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r_symposium_2019 [2019/09/19 14:57]
ph.pereirabraga
r_symposium_2019 [2019/10/12 10:46] (current)
ph.pereirabraga
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-**Le 3e Colloque R du CSBQ aura lieu le 10, 11 et 12 octobre 2019 à la Reserve Naturelle Gault**+**Le 3e Colloque R du CSBQ a eu lieu le 10, 11 et 12 octobre 2019 à la Reserve Naturelle Gault**
 </​WRAP>​ </​WRAP>​
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-**The 3rd QCBS R symposium ​will be held from October 10th to 12th 2019 at the Gault Nature Reserve**+**The 3rd QCBS R symposium ​was held from October 10th to 12th 2019 at the Gault Nature Reserve**
 </​WRAP>​ </​WRAP>​
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-Pour la 3ème année consécutive,​ l'​équipe d'​ateliers R du CSBQ organisera ​l'​**edition 2019 du Colloque R du CSBQ**. ​+Pour la 3ème année consécutive,​ l'​équipe d'​ateliers R du CSBQ a organisé ​l'​**edition 2019 du Colloque R du CSBQ**. ​
  
 L'​objectif du Colloque R du CSBQ est de fournir un cadre structuré pour la discussion et l'​échange d'​idées entre des participants et des présentateurs d'​ateliers concernant l'​utilisation de R dans les analyses de la biodiversité. Pour cela, nous fournissons un lieu d’enseignement et de participation à une série d’ateliers R avancés qui ne sont pas couverts par la série annuelle d’ateliers R du CSBQ. L'​objectif du Colloque R du CSBQ est de fournir un cadre structuré pour la discussion et l'​échange d'​idées entre des participants et des présentateurs d'​ateliers concernant l'​utilisation de R dans les analyses de la biodiversité. Pour cela, nous fournissons un lieu d’enseignement et de participation à une série d’ateliers R avancés qui ne sont pas couverts par la série annuelle d’ateliers R du CSBQ.
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-For the 3rd consecutive year, the QCBS R Workshop cohort ​will hold the **2019 edition of the QCBS R Symposium**. ​+For the 3rd consecutive year, the QCBS R Workshop cohort ​held the **2019 edition of the QCBS R Symposium**. ​
  
 The purpose of the QCBS R Symposium is to provide a structured framework for the discussion and exchange of ideas between participants and presenter in the application of biodiversity science analyses using R. For this, we provide a venue for teaching and participation in a series of advanced R workshops that are not offered during the annual QCBS R Workshop Series. The purpose of the QCBS R Symposium is to provide a structured framework for the discussion and exchange of ideas between participants and presenter in the application of biodiversity science analyses using R. For this, we provide a venue for teaching and participation in a series of advanced R workshops that are not offered during the annual QCBS R Workshop Series.
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-Le 3e Colloque R du CSBQ aura lieu le **10, 11 et 12 octobre 2019** à la [[https://​www.mcgill.ca/​gault/​|Reserve Naturelle Gault]], à la municipalité de Mont-Saint-Hilaire,​ Monterégie,​ Québec.+Le 3e Colloque R du CSBQ a eu lieu le **10, 11 et 12 octobre 2019** à la [[https://​www.mcgill.ca/​gault/​|Reserve Naturelle Gault]], à la municipalité de Mont-Saint-Hilaire,​ Monterégie,​ Québec.
 </​WRAP>​ </​WRAP>​
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-The 3rd QCBS R Symposium ​will be held from **October 10th to 12th 2019** at the [[https://​www.mcgill.ca/​gault/​|Gault Nature Reserve]], in the municipality of Mont-Saint-Hilaire,​ Monterégie,​ Québec.+The 3rd QCBS R Symposium ​was held from **October 10th to 12th 2019** at the [[https://​www.mcgill.ca/​gault/​|Gault Nature Reserve]], in the municipality of Mont-Saint-Hilaire,​ Monterégie,​ Québec.
 </​WRAP>​ </​WRAP>​
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-Les frais d'​inscription au **3ème Colloque R du CSBQ** ​est de:+Les frais d'​inscription au **3ème Colloque R du CSBQ** ​a été de:
   * **25 $** pour les **membres du CSBQ**, et;    * **25 $** pour les **membres du CSBQ**, et; 
   * **150 $** pour les **//​non-membres//​ du CSBQ**.   * **150 $** pour les **//​non-membres//​ du CSBQ**.
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-The attendance fee for the **3rd QCBS R Symposium** ​is:+The attendance fee for the **3rd QCBS R Symposium** ​was:
   * **25 $** for **QCBS members**, and;    * **25 $** for **QCBS members**, and; 
   * **150 $** for **QCBS //​non-members//​**.   * **150 $** for **QCBS //​non-members//​**.
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-Les inscriptions pour le 3ème Colloque R du CSBQ sont **OUVERTES**. \\ +Les inscriptions pour le 3ème Colloque R du CSBQ sont **FERMÉS**. \\
- +
-**[[https://​registration.qcbs.ca/​fr/​colloque-r-2019|INSCRIVEZ-VOUS MAINTENANT!]]**+
  
