convert everything to Quarto + convert spatial stats workshop to a post

.quarto/_freeze/posts/2020-06-15-science-communication/index/execute-results/html.json

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+    "markdown": "---\ntitle: \"Science Communication\"\ndescription: |\n  Recordings, content and handouts from a 6-hour Science Communication workshop held over two days on 15 and 16 June 2020.\nauthor:\n  - name: Gracielle Higino\n  - name: Katherine Hébert\nbase_url: https://bios2.github.io/\nimage: image.jpg\ncategories: [Career, Fellow contributed, EN]\ndate: \"2020-06-15\"\ntoc: true\nnumber-sections: true\nnumber-depth: 1\n---\n\n\n\n\nThe objective of this training is to share and discuss the concepts and tools that contribute to effective science communication. The training is split into two sessions, which cover the basic concepts of effective science communication and how social media tools can be used to boost the signal of your research and extend your research network. Each training takes the form of a presentation interspersed with several short activity modules, where participants are invited to use the tools we will be discussing to kickstart their own science communication.\n\nThis training was given on June 1 and 2, 2020. You can view recordings of each session here:\n\n### Day 1\n\n<iframe width=\"560\" height=\"315\" src=\"https://www.youtube.com/embed/MJCXqsnlHZg\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen>\n\n</iframe>\n\n### Day 2\n\n<iframe width=\"560\" height=\"315\" src=\"https://www.youtube.com/embed/Xo7bbJpj4PQ\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen>\n\n</iframe>\n\n## Session 1: The basics of science communication\n\n#### Objectives:\n\n1.  Discuss what science communication (or SciComm) can be, and its potential role in boosting the signal of your research\n2.  Make an overview of basic concepts and tools that you can use in any medium (blog posts, presentations, conversations, twitter, etc.) to do effective science communication\n\nDuring this session, we:\n\n1.  Discuss the potential pitfalls of science communication (notably, diversity and inclusivity problems).\n2.  Cover the basic concepts of science communication, including the Golden Circle method, the creation of personas, and storytelling techniques.\n3.  Have short activities where participants can try to use some of the techniques we will be covering, such as filling in their own Golden Circle and explaining a blog post as a storyboard.\n\n<object data=\"SciComm_Material/material/Presentation/Slides_Basics.pdf\" type=\"application/pdf\" style=\"height:200%;width:100%\">\n\n</object>\n\n<br> <br> <br> <br> <br> <br>\n\n## Session 2: Social media as a science communication tool\n\n#### Objectives:\n\n1.  Rethink the way we write about science by exploring the world of blog posts\n2.  Clarify the mechanics of Twitter and how it can be used effectively for science communication\n\nDuring this session, we:\n\n1.  Discuss how to create a story structure using titles and the flow of ideas in blog posts, especially when we are used to writing scientific articles\n2.  Cover the basics of how Twitter works (retweets, threads, replies, hashtags, photo captions, etc.) and how to find helpful connections\n3.  Have short activities where participants will be invited to write their own Twitter biographies and to create a Twitter thread explaining a project of their choice.\n\n<object data=\"SciComm_Material/material/Presentation/Slides_SocialMedia.pdf\" type=\"application/pdf\" style=\"height:200%;width:100%\">\n\n</object>\n\n<br> <br> <br> <br>\n",
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.quarto/_freeze/posts/2021-03-25-point-count-data-analysis/index/execute-results/html.json

