Posts by Tags

The specimen workflow: from field to database

21 minute read

A write-up on data collection for large biodiversity surveys

How to use the iDigBio portal to look for taxa?

2 minute read

An illustrated demonstration on how to get taxa from a specific geographic zone using the iDigBio portal.

Demonstration of `tidytext` using Darwin’s “On the Origin of Species”.

12 minute read

A short demonstration of the R package tidytext using the 1st edition of ‘the Origin of Species’.

Migrate from Gmail to HelpScout with R

16 minute read

How R allowed The Carpentries to migrate emails from Gmail to HelpScout using their web APIs

Demonstration of `tidytext` using Darwin’s “On the Origin of Species”.

12 minute read

A short demonstration of the R package tidytext using the 1st edition of ‘the Origin of Species’.

rncl: A new package to import NEXUS and Newick trees in R

4 minute read

rncl’ is now officially on CRAN. This package provides an interface with the NEXUS Class Library (NCL). NCL, written in C++, is included in several popular p...

How to do UBSAN and Valgrind tests on a R package that includes C/C++ code before submitting to CRAN

3 minute read

After a trying to submit phylobase to CRAN, I learned a lot about the quality checks that go into a package before being available to the public. Beyond the ...

Advent of Code 2018

2 minute read

Solutions for the 2018 Advent of Code

Advent of Code: Day 21

2 minute read

Solution for Day 21 of Advent of Code

Advent of Code: Day 20

1 minute read

Solution for Day 20 of Advent of Code

Advent of Code: Day 19

1 minute read

Solution for Day 19 of Advent of Code

Advent of Code: Day 18

2 minute read

Solution for Day 18 of Advent of Code

Advent of Code: Day 17

less than 1 minute read

Solution for Day 17 of Advent of Code

Advent of Code: Day 16

less than 1 minute read

Solution for Day 16 of Advent of Code

Advent of Code: Day 15

1 minute read

Solution for Day 15 of Advent of Code

Advent of Code: Day 14

1 minute read

Solution for Day 14 of Advent of Code

Advent of Code: Day 13

1 minute read

Solution for Day 13 of Advent of Code

Advent of Code: Day 12

less than 1 minute read

Solution for Day 12 of Advent of Code

Advent of Code: Day 11

1 minute read

Solution for Day 11 of Advent of Code

Advent of Code: Day 10

1 minute read

Solution for Day 10 of Advent of Code

Advent of Code: Day 9

1 minute read

Solution for Day 9 of Advent of Code

Advent of Code: Day 8

1 minute read

Solution for Day 8 of Advent of Code

Advent of Code: Day 7

1 minute read

Solution for Day 7 of Advent of Code

Advent of Code: Day 6

1 minute read

Solution for Day 6 of Advent of Code

Advent of Code: Day 5

less than 1 minute read

Solution for Day 5 of Advent of Code

Advent of Code: Day 4

less than 1 minute read

Solution for Day 4 of Advent of Code

Advent of Code: Day 3

4 minute read

Solution for Day 3 of Advent of Code

Advent of Code: Day 2

1 minute read

Solution for Day 2 of Advent of Code

Advent of Code: Day 1

less than 1 minute read

Solution for Advent of Code

How to work with remote Parquet files with the duckdb R package?

1 minute read

Learn how to work with Parquet files over HTTPS using duckdb and dplyr.

How to use Arrow to work with large CSV files?

11 minute read

A short practical guide to load a 15 GB dataset with Apache Arrow using R and Python.

Creating an Arrow dataset (part 2)

9 minute read

How does partitioning impact query performance?

Creating an Arrow dataset

10 minute read

An exploration of the file formats that Arrow can read and write.

Photos: Heron & Egret

less than 1 minute read

<a href= "https://lh3.ggpht.com/_DiOeIryp5ac/TPJ9Rw75iMI/AAAAAAAACLA/g_exTFWqQzU/s800/IMG_8397.jpg" > <img src= ...

