Archive

2025  10

October  2

Writing to linked tables in a transaction

October 21, 2025 · 2 min · Scott Chamberlain

Notes on FastAPI, LiteStar and HTMX

October 9, 2025 · 6 min · Scott Chamberlain

July  1

vcr v2

July 28, 2025 · 6 min · Scott Chamberlain

April  1

sixtyfour: writing robust code against AWS

April 3, 2025 · 8 min · Scott Chamberlain

March  2

Picking a web framework

March 27, 2025 · 7 min · Scott Chamberlain

Notes on The Emperor of All Maladies

March 18, 2025 · 10 min · Scott Chamberlain

February  3

uv notes

February 20, 2025 · 3 min · Scott Chamberlain

webmockr v2: another day, another stub

February 13, 2025 · 4 min · Scott Chamberlain

Keeping internal function examples alive

February 4, 2025 · 3 min · Scott Chamberlai

January  1

Notes on A Biology Primer for Computer Scientists

January 7, 2025 · 4 min · Scott Chamberlain

2024  7

December  1

cowsay v1

December 9, 2024 · 4 min · Scott Chamberlain

September  1

Software rules and Quarto

September 26, 2024 · 4 min · Scott Chamberlain

March  5

Refactoring notes

March 20, 2024 · 3 min · Scott Chamberlain

Moved to Hugo

March 20, 2024 · 1 min · Scott Chamberlain

Shiny file inputs

March 8, 2024 · 3 min · Scott Chamberlain

Shiny button weirdness

March 4, 2024 · 2 min

Avoiding the word footgun(s)

March 3, 2024 · 2 min

2023  4

October  3

Weird thoughts

October 12, 2023 · 2 min · Scott Chamberlain

Job searching notes

October 9, 2023 · 3 min · Scott Chamberlain

Working at Fred Hutchinson Cancer Center

October 6, 2023 · 1 min · Scott Chamberlain

April  1

Python, ast, and redbaron

April 18, 2023 · 4 min · Scott Chamberlain

2022  3

June  1

CRAN Checks API and Badges

June 2, 2022 · 2 min · Scott Chamberlain

April  1

List comprehension vs. filter vs. key lookup

April 18, 2022 · 3 min · Scott Chamberlain

February  1

Notes on Python

February 7, 2022 · 2 min · Scott Chamberlain

2021  1

November  1

Mocking HTTP redirects

November 27, 2021 · 4 min · Scott Chamberlain

2020  5

December  1

API client design: how to deal with lots of parameters?

December 21, 2020 · 8 min · Scott Chamberlain

September  1

stories behind archived packages

September 10, 2020 · 8 min · Scott Chamberlain

August  1

taxizedb: an update

August 17, 2020 · 4 min · Scott Chamberlain

February  1

how many parameters?