 </​WRAP>​ </​WRAP>​
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-Registration for the 3rd QCBS R Symposium ​is **OPEN**.\\+Registration for the 3rd QCBS R Symposium ​are **CLOSED**.\\
  
-**[[https://​registration.qcbs.ca/​r-symposium-2019|REGISTER NOW!]]** 
 </​WRAP>​ </​WRAP>​
 <WRAP clear></​WRAP>​ <WRAP clear></​WRAP>​
  
-==== Programmation ​préliminaire ​| Preliminary ​program  ​====+==== Programmation | Preliminary ====
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 **19:45** - Arrivée à //Maison Gault// \\ **19:45** - Arrivée à //Maison Gault// \\
 **20:00** - //Activité pour briser la glace// \\ **20:00** - //Activité pour briser la glace// \\
 +
 +// Notez qu'un souper traiteur n'est pas prévu pour le jeudi soir. Nous allons avoir quelques crudités et des croustilles dans un cadre détendu. Si vous désirez avoir d'​autres choses à manger et des boissons alcoolisées,​ veuillez les emporter avec vous.//
 +
 \\ \\
 === 11 octobre === === 11 octobre ===
 **8:00** - //​Déjeuner//​ \\ **8:00** - //​Déjeuner//​ \\
 **8:45** - Annonces \\ **8:45** - Annonces \\
-**9:00** - Atelier ​(1h 30min) \\ +**9:00** - **Basics of effective and reproducible data visualization** ​(1h30min) \\ 
-**10:30** - //Pause// \\ +**10:45** - //Pause// \\ 
-**11:00** - Atelier ​(1h 30min) \\ +**11:00** - **Community Phylogenetics - Part #1** (1h) \\ 
-**12:30** - //Dîner// \\ +**12:15** - //Dîner// \\ 
-**13:30** - Atelier ​(1h 30min) \\ +**13:30** - **Community Phylogenetics - Part #2** (1h) \\ 
-**15:00** - //Pause// \\ +**14:45** - //Pause// \\ 
-**15:30** - Atelier ​(2h) \\ +**15:00** - **Mining species-level biodiversity information from published literature** ​(2h) \\ 
-**18:00** - //Souper// \\+**17:15** - //Pause// \\ 
 +**17:30** - **Peer-discussion and code debugging moment** ​\\ 
 +**18:30** - //Souper// \\
 \\ \\
 === 12 octobre === === 12 octobre ===
 **8:00** - //​Déjeuner//​ \\ **8:00** - //​Déjeuner//​ \\
-**9:00** - Atelier ​(2h) \\ +**9:00** - **Touchdown your research!** ​(2h) \\ 
-**12:00** - //Dîner// \\ +**11:00** - //Temps libre// \\ 
-**13:30** - //Temps libre// \\ +**12:45** - //Dîner// \\ 
-**15:30** - Retour à //​Montréal//​ \\+**14:00** - Retour à //​Montréal//​ \\
  
