诺夫想验证上帝不存在，决定自杀成神。斯塔夫罗金摇摆在信与不信之间，心灵饱受折磨，最后也选择自杀。老实说，我从来没有想过上帝存在与否是如此重要的命题，但是我在小说中读懂了失去信仰的恶果——恶念丛生、道德败坏。Finally finished reading! The latter half of the plot was much more exciting than the first half, especially the series of deaths towards the end, which made me feel that this group of five was so sinister that it sent chills down my spine. Overall, the reading experience wasn’t great because the main characters of the novel were not likable. The Verhovensky father and son are by far the most detestable characters I’ve encountered in a novel. One is pretentious and oily, the other is sinister and vicious. And another main character, Stavrogin, is fickle and inexplicable. But they are all not good people, the ‘demons’ as Dostoevsky described. These ‘demons,’ waving the banner of freedom, disrupt society and harm others and themselves, acting as a cancer that affects the normal functioning of society. Additionally, in keeping with Dostoevsky’s usual style, this novel also focuses on the debate over whether God should exist. Kirillov wants to prove God doesn’t exist by committing suicide to become a god. Stavrogin swings between belief and disbelief, his soul tormented, and in the end, he also chooses suicide. Honestly, I never thought the existence of God was such an important proposition, but in the novel, I understood the evil consequences of losing faith—evil thoughts and moral decay.

2024.01.16 陀思妥耶夫斯基《死屋手记》Fyodor Dostoevsky’s “The House of the Dead “：这本书是我读过的陀老的书中最细腻最真挚动人的一部了。能看得出陀老的哲学思想与他的监狱经历密不可分。书里记载了监狱里的众生百态，是一群已经放飞自我的罪犯在不能放飞自我的情况下放飞自我的故事。这些故事令人匪夷所思，但仔细一想他们的社会背景和自身经历，又不由得可笑可叹。This book is the most delicate and genuinely moving one that I have read among Dostoevsky’s works. It’s evident how his philosophical thoughts are inextricably linked to his prison experiences. The book recounts the various facets of life in prison. These stories are astonishing, yet when one considers their social backgrounds and personal experiences, they make me feel ridiculous and sad at the same time.

# Collections of animals and insects in Durrell’s Corfu trilogy (book 1) 希腊三部曲动物昆虫图鉴 1

Among all the books I read in 2020, my favorite is Durrell’s Corfu trilogy. The books humorously described the colorful childhood of naturalist Gerald Durrell when he and his widowed mother, satiric elder brother Larry, gun-mad brother Leslie, and naïve sister Margo stayed in Corfu island in Greece. The beautiful natural scenery of the island and the hospitable locals are beckoning to me so much. The books have been adapted into a great TV series (The Durrells in Corfu) that has pictured many interesting stories of the family with animals and insects in the island. But I think there are still a lot more to see. Therefore, I am making a collection of the animals and insects mentioned in the books. If there is any misinformation, please feel free to leave your comments. 2020 has been a hard year, as we had to stay indoor and quarantined. I wish this article can recall your lovely memories with wildlife.

##### 第一部：《追逐阳光之岛》(the first book: My Family and Other Animals)
1. 草蛉 （Green lacewings）https://en.wikipedia.org/wiki/Neuroptera
```
（截图自草蛉下蛋视频 from the video：https://youtu.be/ByQo-TpYpxg）```

“我在一丛玫瑰上发现一只草蛉在叶间爬来爬去，正欣赏它美丽脆弱如绿玻璃的翅膀，以及它水汪汪的金色大眼睛，它却在玫瑰叶上停下来，把自己的腹部顶端压低。它保持那个姿势好一会儿才举起尾巴，让我大吃一惊的是，从尾巴里居然拉出一条细线，像一根淡色的头发，就在这根线的末端，出现了一颗蛋。母草蛉休息了一会儿，继续重复刚才的动作，直到那片玫瑰叶看起来像覆盖了一片石松森林为止。下完蛋之后，母草蛉动一动触角，就扇着如一片绿色轻纱的翅膀飞走了。”

“I found a lacewing-fly on the roses and watched her as she climbed about the leaves, admiring her beautiful, fragile wings like green glass, and her enormous liquid golden eyes. Presently she stopped on the surface of a rose-leaf and lowered the tip of her abdomen. She remained like that for a moment and then raised her tail, and from it, to my astonishment, rose a slender thread, like a pale hair. Then, on the very tip of this stalk, appeared the egg. The female had a rest, and then repeated the performance until the surface of the rose-leaf looked as though it was covered with a forest of tiny club moss. The laying over, the female rippled her antennae briefly and flew off in a mist of green gauze wings.”

——（第二章 草莓别墅）(From Chapter 2: The Strawberry-Pink Villa)

`有趣的小知识 (interesting facts)：草蛉是捕食性昆虫，可用来防治虫害。其在幼虫时期不会飞，食量最大。Lacewings feed on insects, so that they can be used for pest control. `

2. 蠼螋 （qu (三声) sou (一声)）Earwig https://en.wikipedia.org/wiki/Earwig

```

“我在周围筑起一道石墙，并用红墨水写了一个告示，贴在附近的柱子上，警告全家人：‘主意——蠼螋窝——抱持按静。’很难得，我只写错了三个字，都跟生物学无关。

“I erected a protecting wall of rocks round it, and as an additional precaution I wrote out a notice in red ink and stuck it on a pole nearby as a warning to the family. The notice read: ‘bewar– earwig nest – quiat plese.‘ It was only remarkable in that the two correctly spelt words were biological ones.“

——（第二章 草莓别墅）(From Chapter 2: The Strawberry-Pink Villa)

`有趣的小知识 (interesting facts)：俗称夹板子，剪指甲虫。受到威胁时会装死，也会卷起尾巴示威，尾巴含微毒。When in danger, they will either pretend to be dead, or curl their tails which contain venom.`

3. 金翅雀 （Goldfinch）https://en.wikipedia.org/wiki/American_goldfinch

```

（Public domain photo）```

“在荒置的畦头上，俗丽的金翅雀兴奋地尖声鸣啭，从一个蓟头唱到另一个蓟头。“

“……and the rough headland where the flocks of garish goldfinches fluttered with excited piping from thistle-head to thistle-head.“

——（第四章 勤学）(From Chapter 4: A Bushel of Learning)

`有趣的小知识 (interesting facts)：以植物果实、种子、草子和谷粒等农作物为食，雄鸟颜色比雌鸟明亮。The color of males are brighter than females. 叫声 bird calls：https://www.bird-sounds.net/american-goldfinch/`

4. 活板门蛛 trapdoor spider

```

（截图自视频 screenshot from the video: https://youtu.be/cBdG9t4hltM）```

“我想到蜘蛛守候在它的甬道里，用爪子紧紧扣住门，聆听昆虫在头顶上的苔藓森林里的活动。“

“The facts he told me about the trapdoor spider haunted me: the idea of the creature crouching in its silken tunnel, holding the door closed with its hooked claws, listening to the movement of the insects on the moss above.“

——（第五章 蜘蛛的宝库）(From Chapter 5: A Treasure of Spiders)

`有趣的小知识 (interesting facts)：这种蜘蛛的天敌包括一种会叮咬蜘蛛并在它们身上产卵的蛛蜂。蛋孵化后，幼虫会生吞蜘蛛。A kind of spider wasps can sting and lay eggs on the spiders. When the egg hatches, the larva can devour the spider alive.`

5. 剑水蚤 Cyclops

`Cyclops features a long antennae屁股上带着剑和两个粉色大囊的剑水蚤（图片来源source：https://bettagogogo.blogspot.com/2013/05/blog-post_12.html）`

“一只光怪陆离的虫走进白色的光圈里，梨形的身体，触角愤愤地抖动着，一根像石南茎的尾巴，两侧各有一个被粉红色小珠珠塞得鼓鼓的大囊（就像骡子驮着两袋洋葱）。

“Into the brilliant circle of white light a weird creature would appear, a pear-shaped body, long antennae that twitched indignantly, a tail like sprigs of heather, and on each side of it (slung like sacks of onions on a donkey) the two large sacs bulging with pink beads.”