February 10, 2020 · 5 min · Scott Chamberlain

January  1

finding truffles

January 30, 2020 · 3 min · Scott Chamberlain

2019  4

March  2

text mining, apis, and parsing api logs

March 21, 2019 · 7 min · Scott Chamberlain

Exceptions in control flow in R

March 4, 2019 · 9 min · Scott Chamberlain

February  2

Notes on porting Ruby to R

February 19, 2019 · 4 min · Scott Chamberlain

trailing commas

February 7, 2019 · 3 min · Scott Chamberlain

2018  7

December  1

condition control: I just want that message once

December 6, 2018 · 4 min · Scott Chamberlain

October  1

limiting dependencies in R package development

October 2, 2018 · 5 min · Scott Chamberlain

July  1

Balancing user friendliness and code fragility

July 27, 2018 · 5 min · Scott Chamberlain

June  1

Exploring specimen collections data in Butte County, California

June 12, 2018 · 5 min · Scott Chamberlain

February  1

Exploring git commits with git2r

February 5, 2018 · 4 min · Scott Chamberlain

January  2

My Sublime Text workflow/setup

January 31, 2018 · 3 min · Scott Chamberlain

Playing with Ruby Patterns in R

January 25, 2018 · 4 min · Scott Chamberlain

2017  8

November  1

Web APIs with Sinatra, Mongo, Docker, and Caddy

November 14, 2017 · 8 min · Scott Chamberlain

October  1

habanero update: Crossref data from Python

October 23, 2017 · 3 min · Scott Chamberlain

September  2

cranchecks: an API for CRAN check results

September 27, 2017 · 3 min · Scott Chamberlain

gbifrb: Ruby client for the GBIF API

September 7, 2017 · 1 min · Scott Chamberlain

August  1

hoardr: simple file caching

August 15, 2017 · 4 min · Scott Chamberlain

June  1

Tooling for R package development

June 18, 2017 · 7 min

May  1

Reading in May

May 16, 2017 · 1 min

March  1

CascadiaRConf

March 23, 2017 · 1 min

2016  10

October  1

USDA plants database API in R

October 19, 2016 · 8 min

September  1

gbids - GenBank IDs API is back up!

