Last call for Cladistics workshop in Spain
Dear colleagues: This is the last call for the workshop QUANTITATIVE CLADISTICS AND USE OF TNT, June 3-7, 2013. Instructors: Dr. Goloboff and Dr. Szumik (Conicet, Argentine). More information: http://www.transmittingscience.org/cladistics.htm. The workshop will cover the basics of parsimony analysis and character optimization, tree-searches, diagnosing and summarizing results efficiently, and measuring group supports. It will have extensive hands-on exercises which will help participants get familiar with the main aspects of phylogenetic analysis using TNT. The workshop will make extensive use of TNT. There will also be a demonstration and some practice with GB-TNT, a program to create TNT matrices from GenBank data. This workshop will be held in the Hostalets the Pierola (Barcelona, Spain) and is co-organized by Transmitting Science, Institut Catalá de Paleontologia M. Crusafont and the council of Hostalets de Pierola. Places are limited and will be covered by strict registration order. Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban-Trivigno, Ph.D. -- CLASS-L list. Instructions: http://www.classification-society.org/csna/lists.html#class-l
Course Classification trees and Neural networks with R, 4-7 November, Barcelona (Spain).
Dear colleagues: Registration is open for the course CLASSIFICATION AND REGRESSION TREES AND NEURAL NETWORKS WITH R - Second Edition. INSTRUCTORS: Dr. Llorenç Badiella (UAB, Spain), Dr. Joan Valls (Biomedical Research Institute of Lleida, Spain) and Dr. Montserrat Martínez-Alonso (Biomedical Research Institute of Lleida, Spain). DATES: November 4-7, 2013; 24 teaching hours. PLACE: Premises of Sabadell of the Institut Català de Paleontologia Miquel Crusafont, Sabadell, Barcelona (Spain). Organized by: Transmitting Science and the Institut Catalá de Paleontologia Miquel Crusafont. More information: http://www.transmittingscience.org/cart_with_r.htm or writing to cour...@transmittingscience.org The main goal of the methods such as CART (Classification and Regression Trees), is to model and predict one response variable explained by a set of dependent variables. This methods can be particularly effective to model interactions between explanatory variables. On the other hand, as a statistical model, a neural network is based on linear and non-linear combinations of explanatory variables that interact with other combinations to predict or explain an outcome variable. Both CART and neural networks methods can provide good results to explain or predict an outcome variable, particularly when the number of interactions is important. Nevertheless, these techniques also tend to over-fit the data and a validation of the models is required. ROC methods, including a sensitivity/specificity analyses and/or external validations can be performed to assess the consistency of these techniques. Applications cover a wide range of problems, including species classification in biology, prediction of the prognosis of a patient in biomedicine, etc. With best regards Soledad De Esteban Trivigno, PhD. -- CLASS-L list. Instructions: http://www.classification-society.org/csna/lists.html#class-l
Last call for the course R for Beginners, September 3-6, Spain
Dear colleagues: This is the last call for the course R for beginners - Second edition. end of early registration May 31. INSTRUCTORS: Dr. Klaus Langohr (Universitat Politécnica de Catalunya, Spain) and Dr. Joan Valls (Biomedical Research Institute of Lleida, Spain). DATES: September 3-6, 2013; 24 teaching hours. PLACE: Premises of Sabadell of the Institut Català de Paleontologia Miquel Crusafont, Sabadell, Barcelona (Spain). Organized by: Transmitting Science and the Institut Catalá de Paleontologia Miquel Crusafont. More information: http://www.transmittingscience.org/courses/stats/r-for-beginners/ or writing to cour...@transmittingscience.org The aim of this course is to give an introduction to R to people that has never used R . By the end of the course, the participants should be able to do the following in R: Import/export data bases to/from R, manage data sets, carry out basic statistical analysis with R, draw high quality graphs and, program specific functions. Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban Trivigno, PhD. -- CLASS-L list. Instructions: http://www.classification-society.org/csna/lists.html#class-l
Course on Phylogenetic Analyses, May 4-8 2015, Barcelona, Spain