——（第六章 嬉春）(From Chapter 6: The Sweet Spring)

`有趣的小知识 (interesting facts)：剑水蚤营养丰富，可作为鱼食。Cyclops are rich in nutrition and can be used as fish food.`

6. 地胆 （其实应该翻译成油甲虫）oil-beetle （meloe proscaraboeus

`雄性油甲虫 Male oil-beetle（ 来自维基百科Source: https://en.wikipedia.org/wiki/Meloe_proscarabaeus#/media/File:Meloe_proscarabaeus_(male).jpg）`

“那只蓝黑色，看起来笨兮兮的甲虫，有一个圆头，一对长在一起的长触角和一个圆滚滚的身体。最怪的东西是它的翅鞘，仿佛刚送洗回来缩了水，小得似乎是给它一半大小的甲虫穿的。….我捡起它后，注意到自己的手指头有一丝丝酸味和油味，却没看见它排出什么液体。“

“It was a large, clumsy, blue-black beetle, with a large round head, long jointed antennae, and a bulbous body. The weird thing about it was its wing-cases; it looked as though it had sent them to the laundry and they had shrunk, for they were very small and appeared to have been constructed for a beetle half the size……. I noticed, after I had picked it up, that my fingers smelled faintly acrid and oily, though it had not appeared to have exuded any liquid that I could see.”

——（第七章 黄水仙别墅）(From Chapter 7: The Daffodil-Yellow Villa)

`有趣的小知识 (interesting facts)：它不会飞 Oil beetles can not fly. `

7. 蚁狮 Antlion

```

“蚁狮的幼虫在沙道上挖出圆锥型的小洞，躺在洞里等候大意的蚂蚁踏上陷阱边缘，随着沙粒滚下洞底，被蚁狮幼虫可怕的钳爪攫住。”

“In the sandy paths the ant-lion larvae dug their little cone-shaped pits, and lay in wait to spatter any unwary ant that stepped over the edge with a bombardment of sand that would send it tumbling down to the bottom of the trap, to be seized in the ant-lion larva’s terrible, pincer-like jaws.”

——（第八章 乌龟山丘）(From Chapter 8: The Tortoise Hills)

`有趣的小知识 (interesting facts)：幼虫没有肛门，所有代谢废物都会储存在身体里，一些用于作茧的丝，其余的在蛹阶段结束时作为胎粪排泄。成虫被叫做蚁蛉，长得像蜻蜓。The larva has no anus, and all metabolic wastes are stored in the body. Some of the wastes are used for producing cocoons, and the rest are excreted as meconium at the end of the pupal stage. The adults are called the ant-fly and look like dragonflies.`

8. 帝王蛾 emperor moth

```

“帝王天蚕蛾胖大的毛毛虫在石南丛里慢慢进食，看起来好似一条条会动的皮毛围领。”

“Among the heather-blooms the great, fat, furry caterpillars of emperor moths fed slowly, looking like animated fur collars.”

——（第八章 乌龟山丘）(From Chapter 8: The Tortoise Hills)

`有趣的小知识： 体型很大，翅膀最高纪录有400 平方厘米。前翅末端的图案形态非常像蛇的头部，又被称为蛇头蛾。是《哥斯拉》系列电影中的著名怪兽摩斯拉的原型。It is very large, and the highest recorded wing length is 400 square centimeters. The pattern at the end of the forewing resembles the head of a snake, also known as a snake-headed moth. It is the prototype of the famous monster, Mothla, in the Godzilla films.`

9. 苍头燕雀 chaffinch

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“苍头燕雀在柏树枝丫间筑起灵巧的巢，巢内挤满双眼鼓凸直瞪着你瞧的宝宝。”

“Among the cypress branches the chaffinches had their neat nests, full of gawping, goggle-eyed babies”

——（第八章 乌龟山丘）(From Chapter 8: The Tortoise Hills)

`有趣的小知识 (interesting facts)：特点是喙呈灰色，雄性比雌性鲜艳，幼年食昆虫，成年食种子为生，歌声美妙响亮. It is characterized by a gray beak. Males are brighter than females. The young birds are insect eaters, while the adults are seed-eaters. Bird calls`

```10. 戴菊鸟 Goldcrest

“戴菊鸟在较低的枝丫上，用青苔与毛发编制纤小的杯状巢，或是倒挂枝头搜寻昆虫，在找到小蜘蛛或蚊蚋时，高兴地发出几乎听不见的吱吱声，它们轻盈地在叶间翻转，金冠仿佛一个个小步兵便帽，灿灿生辉。”

“And on the lower branches the goldcrests weaved their tiny, fragile cups of moss and hair, or foraged for insects, hanging upside down on the ends of the branches, giving almost inaudible squeaks of joy at the discovery of a tiny spider or a gnat, their golden crests gleaming like little forage caps as they flipped daintily through the gloom of the tree.”

——（第八章 乌龟山丘）(From Chapter 8: The Tortoise Hills)

`有趣的小知识：性格活泼好动，羽冠只有在特殊时期（危险或求偶）时才展开。Goldcrest has a lively and active character. The crest only stands up at special times (danger or courtship). Bird calls`

11. 石蚕 （其实应该翻译成纹蚤）ceriodaphnia laticaudata

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“‘……有个奇怪的石蚕幼虫…..那里，看到没？…..嗯….它们会用特定软体动物的壳做鞘…实在很漂亮。”

“‘there is rather a curious caddis larva… there, d’you see it?…um… it appears to have made its case of the shells of certain molluscs…. It’s certainly very pretty.’”

——（第九章 墙中世界）(From Chapter 9: The World in a Wall)

`有趣的小知识 (interesting facts): 物尽其用的建筑师 Good architect`

12. 胡狼  jackal

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“有一次，五只胡狼从桃金娘丛中探头出来，看到我便惊愕地停下脚步，然后才像影子般融化在树林中。”

“Once, five jackals appeared out of the murtle bushes, paused in surprise at seeing me, and then melted among the trees, like shadows.”

——（第十章 萤火虫的盛会）(From Chapter 10: The Pageant of Fireflies)

`有趣的小知识 (interesting facts): 阿努比斯是古埃及处置遗体及地狱的神，其形象就是人身胡狼头。Anubis was the ancient Egyptian god of taking charge of dead bodies and hell, whose image was a human with a jackal head.`

13. 夜鹰 Nightjar

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“我看到夜鹰寂静无声地伸展丝缎般的翅膀，仿佛黑色的大燕子穿过一排排的橄榄树，低空掠过草丛，寻觅酩酊打转的大蚊子。”

“The nightjars on silent, silky wings would slide as smoothly as great black swallows along the rows of olives, sweeping across the grass in pursuit of the drunken, whirling crane-flies.”

——（第十章 萤火虫的盛会）(From Chapter 10: The Pageant of Fireflies)

`有趣的小知识 (interesting facts)：从不筑巢。 Nightjar don't make nests. Bird calls`

