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Ethan White ethanwhite @weecology, Univ of Florida Gainesville, FL http://ethanwhite.org Professor at University of Florida. Moore Investigator in Data-Driven Discovery. I work on ecology, data, open science, & open source.

bendmorris/neon_portal 3

Django web app for data entry into the dodobase system.

embaldridge/commonness-and-rarity 2

This repository contains some ideas for several projects exploring the commonness and rarity of species.

ahhurlbert/brubertlab 0

sandbox for learning github for the Brubert lab

aroopsind/data_carpentry 0

UF Course Fall 2015; data computation in r; Professor Ethan White

PR opened weecology/NeonTreeEvaluation_package

Lowercase `w` for org name for devtools install

I know this currently works as is, just a minor tweak for consistency.

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PR opened ethanwhite/NeonTreeEvaluation_package

Lowercase `w` for org name for devtools install

I know this currently works as is, just a minor tweak for consistency.

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R package for evaluating individual tree crown predictions against a diverse benchmark dataset

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PR opened weecology/NeonTreeEvaluation_python

Read the README from the appropriate extension

The README is currently written in markdown but was being read as .rst causing an installation error when using setup.py/pip.

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python benchmark for individual tree crown methods

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Ethan White

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Both exercises for week 6 are optional

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Create the reproducibility lesson

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Add review exercises on vectors, dplyr, and ggplot

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PR opened ropensci/rdataretriever

Add draft of paper for JOSS
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Add JOSS paper structure Update the list of authors

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Merge pull request #249 from henrykironde/paper Add JOSS paper structure

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Update invited workshops

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Add WEC IDEA committee

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Update Sergio's awards

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Add completion dates for Kristina & Shawn

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Updating talks

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Fix talk dates

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Update to publications and preprints

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Update grants

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Add Anaconda badges

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Merge pull request #1519 from henrykironde/badges Add Anaconda badges

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Check for, file path provided as directory with -d

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Check for, file path provided as directory with -d

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Merge pull request #1517 from henrykironde/autocreate-check Autocreate check

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PR merged weecology/retriever

Autocreate check

In case a user provides a path to a file with the flag as a directory -d return and inform the user of the error

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Add review & reproducibility material * Add to schedule for 2020 * Updates to material based on use of RStudio Cloud

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Add video tutorials for intro to forecasting in R

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Ethan White

commit sha c6a3ffd153c6ef76793163f9f1eafd0d57f6a0ab

Typo & video consistency fixes to dplyr material

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issue openedweecology/ogrants

Add note about updates taking time

See: https://twitter.com/_miloj/status/1306671963054669828

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Minor clarification to acacia + ants data manip

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Add prepopulated data text to adult-vs-newborn-size

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Minor ggplot lecture updates

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commit sha 2c97da77a0a1f9969a36cd5d95d9928c977f6698

Minor updates ot Acacia and Ants graphing exercise

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Small clarification to Mass vs Metabolish

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Create datavis lesson

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Add new challenge exercise on graphing data from multiple sources

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issue closeddatacarpentry/semester-biology

Consider moving to a null free dataset for first few weeks

Nulls are important, but they also add a lot of complexities that it might be better to leave until a little later in the semester

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ethanwhite

issue commentdatacarpentry/semester-biology

Consider moving to a null free dataset for first few weeks

We've decided to keep nulls but take extra time to teach about how to interact with them as part of the move from 2 weeks to 3 weeks for Intro R + dplyr.

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issue closeddatacarpentry/semester-biology

Consider 3 Intro + dplyr weeks next year

Weeks 2-3 are currently a bit short for the material for novices. The challenge is that stretching this material to 2-4 is a bit long. Here's one stretch, but then what to do on the 3rd Friday?

Week 1: Course intro + data structure Week 2: Basic intro to R. No assignment. Feel free to skip if you know it all. Week 3: T (Paths, Basic reproducibility), R (dplyr: select, filter, mutate, arrange, adv filter aggregation) Week 4: T (dplyr: joins), F ?

We've gone back and forth on this historically for exactly this reason

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ethanwhite

issue commentdatacarpentry/semester-biology

Consider 3 Intro + dplyr weeks next year

This has been implemented as part of the 2020 course.

