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--- r_symposium_2019 [2019/09/19 14:57]
ph.pereirabraga
+++ r_symposium_2019 [2019/10/12 10:46]
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@@ Line 3: / Line 3: @@
 <WRAP group>
 <WRAP rightalign half column 47%>
-**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 half column 48%>
-**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 clear></WRAP>
@@ Line 16: / Line 16: @@
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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.
@@ Line 22: / Line 22: @@
 <WRAP half column 47%>
-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.
@@ Line 32: / Line 32: @@
 <WRAP group>
 <WRAP half column 48%>
-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 half column 47%>
-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 clear></WRAP>
@@ Line 43: / Line 43: @@
 <WRAP group>
 <WRAP half column 48%>
-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;
   * **150 $** pour les **//non-membres// du CSBQ**.
@@ Line 50: / Line 50: @@
 </WRAP>
 <WRAP half column 47%>
-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;
   * **150 $** for **QCBS //non-members//**.
@@ Line 61: / Line 61: @@
 <WRAP group>
 <WRAP half column 48%>
-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 half column 47%>
-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 clear></WRAP>
-==== Programmation préliminaire | Preliminary program  ====
+==== Programmation | Preliminary ====
 <WRAP group>
 <WRAP half column 48%>
@@ Line 81: / Line 78: @@
 **19:45** - Arrivée à //Maison Gault// \\
 **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 ===
 **8:00** - //Déjeuner// \\
 **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 ===
 **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>
@@ Line 107: / Line 109: @@
 **19:45** - Arrival at //Maison Gault// \\
 **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 ===
 **8:00** - //Breakfast// \\
 **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 ===
 **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>
@@ Line 131: / Line 138: @@
+===== 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 =====
 <WRAP group>
 <WRAP half column 48%>
-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 half column 47%>
-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 clear></WRAP>
 === 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**)
 <WRAP group>
@@ Line 157: / Line 253: @@
 //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]]**)
 <WRAP group>
@@ Line 166: / Line 263: @@
 </WRAP>
 <WRAP clear></WRAP>
 === 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}}]])
+(**[[ToBeIncluded|Workshop Material]]** | **[[ToBeIncluded|Presentation]]**)
 <WRAP group>
@@ Line 183: / Line 281: @@
 === 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}}]])
+(**[[https://pedrohbraga.github.io/CommunityPhylogenetics-Workshop/CommunityPhylogenetics-Workshop.html|Workshop Material]]**)
 <WRAP group>
@@ Line 192: / Line 292: @@
 </WRAP>
 <WRAP clear></WRAP>
-=== And, another workshop to come! ===
 ===== Call for Workshop Proposals | Appel à la proposition d'ateliers =====
@@ Line 282: / Line 380: @@
 </WRAP>
 <WRAP clear></WRAP>