```14. 角鸮 Scops owl （杰瑞的尤利西斯 In the book, Gerry named his owl Ulysses）

“有一天我把手臂伸进一个洞里，手指碰到一个小小软软、拉它出来时会乱动的东西。乍看之下，我以为那是一团超大的蒲公英花球，配上一对金色的大眼睛，仔细观察，才发觉那是一只绒毛还没有蜕的角鸮宝宝。”

“one day I thrust my arm into a hole, and my fingers closed round something small and soft, something that wiggled as I pulled it out. At first glance my capture appeared to be an outsize bundle of dandelion seeds, furnished with a pair of enormous golden eyes; closer inspection proved it to be a young Scops owl, still clad in his baby down.”

——（第十章 萤火虫的盛会）(From Chapter 10: The Pageant of Fireflies)

`有趣的小知识 (interesting facts)：喜欢住在树洞中。Scops owl loves to live in a hollow of trees. Bird calls`

```15. 豆蟹 Pea crab
（图片来源 source：https://www.tastecooking.com/pea-crabs-offal-of-the-sea-the-redneck-toothpick/）```

“偶尔一块块银色沙床上，一小簇一小簇的蛤直立着长着大口，坚硬的壳缘上可见到栖息在上面苍白、细小的青豆蟹。这些羸弱、颓废的软壳动物，躲在贝壳呈波状的城墙里，过着寄生虫的日子。”

“In the patches of silver sand the clams were stuck upright in small clusters, their mouths gaping. Sometimes, perched between the shell’s horny lips, here would be a tiny, pale ivory pea crab, the frail, soft-shelled, degenerate creature that lived a parasitic life in the safety of the great shell’s corrugated walls.”

——（第十一章 销魂群岛）(From Chapter 11: The Enchanted Archipelago)

`有趣的小知识 (interesting facts)：身体略微透明，壳软，有些人认为吃生蚝的时候里面有豆蟹是好运的象征。The body is slightly transparent and the shell is soft. Some people think that eating oysters with pea crab inside is a sign of good luck.`

16. 龙介虫 Serpula

`（图片来源 source：https://alchetron.com/Serpula）`

“错落在蛤之间的是龙介虫。它们生长在灰色粗长管子的顶端，像羽毛般美丽的花瓣永远都在绕着圈子。那些飘逸的橘金与蓝色花瓣看起来和它们肥胖的茎好不搭配，仿佛一朵朵兰花开在香菇茎上。龙介虫也有防盗系统，只不过比蛤的更灵敏，捕蝶网的把手只要伸到距离颤抖中的花海约十几厘米的地方，所有的花瓣就突然指向天空，收拢成一束，头上脚下地钻进沙里，只剩下一截截的茎，像是插在沙床上的水管。“

“Interspersed with the clams were the serpulas, beautiful feathery petals, forever moving round and round, perched on the end of a long, thick, greyish tube. The moving petals, orange-gold and blue, looked curiously out of place on the end of these stubby stalks, like an orchid on a mushroom stem. Again the serpulas had a burglar-alarm system but it was much more sensitive than the clams’; the net handle would get within six inches of the whirpool of shimmering petals, and they would suddenly all point skywards, bunch together, and dive head-first down the stalk, so that all that was left was a series of what looked like bits of miniature hosepipe stuck in the sand.”

——（第十一章 销魂群岛）(From Chapter 11: The Enchanted Archipelago)

`有趣的小知识 (interesting facts)：有一种龙介虫，由于有两个组成像圣诞树的冠，被称为圣诞树管虫（大旋鳃虫）。There is a serpula called the Christmas tree worm (Spirobranchus giganteus), because it has two crowns that resemble Christmas trees.`

17. 蜘蛛蟹 Spider crab

“躲在下方海草丛里的，是长着奇怪刺状蟹壳的蜘蛛蟹，它们的脚又细又长，每一根都披着海草或海绵，偶尔背上也背着一朵它们小心栽种的海葵。“

“There were crabs too, fat, green, shiny ones on the tops of the reef, waving their claws in what appeared to be a friendly manner, and down below, on the weedy bed of the sea, the spider-crabs with their strange spiky-edged shells, their long, thin legs, each wearing a coat of weeds, sponges, or occasionally an anemone which they had carefully planted on their backs.“

——（第十一章 销魂群岛）(From Chapter 11: The Enchanted Archipelago)

`有趣的小知识(interesting facts)：与海葵共生，利用海葵的五彩斑斓伪装自己，并用海葵的毒素保护自己。一生中要经历约14次生长蜕壳。Spider crabs live with anemones, so that they can camouflages themselves with the anemone's colorful colors, and protect themselves with the anemone's toxin. They go through about 14 times of slough in their lifetime.`

```18. 鹬 snipe

“小岛上的沼泽及水塘里踱着纤细的鹬，将它们橡皮似的长喙戳进稀泥里探索，然后自你脚旁突然腾起，像箭似地嗖嗖飞过。”

“On the island the swamps and pools had their wisps of snipe, probing the mushy earth with their long rubbery beaks, humming like arrows as they flipped up from under your feet. “

——（第十二章 山鹬之冬）(From Chapter 12: The Woodcock Winter)

`有趣的小知识 (interesting facts)：这是成语“鹬蚌相争，渔翁得利”里的鹬. There is an ancient Chinese fable describing a story about a snipe and a clam were fighting for food, but both of them turned out to be the food of a fisherman. The fable was used when a quarrel which benefits only a third party.`

```19. 山鹬 （应该翻译成丘鹬）woodcock

（图片来源 source：维基百科 https://en.wikipedia.org/wiki/Woodcock）```

“在橄榄树林、石南丛间，躲着又胖又丑的山鹬，一受惊吓，便鼓噪着羽翼一蹦一跳地走避，仿佛一大捆被风卷起的秋叶。“

“In the olive-groves, among the myrtles, the woodcock lurked, fat and ungainly, leaping away when disturbed with a tremendous purring of wings, looking like bundles of wind-blown autumn leaves.“

——（第十二章 山鹬之冬）(From Chapter 12: The Woodcock Winter)

`有趣的小知识 (interesting facts)：喜欢孤独，不喜欢集群生活。Woodcock likes to be alone.`

```20. 各种雀 Finches

“我很高兴地发现有鲜红、鲜黄、鲜黑画的像小丑的金翅雀以及黄绿相间像仲夏柠檬叶的绿雀；有穿着咖啡色与白色斜呢西装的红雀；有鼓着玫瑰彩红胸膛的红腹黑雀和其他各式各样的鸟。”

“to my delight I found there were goldfinches painted like clowns in vivid scarlet, yellow, and black; greenfinches as green and yellow as lemon leaves in midsummer; linnets in their neat chocolate-and-white tweed suiting; bullfinches with bulging, rose-pink breasts, and a host of other birds.”