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Update acacia-ants graphing exercise to include scale

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Ethan White

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Expand detail in ggplot basics and format code blocks

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Add detailed intro to UHURU data

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Merge remote-tracking branch 'upstream/master'

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Fix copy paste error

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Add grants by Johnson & Sinclair

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Merge pull request #124 from ethanwhite/johnson-sinclair Add grants by Johnson & Sinclair

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PR opened weecology/ogrants

Add grants by Johnson & Sinclair
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issue openeddatacarpentry/semester-biology

Improvements to Joins video

From @andrewmarx:

First, right before the outtakes, you repeat the part about the other types of joins

Second, the only thing I might add would be tying it back to week one more strongly. So right after showing the joined results, something along the lines of: "So what joins do, is they allow us to store our data using good practices like we learned previously, particularly with avoiding duplicate data, but also allow us to efficiently get it into a useful format for working with in R. And now, if we have to update the data for some reason, say we incorrectly typed a species name or the species name was changed, we only have to change it one single place rather than multiple places in our data, which increases the chances of mistakes happening"

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Andrew Marx

commit sha cab24e3b2317824f819d8f3a6f9bb81e18762c41

Update Vectors-bird-banding-R.md Clarify that code is required to find the solutions. It does (rarely) happen that people simply type out the answer

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Andrew Marx

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Update Portal-data-manip-pipes-R.md Add parentheses after `filter`

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Andrew Marx

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Update Portal-data-manip-R.txt Remove output for non-existent exercises

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Merge pull request #890 from andrewmarx/master Week 3 assignment and output fixes

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pull request commentdatacarpentry/semester-biology

Week 3 assignment and output fixes

Thanks @andrewmarx!

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Ethan White

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Remove change note

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Update solution to match current dplyr output

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issue closeddatacarpentry/semester-biology

Providing library imports at top of assigments

I'm proposing that at the top of each assignment we provide a copy/paste code block for students that includes all the needed libraries for that particular assignment. What this would accomplish:

  1. Encourages students to load libraries in a single location at the top of the file. We encourage this behavior but do not enforce it, leading to people having library imports throughout the document, and sometimes students load the same library repeatedly.
  2. Ensures that students are clear about what libraries are needed for the entire assignment. Otherwise, if a student isn't sure about libraries they should be using, this can lead to them wasting time trying to figure out what they need.
  3. Ensures that packages are loaded in the correct order for assignments where multiple packages have functions with the same names. This is a frequent issue; every year multiple students inadvertently override functions midway through an assignment, and it causes reproducibility issues for both them and the instructors. This could also be the source of an optional exercise, where the student is instructed to switch the order that libraries are loaded, the session is cleared, then everything is rerun. They would then describe what occurred and why as a comment, then fix the library order for submission
  4. Prevents students from loading unnecessary packages. For example, while dplyr and tidyr can be installed and loaded individually, some students have submitted answers that load the entire tidyverse package, which does not necessary break things, but can slow down grading. In cases where there are multiple ways to approach a problem, it helps to ensure that students use the approach that results in output that matches the given output. This is potentially an issue when loading csv files using secondary packages that might change things like the order of records.

An example of what the code block might look like:

# Load the necessary libraries for the assignment
library(raster)
library(dplyr)

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Ethan White

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Remove errant data subdirectory

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Ethan White

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Update solution to match exercise

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issue commentdatacarpentry/semester-biology

Providing library imports at top of assigments

Great. I'll try to remember to add these each week, but feel free to remind me if I miss one.

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pull request commentdatacarpentry/semester-biology

Update Dplyr-shrub-volume-join-R.md

Thanks @andrewmarx!

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Andrew Marx

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Update Dplyr-shrub-volume-join-R.md Fix link for sites.csv

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Merge pull request #889 from andrewmarx/master Update Dplyr-shrub-volume-join-R.md

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PR merged datacarpentry/semester-biology

Update Dplyr-shrub-volume-join-R.md

Fix link for sites.csv

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issue commentdatacarpentry/semester-biology

Providing library imports at top of assigments

Oops, wrong link: https://datacarpentry.org/semester-biology/assignments/r-data/

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Add discussion of adding single single value to all rows in data frame

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Add new dataframes-vectors material to week 4 lesson

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Minor cleanup to Week 4 assignment

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Add imports instruction to R Data assignment

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issue commentdatacarpentry/semester-biology

Providing library imports at top of assigments

I think this is a really good idea @andrewmarx. I just pushed an example to https://datacarpentry.org/semester-biology/assignments/r-intro/ Let me know what you think.