 </​WRAP>​ </​WRAP>​
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 **19:45** - Arrival at //Maison Gault// \\ **19:45** - Arrival at //Maison Gault// \\
 **20:00** - //​Icebreaker & Social Event// \\ **20:00** - //​Icebreaker & Social Event// \\
 +
 +// Note that a catered dinner is not predicted for Thursday evening. We will provide a few crudites and chips in a   ​relaxed environment. If you wish to have other food and to drink alcoholic beverages, please bring them with you.//
 +
 \\ \\
 === October 11th === === October 11th ===
 **8:00** - //​Breakfast//​ \\ **8:00** - //​Breakfast//​ \\
 **8:45** - Announcements \\ **8:45** - Announcements \\
-**9:00** - Workshop ​(1h 30min) \\ +**9:00** - **Basics of effective and reproducible data visualization** ​(1h30min) \\ 
-**10:30** - //Break// \\ +**10:45** - //Break// \\ 
-**11:00** - Workshop ​(1h 30min) \\ +**11:00** - **Community Phylogenetics - Part #1** (1h) \\ 
-**12:30** - //Lunch// \\ +**12:15** - //Lunch// \\ 
-**13:30** - Workshop ​(1h 30min) \\ +**13:30** - **Community Phylogenetics - Part #2** (1h) \\ 
-**15:00** - //Break// \\ +**14:45** - //Break// \\ 
-**15:30** - Workshop ​(2h) \\ +**15:00** - **Mining species-level biodiversity information from published literature** ​(2h) \\ 
-**18:00** - //Dinner// \\+**17:15** - //Break// \\ 
 +**17:30** - **Peer-discussion and code debugging moment** ​\\ 
 +**18:30** - //Dinner// \\
 \\ \\
 === October 12th === === October 12th ===
 **8:00** - //​Breakfast//​ \\ **8:00** - //​Breakfast//​ \\
-**9:00** - Workshop ​(2h) \\ +**9:00** - **Touchdown your research!** ​(2h) \\ 
-**12:00** - //Lunch// \\ +**11:00** - //Free time// \\ 
-**13:30** - //Free time// \\ +**12:45** - //Lunch// \\ 
-**15:30** - Return to //​Montréal//​ \\+**14:00** - Return to //​Montréal//​ \\
  