——（第十四章 絮语的花朵）(From Chapter 14: The Talking flowers)

`有趣的小知识 (interesting facts)：这类鸟长得好看，叫声动听，深受鸟类买卖的危害。Finches are generally good looking with lovely voice. They suffer from bird trade.`

```21. 凤头鸫 Cock blackbird

“一间住了一只凤头鸫，羽毛像天鹅绒一般黑，配上一支华丽耀眼、香蕉色的黄喙”

“At each end a large aviary had been built, and in one lived a cock blackbird, black and velvety with a flaunting, banana-yellow beak;”

——（第十四章 絮语的花朵）(From Chapter 14: The Talking flowers)

`有趣的小知识 (interesting facts)：叫声动听 Cock blackbirds have lovely voice. Bird songs`

22. 矶鸫 Rock thrush

`Blue rock thrush（图片来源 source：百度百科 baidu baike）`

“对面住着一只像画眉的鸟，全身披着异常美丽的蓝色系羽毛，奇妙地组合了从深蓝到乳白之间的各种色调。”

“while in the other aviary opposite was a thrush-like bird which was clad in the most gorgeous blue feathering, a celestial combination of shades from navy to opal.”

——（第十四章 絮语的花朵）(From Chapter 14: The Talking flowers)

`有趣的小知识 (interesting facts)：从名字就可以看出这种鸟生活在林地多岩的地方。You can probably tell from its name, that rock thrush lives in places with rocks.`

23. 喜鹊 magpie （杰瑞养的“洗劫”哥俩 （注“洗劫”和“喜鹊”读音相似，在书里，斯皮洛叫它Magenpies，和英文名称magpie相似）In the book, Spiro called them magenpies because of his accent, and magenpies were chose to be the names of Gerry’s two magpie.

`左 left：飞翔的成年喜鹊；adult. 右 right: 喜鹊宝宝 baby bird（图片来源 source：维基百科 https://zh.wikipedia.org/wiki/%E5%96%9C%E9%B9%8A）`

“远远的下方有一小畦金黄色的成熟玉米地，出现了一个黑白相间的小东西，像一支有斑纹的马耳他十字架。它迅速掠过平坦的耕地，很坚决地朝我所在的坡顶飞来。当它接近我的时候，这只喜鹊发出三声短而尖锐的喀喀声，听起来闷闷的，好像鸟喙里含满食物。”

“Far below, over a blond square of ripening maize, a small black and white shape appeared, like a piebald Maltese cross, skimming rapidly across the flat areas of cultivation, heading determinedly for the hill-top on which I sat. As it flew up towards me the magpie uttered three brief, harsh chucks, that sounded rather muffled as though its beak were full of food.”

“我的指头触摸到柔软颤抖的皮肤和细细的绒毛，一阵尖锐的喘息声从巢中传出。我小心翼翼地圈住一只又胖又暖的宝宝，把它拉出来。如此热爱鸟类的我，都不得不承认它实在不漂亮：一支短胖的鸟喙，两个嘴角都有黄色的皱褶，秃头，烂糊糊的眼睛半睁半闭，一副醉醺醺又智力低下的德行，全身皮肤皱巴巴，到处打褶，显然是用黑色的羽翮胡乱钉在肉上的结果。”

“Under my fingers I could feel soft, quivering skin and fluff, while a shrill chorus of wheezes rose from inside the nest. Carefully I curved my fingers round one fat, warm baby and drew it out. Enthusiastic though I was, even I had to admit it was no beauty. Its squat beak, with a yellow fold at each corner, the bald head, and the half-open and bleary eyes gave it a drunken and rather imbecile look. The skin hung in folds and wrinkles all over its body, apparently pinned loosely and haphazardly to its flesh by black feather-stubs.”

——（第十五章 仙客来树林）(From Chapter 15: The Cyclamen Woods)

`有趣的小知识 (interesting facts)：除了代表福气以外，喜鹊还是唯一已知通过镜子测试的非哺乳动物，即它能辨别自己在镜子中的影像。不像红衣主教（就是愤怒的小鸟里的红色小鸟）连自己的水中的倒影都攻击。In addition to representing good fortune, the magpie is the only non-mammal known to have passed the mirror test, as it can recognizing its own reflection in the mirror, unlike the Cardinal (the red bird in Angry Birds) who attacks his own reflection in the water.`

```24. 黑背海鸥 black-backed gull （书里杰瑞的阿力哥Alecko）In the book, the black-backed gull that Gerry kept is called Alecko.

“我们坐在船里吃鸟蛤，我却目不转睛地望着那只鸟，着迷与它雪白的胸膛、它的头、它长长的钩状鸟喙、它凶猛得像春天番红花般鲜黄的眼睛、它宽阔的背和强壮得像煤灰般黑得翅膀。在我眼中，从它有蹼得脚掌，到它鸟喙得尖端，无所不美。”

“We sat in the boat and ate the shellfish, and all the time I watched the bird, fascinated by the snow-white breast and head, his long hooked beak and fierce eyes, as yellow as spring crocuses, the broad back and powerful wings, sooty black. From the soles of his great webbed feet to the tip of his beak he was, in my opinion, quite admirable.“

——（第十七章 棋盘田野）(From Chapter 17: The Chessboard Fields)

`有趣的小知识 (interesting facts)：震耳欲聋的“咿哦”（kee-orr）声是它的特色。Its bird call is characterized as a loud "Kee-orr". Bird calls`

# My R learning notes 2: a simple way to calculate the daily mean from hourly data with a different time interval

Recently I received a surprising email from a scholar that I haven’t met before. He told me that he came across my blog about aggregating minutely data into hourly data when he was trying to calculate the daily mean from a different time interval (e.g., from 09:00 am to 08:00 am at the following day).

At first, I was so surprised, as I thought that this blog could not be indexed by Google. Then, I felt a little bit embarrassed, because I didn’t write the posts very carefully, so the contents must have lots of grammar errors, and might not make sense. However, I felt happy in the end, as it was wonderful to know that my notes had enlightened others who faced the same problem. So I want to express my gratitude to all who have read my posts and borne my poor writing. I also hope to receive opinions from every reader 🙂

In this post, I would like to share my idea with you on how to calculate daily mean with a different time interval (e.g., from 9:00 am to 8:00 at the other day). I think that the quickest way is to calculate the mean of each column by every 24 rows in the data frame. For example, here is the initial data sheet:

```
Fig. 1 Initial data example```

In order to make the R code simple, I delete the first two rows, so that the record started from 9:00 am. Now, let’s put the data frame into R as data1.