September 1, 2016 · 3 min

August  2

nonoyes - text analysis of Reply All podcast transcripts

August 25, 2016 · 4 min

video editing notes

August 12, 2016 · 1 min

June  1

Marine Regions data in R

June 9, 2016 · 6 min

April  1

atomize - make new packages from other packages

April 7, 2016 · 2 min

March  3

GenBank IDs API - get, match, swap id types

March 29, 2016 · 3 min

heythere - a robot to automate GitHub issue comments

March 24, 2016 · 4 min

scrubr - clean species occurrence records

March 4, 2016 · 11 min · Scott Chamberlain

January  1

request - a high level HTTP client for R

January 5, 2016 · 5 min · Scott Chamberlain

2015  26

December  1

binomen - Tools for slicing and dicing taxonomic names

December 8, 2015 · 5 min · Scott Chamberlain

November  2

Crossref programmatic clients

November 30, 2015 · 3 min · Scott Chamberlain

pygbif - GBIF client for Python

November 12, 2015 · 2 min · Scott Chamberlain

October  3

noaa - Integrated Surface Database data

October 21, 2015 · 4 min · Scott Chamberlain

Metrics for open source projects

October 19, 2015 · 5 min · Scott Chamberlain

analogsea - an R client for the Digital Ocean API

October 2, 2015 · 2 min · Scott Chamberlain

September  1

oai - an OAI-PMH client

September 11, 2015 · 3 min · Scott Chamberlain

August  1

fulltext - a package to help you mine text

August 7, 2015 · 10 min · Scott Chamberlain

July  1

rnoaa - Weather data in R

July 7, 2015 · 12 min · Scott Chamberlain

June  2

rerddap - General purpose R client for ERDDAP servers

June 24, 2015 · 8 min · Scott Chamberlain

iDigBio - a new data source in spocc

June 8, 2015 · 3 min · Scott Chamberlain

May  2

lawn - a new package to do geospatial analysis

May 18, 2015 · 5 min · Scott Chamberlain

openadds - open addresses client

May 18, 2015 · 5 min · Scott Chamberlain

April  2

geojsonio - a new package to do geojson things

April 30, 2015 · 5 min · Scott Chamberlain

the new way - httsnap

April 29, 2015 · 4 min · Scott Chamberlain

March  3

Faster solr with csv

March 20, 2015 · 3 min · Scott Chamberlain

PUT dataframes on your couch

March 12, 2015 · 3 min · Scott Chamberlain

csl - an R client for Citation Style Language data

March 11, 2015 · 3 min · Scott Chamberlain

February  2

Elasticsearch backup and restore

February 26, 2015 · 1 min · Scott Chamberlain

note to self, secure elasticsearch

February 26, 2015 · 2 min · Scott Chamberlain

January  6

httping - ping and time http requests

January 30, 2015 · 5 min · Scott Chamberlain

elastic - Elasticsearch from R

January 29, 2015 · 10 min · Scott Chamberlain

binomen - taxonomic classes and parsing

January 19, 2015 · 3 min · Scott Chamberlain

discgolf - Dicourse from R

January 15, 2015 · 4 min · Scott Chamberlain

R I/O for geojson and topojson

January 6, 2015 · 5 min · Scott Chamberlain

gistr - R client for GitHub gists

January 5, 2015 · 7 min · Scott Chamberlain

2014  20

December  8

pytaxize - low level ITIS functions

December 26, 2014 · 3 min · Scott Chamberlain

Museum metadata - the Asian Art Museum of San Francisco

December 10, 2014 · 5 min · Scott Chamberlain

icanhaz altmetrics

December 8, 2014 · 3 min · Scott Chamberlain

Altmetrics from anywhere

December 8, 2014 · 3 min · Scott Chamberlain

Dealing with multi handle errors

December 8, 2014 · 2 min · Scott Chamberlain

Publications by author country

December 3, 2014 · 4 min · Scott Chamberlain

http codes

December 2, 2014 · 4 min · Scott Chamberlain

taxize workflows

December 2, 2014 · 5 min · Scott Chamberlain

November  4

1000 commits to taxize

November 28, 2014 · 3 min · Scott Chamberlain

Intro to alpha ckanr - R client for CKAN RESTful API

November 26, 2014 · 8 min · Scott Chamberlain

Fun with the GitHub API

November 26, 2014 · 3 min · Scott Chamberlain

sofa - reboot

November 18, 2014 · 5 min · Scott Chamberlain

October  1

Conditionality meta-analysis data

October 6, 2014 · 4 min · Scott Chamberlain

August  1

rsunlight - R client for Sunlight Labs APIs

August 11, 2014 · 6 min · Scott Chamberlain

June  1

analogsea - v0.1 notes

June 18, 2014 · 5 min · Scott Chamberlain

May  2

analogsea - an R client for the Digital Ocean API

May 28, 2014 · 5 min · Scott Chamberlain

Logistic plot reboot

May 22, 2014 · 2 min · Scott Chamberlain

February  1

cowsay - ascii messages and warnings for R

February 20, 2014 · 4 min · Scott Chamberlain

January  2

cites - citation stuff from the command line

January 18, 2014 · 5 min · Scott Chamberlain

rgauges - fun with hourly web site analytics

January 17, 2014 · 5 min · Scott Chamberlain

2013  25

November  1

Jekyll - an intro

November 20, 2013 · 3 min · Scott Chamberlain

October  2

Code display in scholarly journals

October 25, 2013 · 2 min · Scott Chamberlain

Guide to using rOpenSci packages during the US Gov’t shutdown

October 8, 2013 · 3 min · Scott Chamberlain

September  2

Taxonomy data from the web in three languages

September 27, 2013 · 2 min · Scott Chamberlain

Pollinator niche breadth and natural enemies

September 19, 2013 · 1 min · Scott Chamberlain

August  3

govdat - SunlightLabs and New York Times Congress data via R

August 28, 2013 · 6 min · Scott Chamberlain

Engaging the public on climate change through phenology data

August 18, 2013 · 3 min · Scott Chamberlain

Working with climate data from the web in R

August 17, 2013 · 5 min · Scott Chamberlain

July  4

R ecology workshop

July 31, 2013 · 1 min · Scott Chamberlain

R resources

July 30, 2013 · 1 min · Scott Chamberlain

Beyond academia

July 25, 2013 · 2 min · Scott Chamberlain

On writing, sharing, collaborating, and hosting code for science

July 20, 2013 · 5 min · Scott Chamberlain

June  4

R to GeoJSON

June 30, 2013 · 3 min · Scott Chamberlain

Coffeehouse - an aggregator for blog posts about data, data management, etc.