Dear Colleagues, Registration is open for the course AN INTRODUCTION TO PHYLOGENETICS ANALYSIS USING R - Second Edition. INSTRUCTORS: Dr. Emmanuel Paradis (Institut de Recherche pour le Développement, France) and Dr. Klaus Schliep (Universidad de Vigo, Spain). DATES: May 4-8, 2015 More information: http://www.transmittingscience.org/courses/phylo/phylogeny-with-r/ or wrtiting to cour...@transmittingscience.org. This course is for biologists dealing with the analysis of multiple molecular sequences at several levels: Populations, species, clades, communities. These biologists address questions relative to the evolutionary relationships among these sequences, as well as the evolutionary forces structuring biodiversity at different scales. The objectives are: (i) to learn the theorical bases phylogenetic analysis, (ii) to know how to choose a strategy of molecular data analysis at the inter‐ or intraspecific levels, (iii) to be able to initiate a phylogenetic analysis starting from the files of molecular sequences until the interpretation of the results and the graphics.The software used for this course will be centered on the R language for statistics. This will include the use of specialized packages particularly ape, phangorn, and adegenet. PLACE: Facilities of the Centre of Restauració i Interpretació Paleontologica, Els Hostalets de Pierola, Barcelona (Spain). Organized by: Transmitting Science, the Institut Catalá de Paleontologia M. Crusafont and the Centre de Restauració i Interpretació Paleontologica de Els Hostalets de Pierola. Places are limited and will be covered by strict registration order. Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Dr. Soledad De Esteban-Trivigno cour...@transmittingscience.org Transmitting Sciencehttp://www.transmittingscience.org/ -- CLASS-L list. Instructions: http://www.classification-society.org/csna/lists.html#class-l
Course on Historical Biogeography, June 15-19, Barcelona, Spain
Dear colleague, Registration is open for the course HISTORICAL BIOGEOGRAPHY: FUNDAMENTALS AND APPLICATIONS, June 15-19, 2015. INSTRUCTORS: Dr. Lone Aagesen (IBODA, CONICET, Argentina) and Dr. Claudia A. Szumik (Miguel Lillo Foundation, CONICET, Argentina). PLACE: Facilities of the Centre of Restauració i Interpretació Paleontologica, Els Hostalets de Pierola, Barcelona (Spain). WEBPAGE: http://www.transmittingscience.org/courses/biog/historic-biogeography/ This course provides basic knowledge on selected theoretical and methodological problems of historical biogeography. We aim to provide the practical skills to enable the students to carry out empirical biographical analyses. A considerable part of the course is therefore allocated to practical problems as well as to the use of computer programs specifically developed for biogeography analyses. Organized by: Transmitting Science, the Institut Catalá de Paleontologia Miquel Crusafont and de Centre de Restauració i Interpretació Paleontologica de Els Hostalets de Pierola. For more information you can write tocour...@transmittingscience.org http://webmail.icp.cat/webmail/basic/index.html?_n[p][main]=win.main.tree_n[p][content]=mail.composeto=cour...@transmittingscience.org . Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban Trivigno Transmitting Science www.transmittingscience.org -- CLASS-L list. Instructions: http://www.classification-society.org/csna/lists.html#class-l
Course Geometric Morphometrics in R, January 26-30, Barcelona, Spain
Dear colleagues, Transmitting Science offers a new course which migth could be of interest for some members of this list: GEOMETRIC MORPHOMETRICS IN R . INSTRUCTOR: Dr. JULIEN CLAUDE ((Institut des Sciences de l’Évolution de Montpellier, France). DATES: January 26-30, 2015; 35 hourse on-site. End early registration: October 31. PLACE: Facilities of the Centre of Restauració i Interpretació Paleontologica, Els Hostalets de Pierola, Barcelona (Spain). Organized by: Transmitting Science, the Institut Catalá de Paleontologia Miquel Crusafont and the Centre of Restauració i Interpretació Paleontologica. More information: http://www.transmittingscience.org/courses/gm/gm-in-r/ or writing to cour...@transmittingscience.org Concepts in geometric morphometrics will be taught using a series of original data sets and working in R for solving a series of tasks. The course will start with an introduction to R and will rapidly go into shape analysis with measurements, landmark data and outlines. The participants are welcome to bring their own data and problems so that we may find R solutions. Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban Trivigno, PhD. Course Director Transmitting Science http://www.transmittingscience.org/ -- CLASS-L list. Instructions: http://www.classification-society.org/csna/lists.html#class-l
Course about Cladistic Analysis by Dr. Goloboff in Barcelona, Spain.