Photos: Thanksgiving birding

less than 1 minute read

<a href= "https://lh6.ggpht.com/_DiOeIryp5ac/TO6Qxn6l4uI/AAAAAAAACJQ/P8Y32Da4r0k/s800/IMG_8574.jpg" > <img src= ...

How to work with remote Parquet files with the duckdb R package?

1 minute read

Learn how to work with Parquet files over HTTPS using duckdb and dplyr.

How to setup magithub if you have GitHub 2-factor authentication enabled?

less than 1 minute read

The steps involved to create the authinfo.gpg file used by magithub when you have 2FA enabled on GitHub

Evolution 3 and offlineimap

2 minute read

I use offlineimap to fetch my emails from my Gmail account. I use labels as folders, some are nested, and some contains a dot in their names. I have about 12...

Happy Halloween – Hibana gracilis

less than 1 minute read

<a href= "https://lh6.ggpht.com/-T_3kkUWVHzw/Tq77B-4IJII/AAAAAAAACZ4/CIdExKGQmG8/s800/IMG_7086%252520%252528Modified%252520in%252520GIMP...

Photos: Heron & Egret

less than 1 minute read

<a href= "https://lh3.ggpht.com/_DiOeIryp5ac/TPJ9Rw75iMI/AAAAAAAACLA/g_exTFWqQzU/s800/IMG_8397.jpg" > <img src= ...

`foghorn` 1.3.1 released

less than 1 minute read

New version of foghorn provides access to Win-builder queue

Migrate from Gmail to HelpScout with R

16 minute read

How R allowed The Carpentries to migrate emails from Gmail to HelpScout using their web APIs

Migrate from Gmail to HelpScout with R

16 minute read

How R allowed The Carpentries to migrate emails from Gmail to HelpScout using their web APIs

How to use the iDigBio portal to look for taxa?

2 minute read

An illustrated demonstration on how to get taxa from a specific geographic zone using the iDigBio portal.

Offlineimap 6.4.1 and nested labels in Gmail

less than 1 minute read

I just upgraded to offlineimap 6.4.1 and I was getting the following error message: “ERROR: INFINITE FOLDER CREATION DETECTED! Folder ‘.foo’ (repository ‘gma...

Evolution 3 and offlineimap

2 minute read

I use offlineimap to fetch my emails from my Gmail account. I use labels as folders, some are nested, and some contains a dot in their names. I have about 12...

Ubuntu color palette for OpenOffice

less than 1 minute read

I like the colors chosen by Ubuntu and I tend to use them for my presentations and posters. So, I created a palette that can be imported in OpenOffice. H...

Photos: Millipedes

less than 1 minute read

<a href= "https://lh5.ggpht.com/_DiOeIryp5ac/TO2zyXreZeI/AAAAAAAACIU/jYCq67x8ZXc/s800/IMG_8547.jpg" > <img src= ...

How to setup magithub if you have GitHub 2-factor authentication enabled?

less than 1 minute read

The steps involved to create the authinfo.gpg file used by magithub when you have 2FA enabled on GitHub

How to setup magithub if you have GitHub 2-factor authentication enabled?

less than 1 minute read

The steps involved to create the authinfo.gpg file used by magithub when you have 2FA enabled on GitHub

Offlineimap 6.4.1 and nested labels in Gmail

less than 1 minute read

I just upgraded to offlineimap 6.4.1 and I was getting the following error message: “ERROR: INFINITE FOLDER CREATION DETECTED! Folder ‘.foo’ (repository ‘gma...

rncl: A new package to import NEXUS and Newick trees in R

4 minute read

rncl’ is now officially on CRAN. This package provides an interface with the NEXUS Class Library (NCL). NCL, written in C++, is included in several popular p...

rncl: A new package to import NEXUS and Newick trees in R

4 minute read

rncl’ is now officially on CRAN. This package provides an interface with the NEXUS Class Library (NCL). NCL, written in C++, is included in several popular p...