```
Fig. 2 Data arrangement in R.```

Then, let’s build a simple function to calculate the mean of every 24 rows.The code was taken from Vlo’s answer from the following website: https://stackoverflow.com/questions/30359427/calculate-the-mean-of-every-13-rows-in-data-frame.  If you would like to calculate the sum instead of the mean, please just adjust the  “FUN=      ” commend.

n.colmeans = function(df, n = 24){
aggregate(x = df,
by = list(gl(ceiling(nrow(df)/n), n)[1:nrow(df)]),
FUN = mean)
} ### because I have 12 column in the data frame, so n > 12. This function will calculate the average of every 24 rows. For example, the result comes from row 1 to row 24, then from row 25 to row 49, etc.)

After we run the above codes, we input the following code:

data2<- n.colmeans(data1, 24) ### this is used to apply the above function to calculate our own dataset.

The daily means of every column in the data2 were calculated with the time interval from 9:00 am to 8:00 at the other day. You can export the result by using the following code:

data2 <-write.xlsx(  )

Finally we got what we want. Yay! However, it is note that If your data have missing rows, then this method is not applicable.

There are definitely other ways to aggregate the data, but the codes in this blog, in my opinion, is the most simple ones. If you have different opinions, or you’d like to share your codes, please feel free to leave your comments.

Thank you for reading it! 🙂

# How does thinning affect key hydrological processes?

High forest stand densities can lead to severe competition on resources (e.g., water, light and nutrients) among trees [1], which causes stress on tree growth and health, and consequently limits forest carbon sequestration and water use [2]. Thinning, as a conventional practice to reduce competition, exerts considerable effects on forest carbon and water cycles [6]. The key hydrological processes under thinning treatments has been studied for decades, but recently gained prominent attention[3] and been adopted as a mitigation of drought in forest ecosystems [4-8]. The effects of thinning on transpiration (T) and evapotranspiration (ET) at the forest stand level, and T, ET and water yield at the watershed level are elaborated below.

Transpiration of thinned stands was less than unthinned counterpart due to decreased basal area (BA) and canopy leaf area [4, 8-13]. The decrease of stand transpiration of the thinned stand was smaller than the reduction of leaf area index (LAI) [9, 10], because of the enhanced transpiration of individual trees in the thinned stand following thinning treatments. Such increase of the remaining trees can be partly explained by the higher leaf water potential due to open canopy exposure, and higher soil water availability caused by decreased canopy interception [5]. However, soil water moisture was not always promoted by thinning treatments. For example, Lopushinsky (1975) reported that thinned logdepole pine underwent slight moisture stress in thinned plots than in unthinned plots, which was due to increased evaporation because of higher exposure to sunlight in thinned plots [11]. Zhu et al (2017) found that thinning increased water content of deep soil, while reduced that of surface soil, resulting from modified soil infiltration under thinning [12].

Although arguments on the effect of thinning on soil moisture exist, the above effects of thinning on transpiration of the individual tree and the stand in the short term were found quite consistent among publication regardless of tree species, thinning intensity, and stand condition. In a long run, the discrepancy on transpiration between thinned and unthinned sites diminishes over time, and transpiration of thinned stand may even exceed that of unthinned stand [13]. Nevertheless, exceptions were reported. For instance, Simonin et al. (2007) observed a higher stand transpiration in the thinned stand during a severe drought, suggesting that higher transpiration of individual trees in the thinned stand during drought overcompensated the loss of LAI [5]. And Black et al. (1980) found that with understory presents, the transpiration of individual trees in the thinned stands was similar to that of the nearby unthinned stand without understory [14].

Understory plants further complicates the response of stand evapotranspiration (SET) to thinning treatments, as understory evapotranspiration was increased by thinning due to greater canopy openness that allows more solar radiation reaches the forest floor. In a forest stand without understory, thinning initiated the regrowth of weeds and promoted bare soil evaporation [15]. When understory was present, thinning increased the herbaceous cover, leading to a surge of understory transpiration which could even be three times more than that in the nearby unthinned stand [5]. But this effect obscured under extreme drought when transpiration and plant growth were suppressed as a result of stomatal closure [15]. Nonetheless, the increasing understory evapotranspiration [16] counterbalances the decreasing overstory transpiration, resulting in SET unaffected [15] or decreased [7, 10, 17-19] under thinning treatments. No observation of SET increase has been report to author’s knowledge. Furthermore, the differences of SET between thinned and unthinned stand could not be detected after four or five years after thinning [7, 19], which suggests that such effect was transient, and highly depends on the thinning intensity [20], understory growth and environmental variables.

The response of watershed-scale transpiration and evapotranspiration (WET) which are derived from site measurements, concords with stand-scale observations under thinning treatment. WET, which decreases with decreasing forest cover (or with increasing thinning intensity) [21-27] because its biggest contributor (i.e., forest transpiration) was largely reduced [28], leads to an increase in the water yield [22, 24, 25, 27-33], regardless the type of thinning treatment (e.g. strip thinning, uniform thinning or patch cutting). A detailed study concluded that strip thinning resulted in highest increase in water yield, followed by uniform thinning and patch cutting [27], but this conclusion may be watershed-depended. Notably that the increase in water yield are revertible when trees regrowth to the pre-disturbance level with increasing canopy interception and WET [27, 34], though the recovery period spans from 9 to more than 34 years [31, 34].

Increasing water yield usually leads to the increasing in the quantity and duration of streamflow, as well as base flow [15] and peak flow [26], but is not a guarantee of increase, as streamflow is highly subject to soil water storage capacity and thinning intensity [35, 36]. The magnitude of streamflow increment is various (some result are summarized in the table below) under similar thinning treatments, suggesting that watershed topographic properties (e.g. slope, area and soil characteristics) and rainfall amount [22, 25, 36, 37] play an important role in regulating the surface runoff.

Table 1. Some research on the effect of thinning on streamflow

 Research Citation Thinning treatment intensity Streamflow increase Stoneman (1986) [30] 66% reduction of forest density 86mm Ruprecht et al. (1991) [24] reduce crown cover from 60 to 14% 260 mm Lesch and Scott (1997) [31] 22-46% reduction of density 19-99 nm Johnson and Kovner (1956) [32] 53% of the basal area 55 mm Baker (1986) [33] 31–68% of the basal area 25–46.3 mm Dung et al. (2012) [25] Reduce 43.2% of the basal area 240.7 mm Hawthrone et al. (2013) [27] Reduce 33-54% basal area ~36% increase Saksa et al. (2017) [22] Reduce LAI from 9.9 to 9.1 130-140mm

As climate change projects a continuous global warming, and an increase in the frequency of hot extremes at the global scale (IPCC Climate Change 2014 Synthesis Report), hydrology-oriented thinning may serve as a temporary makeshift to tackle with drought. Over a longer period, forest LAI recovery and understory growth enhanced by thinning may decrease water yield [27], which further exacerbates the water crisis. Thus, decisions on adopting thinning treatments should be made with cautions.