June 18, 2013 · 2 min · Scott Chamberlain

Stashing and playing with raw data locally from the web

June 17, 2013 · 7 min · Scott Chamberlain

Fylopic, an R wrapper to Phylopic

June 1, 2013 · 3 min · Scott Chamberlain

May  1

BISON USGS species occurrence data

May 27, 2013 · 4 min · Scott Chamberlain

March  2

Scholarly metadata in R

March 16, 2013 · 6 min · Scott Chamberlain

Visualizing rOpenSci collaboration

March 8, 2013 · 3 min · Scott Chamberlain

February  2

Academia reboot

February 22, 2013 · 3 min · Scott Chamberlain

Getting a simple tree via NCBI

February 14, 2013 · 2 min · Scott Chamberlain

January  4

testing ifttt recipe, ignore

January 26, 2013 · 1 min · Scott Chamberlain

Waiting for an API request to complete

January 26, 2013 · 2 min · Scott Chamberlain

Resolving species names when you have a lot of them

January 25, 2013 · 5 min · Scott Chamberlain

Open Science Challenge

January 8, 2013 · 3 min · Scott Chamberlain

2012  29

December  3

Is invasive?

December 13, 2012 · 3 min · Scott Chamberlain

Shiny apps are awesome

December 10, 2012 · 3 min · Scott Chamberlain

One R package for all your taxonomic needs

December 6, 2012 · 10 min · Scott Chamberlain

November  1

Altecology, a call to unconference action

November 15, 2012 · 6 min · Scott Chamberlain

October  4

Displaying Your Data in Google Earth Using R2G2

October 24, 2012 · 6 min · Pascal Mickelson

Getting taxonomic names downstream

October 16, 2012 · 3 min · Scott Chamberlain

Exploring phylogenetic tree balance metrics

October 10, 2012 · 4 min · Scott Chamberlain

GBIF biodiversity data from R - more functions

October 8, 2012 · 5 min · Scott Chamberlain

September  4

Vertnet - getting vertebrate museum record data and a quick map

September 19, 2012 · 2 min · Scott Chamberlain

Getting data from figures in published papers

September 18, 2012 · 5 min · Scott Chamberlain

Scholarly metadata from R

September 17, 2012 · 6 min · Scott Chamberlain

Getting data on your government

September 1, 2012 · 3 min · Scott Chamberlain

August  4

Getting ecology and evolution journal titles from R

August 31, 2012 · 3 min · Scott Chamberlain

Ecology unconference at ESA 2013

August 30, 2012 · 2 min · Scott Chamberlain

Making matrices with zeros and ones

August 30, 2012 · 4 min · Scott Chamberlain

ggplot2 maps with insets

August 22, 2012 · 3 min · Scott Chamberlain

July  1

Hitting the Global Names Resolver API

July 20, 2012 · 2 min · Scott Chamberlain

June  1

Recent R packages for ecology and evolution

June 14, 2012 · 2 min · Scott Chamberlain

May  1

Visualize your Github stats (forks and watchers) in a browser with R!

May 5, 2012 · 2 min · Scott Chamberlain

March  1

mvabund - new R pkg for multivariate abundance data

March 19, 2012 · 1 min · Scott Chamberlain

February  2

Journal Articles Need Interactive Graphics

February 25, 2012 · 4 min · Pascal Mickelson

Take the INNGE survey on math and ecology

February 17, 2012 · 1 min · Scott Chamberlain

January  7

Scraping Flora of North America

January 27, 2012 · 2 min · Scott Chamberlain

RNetLogo - A package for running NetLogo from R

January 23, 2012 · 1 min · Scott Chamberlain

Taking a Closer Look at Peer Review

January 16, 2012 · 7 min · Pascal Mickelson

Function for phylogeny resolution

January 13, 2012 · 2 min · Scott Chamberlain

Moving from blogger and wordpress to jekyll

January 11, 2012 · 3 min · Scott Chamberlain

Presenting results of logistic regression

January 10, 2012 · 3 min · Scott Chamberlain

Testing twitterfeed

January 8, 2012 · 1 min · Scott Chamberlain

2011  77

December  5

Weecology can has new mammal dataset

December 29, 2011 · 1 min · Scott Chamberlain

Recology is 1 yr old

December 23, 2011 · 1 min · Scott Chamberlain

Dynamic views don’t support javascript-so reverting back to simple views

December 22, 2011 · 1 min · Scott Chamberlain

I Work For The Internet !