 </​WRAP>​ </​WRAP>​
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 +===== Preparing for the symposium | Préparez-vous pour le colloque =====
 +
 +++++ R Environment Preparation for the workshop | Please, follow the guidelines below **before** coming to the symposium, to avoid delays due to high internet traffic demand:
 + 
 +  - Update your R and RStudio to the latest versions;
 +  - Run the script below in your R console to install and update the libraries required for the workshops;
 +  - Finally, execute the following: ​
 + 
 +<code rsplus | R Environment Preparation>​
 +#​-------------------------------------------------------------------------------#​
 +###        Install all packages for 2019 QCBS R Symposium workshops ​         ####
 +#​-------------------------------------------------------------------------------#​
 +#### Workshop 1: Basics of effective and reproducible data visualization ####
 +# setwd(""​)
 +#
 +# Download: https://​rstudio.com/​wp-content/​uploads/​2015/​03/​ggplot2-cheatsheet.pdf
 +
 +#####​Install packages and libraries #####
 +# install packages that are not already installed
 +if (!require(datasets)) install.packages('​datasets'​)
 +if (!require(ggplot2)) install.packages('​ggplot2'​)
 +if (!require(plyr)) install.packages('​plyr'​)
 +if (!require(ggpubr)) install.packages('​ggpubr'​)
 +
 +# potential errors for non windows users with these (non-essential)
 +if (!require(rvg)) install.packages('​rvg'​)
 +if (!require(svglite)) install.packages('​svglite'​)
 +if (!require(officer)) install.packages('​officer'​)
 +if (!require(extrafont)) install.packages('​extrafont'​)
 +
 +library(ggplot2)
 +library(datasets)
 +library(plyr)
 +library(ggpubr)
 +
 +# Installation for Windows only, not essential
 +library(rvg) ​
 +library(svglite)
 +library(officer)
 +library(extrafont)
 +
 +
 +#### Workshop 2: Community Phylogenetics in R ####
 +
 +# Check for needed packages, and install the missing ones
 +required.libraries <- c("​ape",​ "​picante", ​
 +                        "​pez",​ "​phytools",​
 +                        "​vegan",​ "​adephylo", ​
 +                        "​phylobase",​ "​geiger", ​
 +                        "​mvMORPH",​ "​OUwie", ​
 +                        "​hisse",​ "​BAMMtools",​
 +                        "​phylosignal",​ "​Biostrings",​
 +                        "​devtools","​ggplot2", ​
 +                        "​kableExtra",​ "​betapart",​ "​gridExtra",​
 +                        "​reshape2"​)
 +
 +needed.libraries <- required.libraries[!(required.libraries %in% installed.packages()[,"​Package"​])]
 +if(length(needed.libraries)) install.packages(needed.libraries)
 +
 +# Load all required libraries at once
 +lapply(required.libraries,​ require, character.only = TRUE)
 +
 +# Download files from Marc Cadotte'​s and Jonathan Davies'​ book 
 +# "​Phylogenies in Ecology: A guide to concepts and methods":​
 +
 +dir.create("​data/​Jasper"​)
 +download.file("​https://​raw.githubusercontent.com/​pedrohbraga/​CommunityPhylogenetics-Workshop/​master/​data/​Jasper/​jasper_data.csv?​token=ACBTNPKQWOFPQW7UT6Z7RCS5UDUMK", ​
 +              "​data/​Jasper/​jasper_data.csv"​)
 +download.file("​https://​raw.githubusercontent.com/​pedrohbraga/​CommunityPhylogenetics-Workshop/​master/​data/​Jasper/​jasper_tree.phy?​token=ACBTNPNS2F5ZYYXLCMGMVCS5UDURO", ​
 +              "​data/​Jasper/​jasper_tree.phy"​)
 +
 +Workshop HTML Markdown Page: https://​pedrohbraga.github.io/​CommunityPhylogenetics-Workshop/​CommunityPhylogenetics-Workshop.html
 +
 +#### Workshop 3: Mining species-level biodiversity information from published literature ####
 +
 +Presentation:​ https://​docs.google.com/​presentation/​d/​1vUt8GdHCS9j3d_VEn-ftYsdayRgkzFIYKMSEGutoEVQ/​edit
 +Examples: https://​drive.google.com/​open?​id=1CNIIWZFXsTLdaL5f82hZX7R_4T-n1Prc
 +Exercise 1: https://​drive.google.com/​file/​d/​1Sp_4oaXPpZvAsC1ymA_aKJxPoWF6KuFX/​view?​usp=sharing
 +Exercise 2: https://​drive.google.com/​file/​d/​1o32RbKgGjaP6MFtc4UZnilt7-F0uMElL/​view?​usp=sharing
 +
 +#### Workshop 4: Touchdown your research! ####
 +
 +Presentation:​ https://​insileco.github.io/​ResearchDown/#​1
 +Requirements:​ https://​github.com/​inSileco/​ResearchDown#​requirements
 +
 +#​-------------------------------------------------------------------------------#​
 +</​code>​
 +++++
 +
 +----
 ===== Registered Workshops | Ateliers Participants ===== ===== Registered Workshops | Ateliers Participants =====
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-Le 3ème Colloque R du CSBQ réunira ​des étudiants à la maîtrise et au doctorat et des stagiaires postdoctoraux associés au CSBQ qui présenteront des concepts et l’application de méthodes pertinents pour les scientifiques travaillant dans plusieurs domaines liés à la recherche sur la biodiversité.+Le 3ème Colloque R du CSBQ a reuni des étudiants à la maîtrise et au doctorat et des stagiaires postdoctoraux associés au CSBQ qui présenteront des concepts et l’application de méthodes pertinents pour les scientifiques travaillant dans plusieurs domaines liés à la recherche sur la biodiversité.
 </​WRAP>​ </​WRAP>​
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-The 3rd QCBS R Symposium ​will have QCBS-associated graduate students and postdoctoral fellows presenting over the concepts and the application of methods addressing relevant questions and content for scientists working in biodiversity research.+The 3rd QCBS R Symposium ​had QCBS-associated graduate students and postdoctoral fellows presenting over the concepts and the application of methods addressing relevant questions and content for scientists working in biodiversity research.
 </​WRAP>​ </​WRAP>​
 <WRAP clear></​WRAP>​ <WRAP clear></​WRAP>​
  
 === Basics of effective and reproducible data visualization === === Basics of effective and reproducible data visualization ===
-//par// | //by// **Tania Maxwell** (Université Laval  | [[https://​twitter.com/​tania_maxwell7|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]]) +//par// | //by// **Tania Maxwell** (Université Laval  | [[https://​twitter.com/​tania_maxwell7|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]]) ​(**Workshop Material** | **Presentation**)
  