Reference:

1. Brix, H. and A.K. Mitchell, Thinning and nitrogen fertilization effects on soil and tree water stress in a Douglas-fir stand. Canadian Journal of Forest Research, 1986. 16(6): p. 1334-1338.
2. Louda, S.M. and S.K. Collinge, Plant resistance to insect herbivores: a field test of the environmental stress hypothesis. Ecology, 1992. 73(1): p. 153-169.
3. del Río, M., et al., A review of thinning effects on Scots pine stands: From growth and yield to new challenges under global change. 2017, 2017. 26(2).
4. Smit, G.N. and N.F.G. Rethman, The influence of tree thinning on the soil water in a semi-arid savanna of southern Africa. Journal of Arid Environments, 2000. 44(1): p. 41-59.
5. Simonin, K., et al., The influence of thinning on components of stand water balance in a ponderosa pine forest stand during and after extreme drought. Agricultural and Forest Meteorology, 2007. 143(3): p. 266-276.
6. Tang, J., et al., Forest thinning and soil respiration in a ponderosa pine plantation in the Sierra Nevada. Tree Physiology, 2005. 25(1): p. 57-66.
7. Dore, S., et al., Recovery of ponderosa pine ecosystem carbon and water fluxes from thinning and stand-replacing fire. Global Change Biology, 2012. 18(10): p. 3171-3185.
8. Fernandes, T.J.G., et al., Simultaneous assessment, through sap flow and stable isotopes, of water use efficiency (WUE) in thinned pines shows improvement in growth, tree-climate sensitivity and WUE, but not in WUEi. Forest Ecology and Management, 2016. 361(Supplement C): p. 298-308.
9. Bréda, N., A. Granier, and G. Aussenac, Effects of thinning on soil and tree water relations, transpiration and growth in an oak forest (Quercus petraea (Matt.) Liebl.). Tree Physiology, 1995. 15(5): p. 295-306.
10. Wang, Y., et al., Water-Yield Reduction After Afforestation and Related Processes in the Semiarid Liupan Mountains, Northwest China1. JAWRA Journal of the American Water Resources Association, 2008. 44(5): p. 1086-1097.
11. Donner, B.L. and S.W. Running, Water Stress Response After Thinning Pinus contorts Stands in Montana. Forest Science, 1986. 32(3): p. 614-625.
12. Zhu, X., et al., Temporal variability in soil moisture after thinning in semi-arid Picea crassifolia plantations in northwestern China. Forest Ecology and Management, 2017. 401(Supplement C): p. 273-285.
13. Lagergren, F., et al., Thinning effects on pine-spruce forest transpiration in central Sweden. Forest Ecology and Management, 2008. 255(7): p. 2312-2323.
14. Black, T.A., U. Nnyamah, and C.S. Tan, TRANSPIRATION RATE OF DOUGLAS FIR TREES IN THINNED AND UNTHINNED STANDS. Canadian Journal of Soil Science, 1980. 60(4): p. 625-631.
15. Skubel, R.A., et al., Short-term selective thinning effects on hydraulic functionality of a temperate pine forest in eastern Canada. Ecohydrology, 2017. 10(1): p. e1780-n/a.
16. Sun, X., et al., The effect of strip thinning on forest floor evaporation in a Japanese cypress plantation. Agricultural and Forest Meteorology, 2016. 216(Supplement C): p. 48-57.
17. Moreaux, V., et al., Paired comparison of water, energy and carbon exchanges over two young maritime pine stands (Pinus pinaster Ait.): effects of thinning and weeding in the early stage of tree growth. Tree Physiology, 2011. 31(9): p. 903-921.
18. Goodell, B.C., Watershed-management aspects of thinned young lodgepole pine stands. Journal of Forestry, 1952. 50: p. 374-378.
19. Aussenac, G. and A. Granier, Effects of thinning on water stress and growth in Douglas-fir. Canadian Journal of Forest Research, 1988. 18(1): p. 100-105.
20. Anderson, H.W., M.D. Hoover, and K.G. Reinhart, Forests and water: effects of forest management on floods, sedimentation, and water supply. 1976.
21. Biederman, J.A., et al., Increased evaporation following widespread tree mortality limits streamflow response. Water Resources Research, 2014. 50(7): p. 5395-5409.
22. Saksa, P.C., et al., Forest thinning impacts on the water balance of Sierra Nevada mixed-conifer headwater basins. Water Resources Research, 2017. 53(7): p. 5364-5381.
23. Bosch, J.M. and J.D. Hewlett, A review of catchment experiments to determine the effect of vegetation changes on water yield and evapotranspiration. Journal of Hydrology, 1982. 55(1): p. 3-23.
24. Ruprecht, J.K., et al., Early hydrological response to intense forest thinning in southwestern Australia. Journal of Hydrology, 1991. 127(1): p. 261-277.
25. Dung, B.X., et al., Runoff responses to forest thinning at plot and catchment scales in a headwater catchment draining Japanese cypress forest. Journal of Hydrology, 2012. 444(Supplement C): p. 51-62.
26. M. Grace Iii, J., R. W. Skaggs, and G. M. Chescheir, HYDROLOGIC AND WATER QUALITY EFFECTS OF THINNING LOBLOLLY PINE. Transactions of the ASABE, 2006. 49(3): p. 645.
27. Hawthorne, S.N.D., et al., The long term effects of thinning treatments on vegetation structure and water yield. Forest Ecology and Management, 2013. 310(Supplement C): p. 983-993.
28. Ruprecht, J.K. and G.L. Stoneman, Water yield issues in the jarrah forest of south-western Australia. Journal of Hydrology, 1993. 150(2): p. 369-391.
29. Moran, R.J. and P.J. O’Shaughnessy, Determination of the evapotranspiration of E. regnans forested catchments using hydrological measurements. Agricultural Water Management, 1984. 8(1): p. 57-76.
30. Stoneman, G. Thinning a Small Jarrah Forest Catchment: Steamflow and Groundwater Response After 2 Years. in Hydrology and Water Resources Symposium 1986: River Basin Management; Preprints of Papers. 1986. Institution of Engineers, Australia.
31. Lesch, W. and D.F. Scott, The response in water yield to the thinning of Pinus radiata, Pinus patula and Eucalyptus grandis plantations. Forest Ecology and Management, 1997. 99(3): p. 295-307.
32. Johnson, E.A. and J.L. Kovner, Effect on streamflow of cutting a forest understory. Forest Science, 1956. 2(2): p. 82-91.
33. Baker, M.B., Effects of ponderosa pine treatments on water yield in Arizona. Water Resources Research, 1986. 22(1): p. 67-73.
34. Bren, L., P. Lane, and G. Hepworth, Longer-term water use of native eucalyptus forest after logging and regeneration: The Coranderrk experiment. Journal of Hydrology, 2010. 384(1): p. 52-64.
35. Stokes, R.A., Streamflow and groundwater responses to logging in Wellbucket catchment, south Western Australia / R.A. Stokes, F.E. Batini. Report (Water Authority of Western Australia) ; no. WH3., ed. F.E. Batini and B. Water Authority of Western Australia. Hydrology. 1985, Leederville, W.A: Water Authority of Western Australia.
36. Rahman, A., et al., Effects of forest thinning on direct runoff and peak runoff properties in a small mountainous watershed in Kochi Prefecture, Japan. Pakistan Journal of Biological Sciences, 2005. 8: p. 259-266.
37. Stoneman, G.L., Hydrological response to thinning a small jarrah (Eucalyptus marginata) forest catchment. Journal of Hydrology, 1993. 150(2): p. 393-407.