Dear colleagues, Registration is open for the workshop QUANTITATIVE CLADISTICS AND USE OF TNT - 2nd Edition, June 29 - July 3, 2015. Instructors: Dr. Goloboff and Dr. Szumik (Conicet, Argentine). PLACE: Facilities of the Centre de Restauració i Interpretació Paleontologica, Els Hostalets de Pierola, Barcelona (Spain). WEBPAGE: http://www.transmittingscience.org/courses/phylo/cladistics/ PROGRAM: - Intro and Basics. Parsimony and phylogenetic systematics. Character optimisation and mapping. Most parsimonious reconstructions and specific changes. Input/output in TNT. Dataset formats. Using GB-TNT to create matrices. Instruction files. Options for graphic output (SVG, metafiles). Creation of “batch” files. Editing trees. Handling tree files. Groups of trees, characters and taxa. - Tree calculation. Tree searches. Exact solutions, Wagner trees, branch-swapping. Local and global optima. Use of multiple addition sequences. Improving search strategies. Factors which affect the efficiency of tree-searches. Constraints and “timeouts”. - Ambiguity and consensus; summarizing results. Zero-length branches and collapsing rules. Types of consensus and their use; improving consensus trees; supertrees. Pruned consensus. Comparison of tree-topologies; SPR distances. - Character weighting. Successive and implied weighting. Auto-weighted optimization. Refining character weighting with blocks; taking into account missing entries. User-defined weighting functions. - Group supports. Concept of group support. Bremer supports; how to calculate them; search of suboptimal trees. Problems with Bremer supports; absolute and relative Bremer support. Partitioned Bremer support and individual Bremer supports. Measures based on resampling; effect of search strategies and collapsing rules. Problems with resampling methods. - Tree search in large and difficult data sets. Special search algorithms. Sectorial searches. Ratchet and drifting. Tree fusing. Combining different algorithms. Driven searches and stabilization of consensus. - Scripting. Automation of decisions to go beyond simple commands. Flow control. Decisions. Expressions, user variables, and internal variables. Design of simple scripts. This course is co-organized by Transmitting Science, the Institut Catalá de Paleontologia M. Crusafont and the Centre de Restauració i Interpretació Paleontologica. Places are limited and will be covered by strict registration order. Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban-Trivigno, PhD. soledad.este...@transmittingscience.org Transmitting Science www.transmittingscience.org -- CLASS-L list. Instructions: http://www.classification-society.org/csna/lists.html#class-l
Course R Without Fear: Applied R, September 21-25, Barcelona, Spain
Dear colleagues, Registration is open for the workshop R Without Fear: Applied R for Biologists, September 21-25, 2015. Instructor: Dr. Jordi Moya-Laraño (Estación Experimental de Zonas Áridas - CSIC, Spain). PLACE: Facilities of the Centre de Restauració i Interpretació Paleontologica, Els Hostalets de Pierola, Barcelona (Spain). WEBPAGE: http://www.transmittingscience.org/courses/stats/applied-r-for-bio/ PROGRAM: Introduction to the R working environment. - Variable types in R. - Statistical populations and samples through working examples. - Measurements of central tendency and variability. - Precision, accuracy and bias. - Hypothesis testing: Falsability, Type-I and II errors and statistical power. - Correlation and simple regression. - P-value vs. effect magnitude. - Linear Models: Residuals, assumptions and interpretation. - Explained vs. unexplained variance of a model (the coefficient of determination). - Building functions in R. - Introduction to graphics in R. - The concept of partial effect: Partial regression and correlation. - General Linear Models (GLM). - Curve fitting in linear models and General Additive Models (GAMs). - The problem of spatial autocorrelation in ecology and evolution. - Multicolinearity: When is there a problem? - Additive vs. multiplicative effects: Checking and plotting interactions. - Introduction to General and Generalized Linear Mixed Models (GLMM). - Fixed vs. Random effects and implications for analysis: Main R functions. - Introduction to Bayesian statistics: The function MCMCglmm. - Practical examples in evolutionary ecology: The study of natural selection. Applications of linear models for quantitative genetics. - Student’s case studies. Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban-Trivigno, Ph.D. Transmitting Science www.transmittingscience.org -- CLASS-L list. Instructions: http://www.classification-society.org/csna/lists.html#class-l
Course Phylogenetic Analysis using R, March 6-10, Barcelona (Spain).