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Add imports instruction to R Data assignment

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Minor cleanup to Week 4 assignment

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Add new dataframes-vectors material to week 4 lesson

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Split out integrative dplyr review exercise

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Add exercises on moving between vectors and data frames

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Finish extracting integrative problem from Portal Data Joins

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Add lecture material on converting between data frames & vectors

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Merge pull request #887 from ethanwhite/week-4-updates Week 4 updates

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PR opened datacarpentry/semester-biology

Week 4 updates
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Fix exercise description of how to calculate area

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Merge pull request #886 from ethanwhite/exercise-fix Fix exercise description of how to calculate area

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pull request commentdatacarpentry/semester-biology

Fix exercise description of how to calculate area

@andrewmarx notifying you that a student caught this error in the question. I'm merging this in since most students won't have started on this yet, but if anyone does width * height on the assignment they should get full credit.

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Bump http-proxy from 1.18.0 to 1.18.1 Bumps [http-proxy](https://github.com/http-party/node-http-proxy) from 1.18.0 to 1.18.1. - [Release notes](https://github.com/http-party/node-http-proxy/releases) - [Changelog](https://github.com/http-party/node-http-proxy/blob/master/CHANGELOG.md) - [Commits](https://github.com/http-party/node-http-proxy/compare/1.18.0...1.18.1) Signed-off-by: dependabot[bot] <support@github.com>

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commit sha 0c5bcfe8e0d11fc6f0a310257bce64b1c71e9c58

Merge pull request #3 from ethanwhite/dependabot/npm_and_yarn/http-proxy-1.18.1 Bump http-proxy from 1.18.0 to 1.18.1

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Bump http-proxy from 1.18.0 to 1.18.1 dependencies

Bumps http-proxy from 1.18.0 to 1.18.1. <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/http-party/node-http-proxy/blob/master/CHANGELOG.md">http-proxy's changelog</a>.</em></p> <blockquote> <h2><a href="https://github.com/http-party/node-http-proxy/compare/1.18.0...v1.18.1">v1.18.1</a> - 2020-05-17</h2> <h3>Merged</h3> <ul> <li>Skip sending the proxyReq event when the expect header is present <a href="https://github-redirect.dependabot.com/http-party/node-http-proxy/pull/1447"><code>#1447</code></a></li> <li>Remove node6 support, add node12 to build <a href="https://github-redirect.dependabot.com/http-party/node-http-proxy/pull/1397"><code>#1397</code></a></li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/http-party/node-http-proxy/commit/9b96cd725127a024dabebec6c7ea8c807272223d"><code>9b96cd7</code></a> 1.18.1</li> <li><a href="https://github.com/http-party/node-http-proxy/commit/335aeeba2f0c286dc89c402eeb76af47834c89a3"><code>335aeeb</code></a> Skip sending the proxyReq event when the expect header is present (<a href="https://github-redirect.dependabot.com/http-party/node-http-proxy/issues/1447">#1447</a>)</li> <li><a href="https://github.com/http-party/node-http-proxy/commit/dba39668ba4c9ad461316e834b2d64b77e1ca88e"><code>dba3966</code></a> Remove node6 support, add node12 to build (<a href="https://github-redirect.dependabot.com/http-party/node-http-proxy/issues/1397">#1397</a>)</li> <li>See full diff in <a href="https://github.com/http-party/node-http-proxy/compare/1.18.0...1.18.1">compare view</a></li> </ul> </details> <br />

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Short name for shrub-volume-experiments data

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issue openedweecology/portal-forecast-web

Setup Shiny hosting

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issue openedweecology/portal-forecast-web

Decide on initial hosting

Shinyapps.io vs. self-hosting

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issue openedweecology/portal-forecast-web

Implement basic Shiny website

  • [ ] Existing markdown pages: Models, Rodents, About
  • [ ] Dynamic version of time-series forecast plot with species selection

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