How to install BEAGLE on Ubuntu 14.04 (and make it work with BEAST)

2 minute read

BEAGLE is a library that computes efficiently the likelihoods needed during maximum-likelihood or Bayesian phylogenetic tree estimation. It is used by MrBaye...

How to work with remote Parquet files with the duckdb R package?

1 minute read

Learn how to work with Parquet files over HTTPS using duckdb and dplyr.

How to use Arrow to work with large CSV files?

11 minute read

A short practical guide to load a 15 GB dataset with Apache Arrow using R and Python.

Creating an Arrow dataset (part 2)

9 minute read

How does partitioning impact query performance?

Creating an Arrow dataset

10 minute read

An exploration of the file formats that Arrow can read and write.

`foghorn` 1.3.1 released

less than 1 minute read

New version of foghorn provides access to Win-builder queue

Reproducible Science Workshop at iDigBio

5 minute read

Cross-posted from the iDigBio blog. Reproducibility is one of the corner stones of the scientific process. Readers should be able to figure out how you gen...

A list of resources to learn more about R programming (and other things)

less than 1 minute read

A non-exhaustive semi-curated list of useful books/websites for R programming, data analysis, and working at the shell.

rncl: A new package to import NEXUS and Newick trees in R

4 minute read

rncl’ is now officially on CRAN. This package provides an interface with the NEXUS Class Library (NCL). NCL, written in C++, is included in several popular p...

A tutorial to get started with species delineation methods using GMYC

less than 1 minute read

I wrote a tutorial to get started using GMYC (the Generalized Mixed Yule Coalescent). GMYC is a popular method for species delineation based on a single locu...

Happy Halloween – Hibana gracilis

less than 1 minute read

<a href= "https://lh6.ggpht.com/-T_3kkUWVHzw/Tq77B-4IJII/AAAAAAAACZ4/CIdExKGQmG8/s800/IMG_7086%252520%252528Modified%252520in%252520GIMP...

A tutorial to get started with species delineation methods using GMYC

less than 1 minute read

I wrote a tutorial to get started using GMYC (the Generalized Mixed Yule Coalescent). GMYC is a popular method for species delineation based on a single locu...

Reproducible Science Workshop at iDigBio

5 minute read

Cross-posted from the iDigBio blog. Reproducibility is one of the corner stones of the scientific process. Readers should be able to figure out how you gen...

Photos: Millipedes

less than 1 minute read

<a href= "https://lh5.ggpht.com/_DiOeIryp5ac/TO2zyXreZeI/AAAAAAAACIU/jYCq67x8ZXc/s800/IMG_8547.jpg" > <img src= ...

Demonstration of `tidytext` using Darwin’s “On the Origin of Species”.

12 minute read

A short demonstration of the R package tidytext using the 1st edition of ‘the Origin of Species’.

Evolution 3 and offlineimap

2 minute read

I use offlineimap to fetch my emails from my Gmail account. I use labels as folders, some are nested, and some contains a dot in their names. I have about 12...

Photos: Millipedes

less than 1 minute read

<a href= "https://lh5.ggpht.com/_DiOeIryp5ac/TO2zyXreZeI/AAAAAAAACIU/jYCq67x8ZXc/s800/IMG_8547.jpg" > <img src= ...

Reproducible Science Workshop at iDigBio

5 minute read

Cross-posted from the iDigBio blog. Reproducibility is one of the corner stones of the scientific process. Readers should be able to figure out how you gen...

François Michonneau

Posts by Tags

See also:

Biodiversity

Demonstration

R

advent of code

arrow

birds

duckdb

emacs

evolution

florida

foghorn

gmailr

helpscout

iDigBio

linux

macro

magit

magithub

offlineimap

phylobase

phylogenetics

r

reproducible science

resources

rncl

species delineation

spider

teaching

terrestrial arthropod

tidytext

ubuntu

white box

workshop