Dear Colleague, Registration is open for the fourth edition of the course PHYLOGENETIC ANALYSIS USING R, March 6th-10th, 2017. INSTRUCTORS: Dr. Emmanuel Paradis (Institut de Recherche pour le Développement, France) and Dr. Klaus Schliep (University of Massachusetts, USA). More information: http://www.transmittingscience.org/courses/phylogeny/phylogenetic-analysis-using-r/ This course is for biologists dealing with the analysis of multiple molecular sequences at several levels: Populations, species, clades, communities. These biologists address questions relative to the evolutionary relationships among these sequences, as well as the evolutionary forces structuring biodiversity at different scales. The objectives are: (i) to learn the theorical bases phylogenetic analysis, (ii) to know how to choose a strategy of molecular data analysis at the inter‐ or intraspecific levels, (iii) to be able to initiate a phylogenetic analysis starting from the files of molecular sequences until the interpretation of the results and the graphics. The software used for this course will be centered on the R language for statistics. This will include the use of specialized packages particularly ape, phangorn, and adegenet. Requeriments: Knowledge of multivariate statistics, phylogenetics and molecular evolution. User level of R. PLACE: Facilities of the Centre of Restauració i Interpretació Paleontologica, Els Hostalets de Pierola, Barcelona (Spain). Organized by: Transmitting Science, the Institut Catalá de Paleontologia M. Crusafont and the Centre de Restauració i Interpretació Paleontologica de Els Hostalets de Pierola. Places are limited and will be covered by strict registration order. With best regards Soledad De Esteban-Trivigno, PhD. Scientific Director Transmitting Science www.transmittingscience.org -- CLASS-L list. Instructions: http://www.classification-society.org/csna/lists.html#class-l
Course Introduction to R, May 22-26, Barcelona.
Dear colleague, Registration is open for the fourth edition of the course "Introduction to R ". INSTRUCTOR: Dr. Ashton Drew (KDV Decision Analysis LLC, USA). DATES: May 22nd – 26th, 2017. PLACE: Premises of Sabadell of the Institut Català de Paleontologia Miquel Crusafont, Sabadell, Barcelona (Spain). Organized by: Transmitting Science and the Institut Catalá de Paleontologia Miquel Crusafont. More information: http://www.transmittingscience.org/courses/statistics/introduction-r/ The aim of this course is to give an introduction to R to people that has never used R. By the end of the course, the participants should be able to do the following in R: Import/export data bases to/from R, manage data sets, carry out basic statistical analysis with R, draw high quality graphs and, program specific functions. Guided practice with R – Students are encouraged to bring a dataset with them along with a “previously completed” statistical analysis or graphic. Ideally something fairly introductory and simple from the student’s own field of practice that you’ve worked with in Excel, SAS, or elsewhere. We will use last lesson session to review all the steps to ensure students can load, check, tidy data and then perform the basic statistics or generate the graphs common in their respective disciplines. This time also usually provides opportunity to troubleshoot and learn to navigate web resources to find solutions to errors. Extra datasets will be available for students that prefer not to bring their own work or who want extra practice at specific skills. Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Sole Soledad De Esteban-Trivigno, PhD. Scientific Director Transmitting Science www.transmittingscience.org -- CLASS-L list. Instructions: http://www.classification-society.org/csna/lists.html#class-l
Course on Data Manipulation and Visualization in R – scholarships available
Dear colleagues,Transmitting Science course DATA MANIPULATION, ANALYSIS, AND VISUALIZATION IN R USING THE TIDYVERSE has some scholarships available. You can apply here (free course attendance) here: https://www.transmittingscience.org/funding/scholarships-application/Deadline: October 15th.Course dates: November 4th-8th, 2019.Instructors: Dr. Ashton Drew (KDV Decision Analysis LLC United States of America) and Dr. Sheila Saia (United States Forest Service Center for Integrated Forest Science, United States of America)Place: Sabadell, Barcelona (Spain)Registration and more info: https://www.transmittingscience.org/courses/statistics-and-bioinformatics/data-manipulation-analysis-visualization-in-r-using-tidyverse/Course OverviewThis intermediate course exposes students to the breadth of resources available in the R tidyverse to build their fluency and confidence when working in R. The tidyverse is a collection of libraries and functions in R sharing an underlying design (philosophy, grammar, and data structures) that aims to help users create efficient, "tidy" code. Many of the libraries address the common data wrangling tasks (read, select, filter, gather, spread, modify, recode, summarize) that are the precursors to both data analysis and visualization. Other libraries address specific tasks (e.g., ggplot2 to create graphs; purr to create functions; broom to tabulate model results) or specific data types (e.g., sf for spatial data, tibbletime for temporal data).A mix of lectures and exercises will walk students through a series of increasingly complex data manipulation and visualization tasks. These exercises will emphasize the underlying principles and grammar of the tidyverse to help students transfer what they learn in the examples to their own research coding projects.Import tabular, spatial, and temporal data (readr, readxl, haven, sf, tibbletime)Manage data structure (dplyr, tidyr, magrittr, forcats, lubridate, stringr)Introduction to functional programming (purr)Visualize data and model results (broom, ggplot2)Please feel free to distribute this information between your colleagues if you consider it appropriate.Soledad De Esteban-Trivigno, PhDScientific DirectorTransmitting Sciencewww.transmittingscience.org
Course: Interactive Data Analysis and Visualization with R Shiny, March 23-27, Barcelona (Spain).