December 13, 2011 · 1 min · Scott Chamberlain

LondonR meetings presentations

December 11, 2011 · 1 min · Scott Chamberlain

November  4

rOpenSci won 3rd place in the PLoS-Mendeley Binary Battle!

November 30, 2011 · 1 min · Scott Chamberlain

Public vote open for Mendely-PLoS Binary Battle: vote rOpenSci!

November 19, 2011 · 1 min · Scott Chamberlain

My talk on doing phylogenetics in R

November 18, 2011 · 1 min · Scott Chamberlain

Check out a video of my research at RocketHub

November 1, 2011 · 1 min · Scott Chamberlain

October  6

My little presentation on getting web data through R

October 28, 2011 · 1 min · Scott Chamberlain

Two new rOpenSci R packages are on CRAN

October 27, 2011 · 1 min · Scott Chamberlain

Two-sex demographic models in R

October 26, 2011 · 1 min · Scott Chamberlain

New food web dataset

October 14, 2011 · 1 min · Scott Chamberlain

Phylogenetic community structure: PGLMMs

October 13, 2011 · 1 min · Scott Chamberlain

R talk on regular expressions (regex)

October 6, 2011 · 1 min · Scott Chamberlain

September  9

R tutorial on visualizations/graphics

September 30, 2011 · 1 min · Scott Chamberlain

Short on funding? Can’t get a grant? Crowdfunding! #SciFund

September 27, 2011 · 1 min · Scott Chamberlain

Ten Simple Rules for OA Publishers talk by Philip Bourne

September 23, 2011 · 1 min · Scott Chamberlain

@drewconway interview on @DataNoBorders at the Strata conference

September 22, 2011 · 1 min · Scott Chamberlain

Open science talk by Carl Boettiger

September 22, 2011 · 1 min · Scott Chamberlain

My take on an R introduction talk

September 9, 2011 · 1 min · Scott Chamberlain

A Data Visualization Book

September 9, 2011 · 5 min · Pascal Mickelson

FigShare Talk

September 8, 2011 · 1 min · Scott Chamberlain

Jonathan Eisen on the Fourth Domain and Open Science

September 6, 2011 · 1 min · Scott Chamberlain

August  6

rnpn: An R interface for the National Phenology Network

August 31, 2011 · 2 min · Scott Chamberlain

Tenure track position in systematics at the University of Vermont

August 22, 2011 · 3 min · Scott Chamberlain

Thursday at #ESA11

August 12, 2011 · 2 min · Scott Chamberlain

Wednesday at #ESA11

August 11, 2011 · 2 min · Scott Chamberlain

Monday at ESA11

August 8, 2011 · 2 min · Scott Chamberlain

(#ESA11) rOpenSci: a collaborative effort to develop R-based tools for facilitating Open Science

August 8, 2011 · 1 min · Scott Chamberlain

July  4

Blogging/tweeting from ESA11

July 31, 2011 · 1 min · Scott Chamberlain

Models in Evolutionary Ecology seminar, organized by Timothee Poisot

July 18, 2011 · 1 min · Scott Chamberlain

Archiving ecology/evolution data sets online

July 15, 2011 · 2 min · Scott Chamberlain

CRdata vs. Cloudnumbers

July 14, 2011 · 3 min · Scott Chamberlain

June  8

rbold: An R Interface for Bold Systems barcode repository

June 28, 2011 · 1 min · Scott Chamberlain

iEvoBio 2011 Synopsis

June 22, 2011 · 2 min · Scott Chamberlain

PLoS journals API from R: “rplos”

June 21, 2011 · 1 min · Scott Chamberlain

ggplot2 talk by Hadley Whickam at Google

June 17, 2011 · 0 min · Scott Chamberlain

OpenStates from R via API: watch your elected representatives

June 10, 2011 · 2 min · Scott Chamberlain

More than 10,000 visits to Recology!!!!