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 //par// | //by// **Steve Vissault** (Université de Sherbrooke | [[https://​github.com/​SteveViss|{{https://​github.githubassets.com/​images/​modules/​logos_page/​GitHub-Mark.png?​25x25}}]] | [[https://​twitter.com/​SVissault|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]]) & **Marie-Hélène Brice** (Université de Montréal | [[https://​github.com/​mhbrice|{{https://​github.githubassets.com/​images/​modules/​logos_page/​GitHub-Mark.png?​25x25}}]] | [[https://​twitter.com/​mariehbrice|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]]) //par// | //by// **Steve Vissault** (Université de Sherbrooke | [[https://​github.com/​SteveViss|{{https://​github.githubassets.com/​images/​modules/​logos_page/​GitHub-Mark.png?​25x25}}]] | [[https://​twitter.com/​SVissault|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]]) & **Marie-Hélène Brice** (Université de Montréal | [[https://​github.com/​mhbrice|{{https://​github.githubassets.com/​images/​modules/​logos_page/​GitHub-Mark.png?​25x25}}]] | [[https://​twitter.com/​mariehbrice|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]])
  
 +(**[[https://​insileco.github.io/​ResearchDown/#​requirements|Workshop Material]]** | **[[https://​insileco.github.io/​ResearchDown/#​1|Presentation]]**)
  
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- 
  
 === Mining species-level biodiversity information from published literature === === Mining species-level biodiversity information from published literature ===
-//par// | //by// **Gabriel Muñoz** (Concordia University | [[https://​github.com/​fgabriel1891|{{https://​github.githubassets.com/​images/​modules/​logos_page/​GitHub-Mark.png?​25x25}}]] | [[https://​twitter.com/​NasuaResearch|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]])+//par// | //by// **Gabriel Muñoz** (Concordia University | [[https://​github.com/​fgabriel1891|{{https://​github.githubassets.com/​images/​modules/​logos_page/​GitHub-Mark.png?​25x25}}]] | [[https://​twitter.com/​NasuaResearch|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]])  
 + 
 +(**[[ToBeIncluded|Workshop Material]]** | **[[ToBeIncluded|Presentation]]**)
  
 <WRAP group> <WRAP group>
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 === Community Phylogenetics:​ linking community ecology and evolutionary biology to your programming skills === === Community Phylogenetics:​ linking community ecology and evolutionary biology to your programming skills ===
 //par// | //by// **Pedro Henrique P. Braga** (Concordia University | [[https://​github.com/​pedrohbraga|{{https://​github.githubassets.com/​images/​modules/​logos_page/​GitHub-Mark.png?​25x25}}]] | [[https://​twitter.com/​pedrohp_braga|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]]) & **Katherine Hébert** (Université de Sherbrooke | [[https://​github.com/​katherinehebert|{{https://​github.githubassets.com/​images/​modules/​logos_page/​GitHub-Mark.png?​25x25}}]] | [[https://​twitter.com/​hebert_kat|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]]) //par// | //by// **Pedro Henrique P. Braga** (Concordia University | [[https://​github.com/​pedrohbraga|{{https://​github.githubassets.com/​images/​modules/​logos_page/​GitHub-Mark.png?​25x25}}]] | [[https://​twitter.com/​pedrohp_braga|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]]) & **Katherine Hébert** (Université de Sherbrooke | [[https://​github.com/​katherinehebert|{{https://​github.githubassets.com/​images/​modules/​logos_page/​GitHub-Mark.png?​25x25}}]] | [[https://​twitter.com/​hebert_kat|{{https://​img.icons8.com/​android/​24/​000000/​twitter.png?​22x22}}]])
 +
 +(**[[https://​pedrohbraga.github.io/​CommunityPhylogenetics-Workshop/​CommunityPhylogenetics-Workshop.html|Workshop Material]]**)
  
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- 
-=== And, another workshop to come! === 
  
 ===== Call for Workshop Proposals | Appel à la proposition d'​ateliers ===== ===== Call for Workshop Proposals | Appel à la proposition d'​ateliers =====
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-