Dear colleagues, Registration is open for the third edition of the Transmitting Science course INTERACTIVE DATA ANALYSIS AND VISUALIZATION WITH R SHINY. Dates: March 23rd-27th, 2020, Barcelona (Spain). Instructor: Dr. Ashton Drew (KDV Decision Analysis LLC, USA) Place: Sabadell, Barcelona (Spain) Scholarships: there are some scholarships available for PhDs and Postdocs. Deadline: February 15 th. To apply please fill this form: https://www.transmittingscience.org/funding/scholarships-application/ R Shiny (https://shiny.rstudio.com/) turns static data (R code) into interactive web apps. With interactive and reactive data visualizations, others will directly engage with your data for stronger communication and better understanding. The Shiny apps can easily be launched directly to the web via shinyapps.io or Shiny Server to be run by anyone (they don’t need to download your data or have R!). This course is for individuals considering developing Shiny apps to deliver their research. Thus, the goal will be to teach the skills necessary to translate static products (your current analysis in R) to dynamic products delivered via a simple web-based graphic-user interface. By the end of the course, students will have built a portfolio of example code and will have designed, constructed, and published at least one example Shiny app. Why Shiny? Some Shiny examples: K-means ( https://shiny.rstudio.com/gallery/kmeans-example.html) and TreeViewer (https://klash.shinyapps.io/shinyTreeViewer/). Registration and more information: https://www.transmittingscience.org/courses/drawing-and-communication/interactive-data-analysis-visualization-r-shiny/ This course is organized by Transmitting Science and the Institut Català de Paleontologia. Please feel free to distribute this information between your colleagues if you consider it appropriate. Best wishes, Sole Soledad De Esteban-Trivigno, PhD Scientific Director Transmitting Science www.transmittingscience.org
Course Communicating Science Effectively, May 18-22, Barcelona (Spain).
Dear colleagues, Registration is open for the first edition of the Transmitting Science course COMMUNICATING SCIENCE EFFECTIVELY. Dates: May 18th-22nd, 2020, Barcelona (Spain). Instructor: Laura Berdejo (Agence France Presse, Uruguay) Place: Capellades, Barcelona (Spain) Registration and more information: https://www.transmittingscience.org/courses/drawing-and-communication/communication-science-effectively/ Course Overview This course is for scientists who want to communicate effectively at several levels (traditional media, social media, activities), in different formats (text, photos, video, graphics) to a heterogeneous audience (general public, peers, potential donors, children, international organisations, public institutions, etc.). The main goal of the course is to provide them with the necessary skills to define their objectives, to identify already existing networks and instruments in order to create links with them and to produce effective messages. This course is organized by Transmitting Science Please feel free to distribute this information between your colleagues if you consider it appropriate. Best wishes, Sole Soledad De Esteban-Trivigno, PhD Scientific Director Transmitting Science www.transmittingscience.org
Live Online Course Interactive Data Analysis and Visualization with R Shiny, October 26-30.
Dear colleagues, Registration is open for the third edition of the Transmitting Science course INTERACTIVE DATA ANALYSIS AND VISUALIZATION WITH R SHINY. This course will be offered online live. Dates: October 26th-30th, 2020 Instructor: Dr. Ashton Drew (KDV Decision Analysis LLC, USA) Course Overview: R Shiny (https://shiny.rstudio.com/) turns static data (R code) into interactive web apps. With interactive and reactive data visualizations, others will directly engage with your data for stronger communication and better understanding. The Shiny apps can easily be launched directly to the web via shinyapps.io or Shiny Server to be run by anyone (they don’t need to download your data or have R!). This course is for individuals considering developing Shiny apps to deliver their research. Thus, the goal will be to teach the skills necessary to translate static products (your current analysis in R) to dynamic products delivered via a simple web-based graphic-user interface. By the end of the course, students will have built a portfolio of example code and will have designed, constructed, and published at least one example Shiny app. Why Shiny? Some Shiny examples: K-means (https://shiny.rstudio.com/gallery/kmeans-example.html) and TreeViewer (https://klash.shinyapps.io/shinyTreeViewer/). Registration and more information: https://www.transmittingscience.com/courses/scientific-communication/interactive-data-analysis-visualization-r-shiny/ Please feel free to distribute this information between your colleagues if you consider it appropriate. Best wishes, Sole