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+    "markdown": "---\ntitle: \"Point-count Data Analysis\"\ndescription: |\n  Analysis of point-count data in the presence of variable survey methodologies and detection error offered by Peter Solymos to BIOS2 Fellows in March 2021.\nauthor: Peter Solymos\nimage: thumb.jpeg\ndate: \"2021-03-25\"\ncategories: [Technical, EN]\ntoc: true\nnumber-sections: true\nnumber-depth: 1\n---\n\n\n\n\nThis course is aimed towards researchers analyzing field observations, who are often faced by data heterogeneities due to field sampling protocols changing from one project to another, or through time over the lifespan of projects, or trying to combine 'legacy' data sets with new data collected by recording units.\n\nSuch heterogeneities can bias analyses when data sets are integrated inadequately, or can lead to information loss when filtered and standardized to common standards. Accounting for these issues is important for better inference regarding status and trend of species and communities.\n\nAnalysts of such 'messy' data sets need to feel comfortable with manipulating the data, need a full understanding the mechanics of the models being used (i.e. critically interpreting the results and acknowledging assumptions and limitations), and should be able to make informed choices when faced with methodological challenges.\n\nThe course emphasizes critical thinking and active learning through hands on programming exercises. We will use publicly available data sets to demonstrate the data manipulation and analysis. We will use freely available and open-source R packages.\n\nThe expected outcome of the course is a solid foundation for further professional development via increased confidence in applying these methods for field observations.\n\n## Instructor\n\n[**Dr. Peter Solymos**](https://peter.solymos.org)\\\n[Boreal Avian Modelling Project](https://borealbirds.ca) and the [Alberta Biodiversity Monitoring Institute](https://abmi.ca)\\\n[Department of Biological Sciences](https://www.ualberta.ca/biological-sciences/), [University of Alberta](https://ualberta.ca)\n\n## Outline\n\nEach day will consist of 3 sessions, roughly one hour each, with short breaks in between.\n\n> The video recordings from the workshop can be found on [YouTube](https://www.youtube.com/watch?v=cXGXvAOqEng&list=PLH424kyZX5ip0PfOo7g13nJEQNVxZlMOh).\n\n| Session   | Topic                                              |                                    Files                                     |                                      Videos                                       |\n|-----------|----------------------------------------------------|:----------------------------------------------------------------------------:|:---------------------------------------------------------------------------------:|\n| **Day 1** | **Naive techniques**                               |                                                                              |                                                                                   |\n|           | 1\\. Introductions                                  |      [Slides](https://peter.solymos.org/qpad-workshop/day1-1-intro.pdf)      |                       [Video](https://youtu.be/cXGXvAOqEng)                       |\n|           | 2\\. Organizing point count data                    | [Notes](https://peter.solymos.org/qpad-workshop/day1-2-data-processing.html) |  [Part 1](https://youtu.be/4PLyaU6bqRc), [Part 2](https://youtu.be/dcsiv-v0UgA)   |\n|           | 3\\. Regression techniques                          |   [Notes](https://peter.solymos.org/qpad-workshop/day1-3-regression.html)    |  [Part 1](https://youtu.be/z_TpcF0FD4o), [Part 2](https://youtu.be/ZdTgdTqxFSM)   |\n| **Day 2** | **Behavioral complexities**                        |                                                                              |                                                                                   |\n|           | 1\\. Statistical assumptions and nuisance variables |      [Slides](https://peter.solymos.org/qpad-workshop/day2-1-intro.pdf)      |                       [Video](https://youtu.be/8v3Uf_aILxI)                       |\n|           | 2\\. Behavioral complexities                        |    [Notes](https://peter.solymos.org/qpad-workshop/day2-2-behavior.html)     |   [bSims](https://youtu.be/gJ11_wlsEfU), [Video](https://youtu.be/UgGeaxMCs2c)    |\n|           | 3\\. Removal modeling techniques                    |     [Notes](https://peter.solymos.org/qpad-workshop/day2-3-removal.html)     |                       [Video](https://youtu.be/ny0ED9cxzeg)                       |\n|           | 4\\. Finite mixture models and testing assumptions  |    [Notes](https://peter.solymos.org/qpad-workshop/day2-4-mixtures.html)     | [Mixtures](https://youtu.be/A1cnzXMMlxU), [Testing](https://youtu.be/flF5NL73ZZE) |\n| **Day 3** | **The detection process**                          |                                                                              |                                                                                   |\n|           | 1\\. The detection process                          |      [Slides](https://peter.solymos.org/qpad-workshop/day3-1-intro.pdf)      |                       [Video](https://youtu.be/CkdYEF_hZqY)                       |\n|           | 2\\. Distance sampling and density                  |    [Notes](https://peter.solymos.org/qpad-workshop/day3-2-detection.html)    |                       [Video](https://youtu.be/x8GfKDEJcrA)                       |\n|           | 3\\. Estimating population density                  |    [Notes](https://peter.solymos.org/qpad-workshop/day3-2-detection.html)    |                       [Video](https://youtu.be/yeoGxRQd6o0)                       |\n|           | 4\\. Assumptions                                    |    [Notes](https://peter.solymos.org/qpad-workshop/day3-2-detection.html)    |                       [Video](https://youtu.be/o0bx-vNCaL0)                       |\n| **Day 4** | **Coming full circle**                             |                                                                              |                                                                                   |\n|           | 1\\. QPAD overview                                  |      [Slides](https://peter.solymos.org/qpad-workshop/day4-1-intro.pdf)      |                       [Video](https://youtu.be/TU9rcwY2Y-g)                       |\n|           | 2\\. Models with detectability offsets              |      [Notes](https://peter.solymos.org/qpad-workshop/day4-2-qpad.html)       |  [Offsets](https://youtu.be/vw_WO2hgNwk), [Models](https://youtu.be/Cy68E1GyNVU)  |\n|           | 3\\. Model validation and error propagation         |      [Notes](https://peter.solymos.org/qpad-workshop/day4-2-qpad.html)       | [Validation](https://youtu.be/lRcJzfE838k), [Error](https://youtu.be/na5cTYNq2HM) |\n|           | 4\\. Recordings, roadsides, closing remarks         |   [Notes](https://peter.solymos.org/qpad-workshop/day4-3-recordings.html)    |                       [Video](https://youtu.be/ckEDGdLA_J4)                       |\n\n## Get course materials\n\n### Install required software\n\nFollow the instructions at the [R website](http://cran.r-project.org) to download and install the most up-to-date base R version suitable for your operating system (the latest R version at the time of writing these instructions is 4.0.4).\n\nThen run the following script in R:\n\n``` r\nsource(\"https://raw.githubusercontent.com/psolymos/qpad-workshop/main/src/install.R\")\n```\n\nHaving RStudio is not absolutely necessary, but it will make life easier. RStudio is also available for different operating systems. Pick the open source desktop edition from [here](http://www.rstudio.com/products/rstudio/download/) (the latest RStudio Desktop version at the time of writing these instructions is 1.4.1106).\n\nPrior exposure to R programming is not necessary, but knowledge of basic R object types and their manipulation (arrays, data frames, indexing) is useful for following hands-on exercises. Software Carpentry's [Data types and structures in R](http://swcarpentry.github.io/r-novice-inflammation/13-supp-data-structures/index.html) is a good resource to brush up your R skills.\n\n### Get the notes\n\nIf you don't want to use git:\n\n1.  Download the [workshop archive](qpad-workshop-Final.zip) release into a folder\n2.  