# Journal 8 – July 29, 2016 – Set three climate stations

Before going to the field, I read the instruction carefully and package the tools that we might use in the field. So things went well when We carried three sets of HOBO climate station to the field and established one of them at each plot in B1. The climate station would measure rain (only at B1T2), solar radiation, wind speed and direction, temperature, humidity continuously at a 20-minute step.

# Measuring photosynthesis and stomatal conductance – June, 23, 2017

Last time I spent nearly a whole day on connecting and adjusting band dandrometer sensors. On our way back, Adam suggested me to put aside the problem of band dendrometer, and measure photosynthesis and stomatal conductance instead, because data from band dandrometer are not as important as those of photosynthesis and stomatal conductance, since I can use tree monthly DBH as tree growth indicator. I strongly agreed with it, and guaranteed to him that I would give photosynthesis and stomatal conductance priority in my next field, no matter band dandrometer sensors work normally or not.

Unfortunately, the band dandrometer sensors still performed badly at this time. But I gave up fixing it, and turned to measure photosynthesis and stomatal conductance by LICOR 6400 XT, with the help of Dr. Wu. (Only Dr. Wu and I went to the field.)

We set off from Kelowna around 8:30 am, and arrived at the site at around 10:30 am. It was a sunny day.

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Fig. 1 Photo of B1C at June, 26, 2017```

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Fig. 2 Photo of B1T1 at June, 26, 2017```
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Fig. 3 Photo of B1T2 at June, 26, 2017```

We carried equipment to the plot T1 at the Block 1. Dr. Wu was interested in learning this photosynthesis system, so I introduced the mechanism to him, while we assembled the machine. After waiting for around 10 minutes to stabilize the machine, we started to measure selected conifer clusters. The time was around 11:00 am.

In my experiment design, I randomly select five trees per plot, and four directions (north, south, west and east) per tree at the 1.5-1.7 m height.  Choosing five trees in each plot is due to the limitation of battery. I only have four batteries which can sustain field measurement up to 5 hours in total. Each clusters may take about 5 minutes, so finishing one block (3 plots) may require 300 minutes, which is equally to the sustainable time of four batteries. Assuming that there will be different solar radiation intensities and temperatures which affect photosynthesis rate and stomatal conductance in different positions, I measure the north, south, west and east sides of the tree branch clusters at the same height, to test this hypothesis. I will average the photosynthesis rate and stomatal conductance from four sides for the future analysis of scalling relationship at the leaf and individual tree level. There are less healthy branches of lodgepole pine that are lower than 1m, and I cannot measure branches that are too high for me since I have to hold heavy connifer chamber all the time, so I choose the healthy branches at the height of 1.5-1.7m.

My goal was to measure instantaneous photosynthesis rate and stomatal conductance. So I tried to set the leaf chamber environment the same with as the real outside condition. Here are the settings I used in my measurement:

```(1) block temperature as 20 ℃ (It is the same with outside temperature which can be read from the machine).

(2) Set light intensity as track the ambient light.

(3) Set the block CO2 as 400 umol/mol.

(4) Set the flow rate as 500 umol/s.

(5) Control the humidity at around 30-60%.```

At first I used compressed gas cylinders as CO2 supply, but then we found a severe leaking problem in the first four measurements by observing that the photosynthesis rates were negative, and the CO2 concentration at the chamber was really low (around 20 umol/mol). Then, I checked the equipment, and found that the O-ring which was supposed to stick at the conjunction between CO2 Cylinders and console was disappeared. As I did not bring any other O-ring, I decided to use air as CO2 supply. in fact, the ambient CO2 was not considered a good supply, because it was easily affected by breath. However, I found that it was acceptable in my experiments, as readouts were quite stable. So we re-measured the clusters with the wrong photosynthesis readings.

Dr. Wu and I took turns to hold the connifer chamber, because it was heavy. We measured clusters while chatted. Time flied fast. At around 1:30, we finished two plot (T1 and T2). We then had a lunch break, and continued to measure the Control plot. At around 3:00 pm, we finished the whole block (Block 1).

```

Fig. 4 Dr. Wu and I took turns to hold the conifer chamber.```

Then, I checked the condition of band dandrometers. Sadly, I found that band dandrometers of tree No. 5, 7, 9, 13, 14, 15 were all out of position. So I adjusted them.

I download the data of sap flow, soil moisture, band dandrometer, evnironmental variables from XM 1000 datalogger and Hobo climate stations. I did not checked them at the field. At around 3:40 pm, we returned home.

Extra bonus: The nesting feathered out! Did you know who they are? the answer is American Robin! I even took the picture of the parent birds.

# New problem: wired pattern of sap flux, disconnection and broken sensors – June, 14, 2017

Since I have succeed in reinstalling the equipment, I set three goals for field trip this time:

(1) Check data of sap flow, band dendrometer and soil moisture.

(2) Measure tree heights and DBHs in Block 2 and 3.

(3) Measuring photosynthesis by Li-cor 6400 XT.

Before going to the field, I checked the condition of Li-cor 6400 XT, and was glad to find that it worked well, though it has not been in use since November last year. I also charge the batteries of Li-cor 6400 XT.

Adam, Dr. Wu and I went to the field  on June, 14, 2017.  It was a sunny day, not cold nor hot. On arrival, I brought my laptop and download the data, while Adam and Dr. Wu measured tree heights and DBHs in Block 2 and 3.

I was so sad to find that the No.3 tree did not give any sap flow signals, indicating a disconnection between tree No.3 and the datalogger. So I  checked mainline of datalogger, the connectors were all connected. Then I went to B1T2 site where the No.3 tree was, to check the connection between sap flow probe and the extension line. It was connected, indicating that there might be broken in the middle of the wire.

The way to find out where was broken was very tough, because there were a bunch of wires connecting sap flow probes, band dendrometers and soil moisture from various trees, and to various extension cables in three plots . Identify the specific broken wire and the position needed at least two people, use electricity meter, section by section at those wires. Adam and Dr. Wu were all at Block 2 which is at least 30 meter away at that time, so I decided to put aside, and check for the other data.

Tree No. 1, 10 and 15 showed a wired sap flux pattern, though the data were in a normal range and shape. It seemed that the three trees has no any sap flowing through trunk at the day time, but transpired at the midnight. However, compared with other trees under the same treatment, the shape and the range were all similar. Thus, I did not think that there were connection problems in the three trees. Rather, I supposed that either trees responded abnormally, or the probes were dis-functional. I could not solve either of them, so I put them aside as well.