June 9, 2011 · 1 min · Scott Chamberlain

How to fit power laws

June 7, 2011 · 1 min · Scott Chamberlain

searching ITIS and fetching Phylomatic trees

June 3, 2011 · 1 min · Scott Chamberlain

May  7

phylogenetic signal simulations

May 18, 2011 · 2 min · Scott Chamberlain

A simple function for plotting phylogenies in ggplot2

May 17, 2011 · 1 min · Scott Chamberlain

plyr’s idata.frame VS. data.frame

May 13, 2011 · 4 min · Scott Chamberlain

google reader

May 12, 2011 · 1 min · Scott Chamberlain

Comparison of functions for comparative phylogenetics

May 11, 2011 · 2 min · Scott Chamberlain

RHIPE package in R for interfacing between Hadoop and R

May 4, 2011 · 1 min · Scott Chamberlain

Treebase trees from R

May 3, 2011 · 1 min · Scott Chamberlain

April  6

Processing nested lists

April 28, 2011 · 1 min · Scott Chamberlain

Running Phylip’s contrast application for trait pairs from R

April 26, 2011 · 2 min · Scott Chamberlain

Phylometa from R: Randomization via Tip Shuffle

April 16, 2011 · 2 min · Scott Chamberlain

RStudio Beta 2 is Out!

April 11, 2011 · 1 min · Scott Chamberlain

Adjust branch lengths with node ages: comparison of two methods

April 10, 2011 · 2 min · Scott Chamberlain

Phylometa from R - UDPATE

April 1, 2011 · 2 min · Scott Chamberlain

March  7

Bio-ORACLE

March 25, 2011 · 1 min · Scott Chamberlain

basic ggplot2 network graphs ver2

March 23, 2011 · 5 min · Scott Chamberlain

basic ggplot2 network graphs

March 17, 2011 · 2 min · Scott Chamberlain

Species abundance distributions and basketball

March 13, 2011 · 2 min · Scott Chamberlain

cloudnumbers.com

March 11, 2011 · 1 min · Scott Chamberlain

Five ways to visualize your pairwise comparisons

March 5, 2011 · 3 min · Scott Chamberlain

Check out Phyloseminar.org

March 4, 2011 · 1 min · Scott Chamberlain

February  7

RStudio

February 28, 2011 · 1 min · Scott Chamberlain

R overtakes SAS in popularity

February 25, 2011 · 1 min · Scott Chamberlain

Phenotypic selection analysis in R

February 24, 2011 · 2 min · Scott Chamberlain

Phylogenetic analysis with the phangorn package: an example

February 21, 2011 · 1 min · Scott Chamberlain

Farmer’s markets data

February 16, 2011 · 2 min · Scott Chamberlain

Troubling news for the teaching of evolution

February 9, 2011 · 3 min · Scott Chamberlain

Plants are less sex deprived when next to closely related neighbors

February 1, 2011 · 2 min · Scott Chamberlain

January  8

Good riddance to Excel pivot tables

January 30, 2011 · 3 min · Scott Chamberlain

R and Google Visualization API: Fish harvests

January 17, 2011 · 1 min · Scott Chamberlain

R and Google Visualization API: Wikispeedia

January 17, 2011 · 1 min · Scott Chamberlain

Bipartite networks and R

January 14, 2011 · 1 min · Scott Chamberlain

Just for fun: Recovery.gov data snooping

January 11, 2011 · 2 min · Scott Chamberlain

Ecological networks from abundance distributions

January 6, 2011 · 1 min · Scott Chamberlain

R-bloggers

January 5, 2011 · 1 min · Scott Chamberlain

New approach to analysis of phylogenetic community structure

January 5, 2011 · 1 min · Scott Chamberlain

2010  3

December  3

Ngram ecological terms

December 29, 2010 · 1 min · Scott Chamberlain

Phylogenetic meta-analysis in R using Phylometa

December 28, 2010 · 3 min · Scott Chamberlain

A new blog about using R for ecology and evolution

December 27, 2010 · 1 min · Scott Chamberlain