Extract the zip archive\n3.  Open the `workshop.Rproj` file in RStudio (or open any other R GUI/console and `setwd()` to the directory where you downloaded the file)\n4.  (You can delete the archive)\n\nIf you want to use git: fork or clone the repository\n\n``` bash\ncd into/your/dir\ngit clone https://github.com/psolymos/qpad-workshop.git\n```\n\n## Useful resources\n\n-   [Using the QPAD package to get offsets based on estimates from the Boreal Avian Modelling Project's database](https://github.com/ABbiodiversity/recurring/blob/master/offset/README.md)\n-   [NA-POPS: Point count Offsets for Population Sizes of North America landbirds](http://na-pops.org/)\n\n## References\n\nSólymos, P., Toms, J. D., Matsuoka, S. M., Cumming, S. G., Barker, N. K. S., Thogmartin, W. E., Stralberg, D., Crosby, A. D., Dénes, F. V., Haché, S., Mahon, C. L., Schmiegelow, F. K. A., and Bayne, E. M., 2020. Lessons learned from comparing spatially explicit models and the Partners in Flight approach to estimate population sizes of boreal birds in Alberta, Canada. *Condor*, 122: 1-22. [PDF](https://drive.google.com/file/d/115WgtPd4zUSIFfSTHbWYs8OCHNdpKkh5/view?usp=sharing)\n\nSólymos, P., Matsuoka, S. M., Cumming, S. G., Stralberg, D., Fontaine, P., Schmiegelow, F. K. A., Song, S. J., and Bayne, E. M., 2018. Evaluating time-removal models for estimating availability of boreal birds during point-count surveys: sample size requirements and model complexity. *Condor*, 120: 765-786. [PDF](https://drive.google.com/file/d/13Czd_A82P0ZhIlvAEabxdHfmaZcJaNU3/view?usp=sharing)\n\nSólymos, P., Matsuoka, S. M., Stralberg, D., Barker, N. K. S., and Bayne, E. M., 2018. Phylogeny and species traits predict bird detectability. *Ecography*, 41: 1595-1603. [PDF](https://drive.google.com/file/d/1CRKl-bh1tqxddijEWZoNcDO_xFIgOfWZ/view?usp=sharing)\n\nVan Wilgenburg, S. L., Sólymos, P., Kardynal, K. J. and Frey, M. D., 2017. Paired sampling standardizes point count data from humans and acoustic recorders. *Avian Conservation and Ecology*, 12(1):13. [PDF](https://drive.google.com/file/d/0B-q59n6LIwYPOTZyTXlDb0xFQTA/view?usp=sharing)\n\nYip, D. A., Leston, L., Bayne, E. M., Sólymos, P. and Grover, A., 2017. Experimentally derived detection distances from audio recordings and human observers enable integrated analysis of point count data. *Avian Conservation and Ecology*, 12(1):11. [PDF](https://drive.google.com/file/d/0B-q59n6LIwYPQ2F6d1llQ3lPTzg/view?usp=sharing)\n\nSólymos, P., and Lele, S. R., 2016. Revisiting resource selection probability functions and single-visit methods: clarification and extensions. *Methods in Ecology and Evolution*, 7:196-205. [PDF](https://drive.google.com/file/d/0B-q59n6LIwYPRE5tVlRMSmhLWmM/view?usp=sharing)\n\nMatsuoka, S. M., Mahon, C. L., Handel, C. M., Sólymos, P., Bayne, E. M., Fontaine, P. C., and Ralph, C. J., 2014. Reviving common standards in point-count surveys for broad inference across studies. *Condor* 116:599-608. [PDF](https://drive.google.com/file/d/0B-q59n6LIwYPcGZNS3JSRUlBdDQ/view?usp=sharing)\n\nSólymos, P., Matsuoka, S. M., Bayne, E. M., Lele, S. R., Fontaine, P., Cumming, S. G., Stralberg, D., Schmiegelow, F. K. A. & Song, S. J., 2013. Calibrating indices of avian density from non-standardized survey data: making the most of a messy situation. *Methods in Ecology and Evolution* 4:1047-1058. [PDF](https://drive.google.com/file/d/0B-q59n6LIwYPV0RNUFU1N1dmS1E/view?usp=sharing)\n\nMatsuoka, S. M., Bayne, E. M., Sólymos, P., Fontaine, P., Cumming, S. G., Schmiegelow, F. K. A., & Song, S. A., 2012. Using binomial distance-sampling models to estimate the effective detection radius of point-counts surveys across boreal Canada. *Auk* 129:268-282. [PDF](https://drive.google.com/file/d/0B-q59n6LIwYPbFhhRUtZNWQyMk0/view?usp=sharing)\n\n## License\n\nThe course material is licensed under [Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)](https://creativecommons.org/licenses/by-nc-sa/4.0/) license. Source code is under [MIT](LICENSE) license.\n",
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