Only one band dendrometer worked well (Tree. No. 13). Then, I found that most problems came from a bad connection in the connector. This was the top lesson I learn at this field trip: DO NOT TRY TO DO SOMETHING BEYOND WHAT YOU HAVE MASTERED IN A IMPORTANT EVENT. The field experiment this year is so important to me, I will not be able to afford any failure. But I used a novel detachable connector which I just got to know one day before my field installation. I could not handle them well, but I applied them in all my band dendrometers connection. In fact, installing this novel connector consumed more time than that of an ordinary one.  I should not use them at all until I mastered them.  How stupid I was!!! Anyway, I cut the connectors off, and replace it with the ordinary ones and junction boxes.

```

Fig. 1 replacing detachable connectors with ordinary ones and junction boxes```

So it took me double time to install the band dendrometers, let alone the expenses on them. I felt so sad… 🙁

Besides, one soil moisture sensor which is located at B1C at the depth of 40 cm gave negative value. After excluding the connection problems in the wire connecting to the datalogger, I thought it was a disconnection at the multiplexer inside the datalogger, by observing an apparent disconnected wire tip in it. However, I did not where channel should I put the tip into, so I took a photo and would ask Antonio for help.

Measure tree DBH and heights was time-consuming, too. Adam and Dr. Wu spent four hours on it. At around 2:30 pm, they came back and asked me about the connection. I was almost finishing replacing the connectors of band dendrometer. So I told them about the disconnection of tree No.3. To my surprise, they suggested to look at the probes first, by disengaging all the foil and foam isolations around it. This suggestion was really good! We found the wire of probe of tree No.3 was broken, as a result of pulling the short wire so hard in order to connect it to the mainline. So we tried our best to re-connect it. However, we failed.

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Fig. 2 Broken sap flow probe in tree No.3```

By the end of that day, we went home with pity. The only achievement today is that tree heights and DBHs in Block 2 and 3 were measured, and all connectors of band dendrometers were replaced. I did not measure photosynthesis as I planed. I hope that field trip next week could be better!

Extra bonus: Blue eggs turned into nesting. Do you know who they are?

# My experiment of 2017 begun! – June, 09, 2017

Two weeks ago,  John and I went to Upper Penticton Watershed to check for the site. We figured out that snow almost disappeared there, but part of the road on the way was covered by snow. Due to snow melting, the road was quite soft, moisture and muddy, thus our truck could not be able to drive on it. However, we speculated that two weeks later the road would be dry up completely according to the abruptly increasing temperature in Kelowna, and we would reinstall the equipment then.

The equipment that we planted to reinstall were: a XM1000 datalogger (Dynamax) with a modified multiplexer for EC-5 soil moisture (Decagon) and self-made tree band dandrometers (for measuring tree basal area increment), 15 band dandrometer sensors (linear position sensors, BEI sensors), and all wire connections on the field including solar panel and battery.

Before going to the field, it is better to make some preparations. since wire connection would be tedious and time-consuming, and easier in the lab than in the field, stripping the wires was the most important preparation this time. I did it in my lab, with around 40 minutes for 15 band dandrometer sensors (60 wires). I took the picture of what i have done. It is quite easy.

```
Fig. 1 Wire preparation in the labs```

The second preparation was make sure that wire connectors is enough. Since I didn’t have enough connectors, I went to tool stores to buy it. I checked for Home Depot and Canadian Tire, but I couldn’t be able to find wire connectors. So I went to Interior Electronics instead. In that store, I also asked if there were some types of connectors that would be easy to disconnect and connect easily, because I will cut the wires and take my sensors back during the winter in which the temperature will be too cold for the sensor. I got a suggest of using a detachable wire connector, which is not much more expensive than what I planed to buy.  So I bought both.

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Fig. 2 Non-detachable connectors (left) and detachable connectors (right).```

Third, I need to consider water-proof protection after wires are connected. I prepared enough junction boxes for keeping wires from rain and insect bites.

`       Fig. 3 Junction boxes I put on the desk in my lab.`

I also prepared the tools that we might use, like various types of scissor, knife, screwdrivers, pliers, tapes, and extra wires. I believed that a good preparation makes a good start, and well begun is half done!

On June, 09, 2017 at 8:00 am, John, Dr. Wu and I headed to the experimental site! Excited! Dr. Wu is a visiting professor from China and just arrived in Canada a few days ago. It was the first time that he went to my site. I couldn’t wait to receive his opinions and suggestions on my research!

On our way to the site, we found that all snows were gone, and soils was dry. Our truck could easily drive to the destination. Standing among the trees, with cool breezes in the sunny, blue sky was so beautiful, but only one deficiency is that the weather was still a little cold (around 7 to 10 ℃), as the elevation is above 1600 m asl.

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Fig. 4 Site condition at June, 09, 2017```

Dr. Wu showed a strong curiosity on my site, and helped me measure sampled tree height and DBH of Block 1 with John, while I was focused on connecting band dandrometer sensors. Connecting those wires took longer time than I expected. So after Dr.Wu and John finished measurement, they came and helped me connect the wire as well. Around 1:30 pm, we succeed in connecting all the band dendrometer sensors. However, I didn’t use the junction box, because it would be more easy and saving time to use water-proof plastic tapes wrapping around the connectors to protect it.

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Fig.5 Band dendrometer sensor connection.```

After lunch, we started to install datalogger. It was may more simple than wire connections. Then, we connected datalogger with solar panel and battery. The datalogger started working. While the datalogger was collecting data, I went to each trees to check the band dendrometer in the right position, and download the data from climate station. Dr. Wu and John was making protections for wires and datalogger.

Later, I connected datalogger with my laptop to download the data. The datalogger worked well, but data indicted that No.3 trees has not been connected to the datalogger, and No.10, 15 trees gave some erratic data. Band dandrometers and soil moisture also gave signals, but right now it was hard to tell if they worked fine. So after we checking for the connections again to make sure everything was connected correctly, we decided to let the equipment work for a while and we would examine the data next week.

At around 5:30 pm, we went back home.  Overall it was a fullfillment field trip, we set up everything! Yay!!!

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Fig .6 It was hard to take a selfie in the field!!!```

Extra bonus: Dr. Wu found a bird nest with two blue eggs. Guess whose eggs are them? ;p

# Journal of field experiments – May, 26, 2017

I went to our experiment site with John on May, 26, 2017. Part of the road was still covered by snow, so the car couldn’t drive all the way there. Anyway, it was not too far, so we walked around 25 minutes to reach the plot.
`               Fig.1 Main road that was still covered by snow`
Upon arrival, we was so surprised to see a small creek running through B1T1, from uphill of the T1, along the path where we entered in B1, and to the creek that is outside of B1. I realized that the sluggish response of soil moisture sensors to the rain event in T1 may be resulted from this depression area in T1.
```

Fig. 2 The intermittent creek at B1T1 (left) and at the path along B1C (right)
​```

​But soils in B1C and B1T2 were pretty dry,and not covered by much snow, which is totally different from soil conditions in T1.

`                                  Fig. 3 B1C`
```                                   Fig. 4 B1T2
​```
Then, we were glad to see that all equipment were protected well, and that climate station worked well. Since the weather in Kelowna turned into Summer so abruptly these days, we decided to install equipment next week. I hope snows would be melt down completely at that time.
`                       Fig. 5 Climate station at B1T1`
We were also glad to see that trees grow well in all the blocks including those that were inserted with sap flow probes, and they were much taller than those in the last year. I guess measuring tree heights will be a tough job….
Extra bonus: I found two footprints in the snow. Guess what animal they are?