In this blog article, I propose a way to look at the spatial repartition of correlation between two rasters. This is an update of a blog post I wrote in 2018 : Spatial correlation between rasters. The main difference is that I use the new {terra} package instead of the old {raster} package. The …
Rstats
How to debug your package in a {rhub} fedora container before sending to CRAN?
It is not the first time I present how to debug on an other platform before sending your package to CRAN. This time, before submission {checkhelper} failed on ‘fedora’ image provided by {rhub}. How to debug your package using this platform when your using an other OS? Let’s speak about docker and …
Share your R work following good dev practices from a single notebook
You write R scripts and you would like to share them with other users, in a sustainable and maintainable way. You already write your code in a notebook (Rmarkdown or Quarto) and share its HTML output. You would like to document the chunks, and make this documentation visible in a separate HTML page. …
Add {tmap} point layer with multiple symbol border colors and width
It’s been a while since my last blog post. Indeed, my free time is used to improve packages like “{fusen}: Inflate your package from a simple flat Rmd” , “{attachment}: Tools to deal with dependencies in scripts, Rmd and packages” or “{gitlabr}: An R client for the GitLab API”. Hence, drawing some …
I do not have time (to practice)
I’d really like to be able to do this, and I know I will benefit from it, but I do not have time or I did not find time to try it… […] How much time do you plan to take to read this blog post? Will you read until the end? Completely or the headlines only? […] If you do not have time …
How not to be lost with VSCode when coming from RStudio?
VSCode is popular these days in the #rstats community. I know how to find everything I need in RStudio and I have my small habits, then how to find my way with VSCode? Here, I present the answers to my first exploration in using VSCode as a R user. […] You first need to install VSCode and …
Debug your package that failed on CRAN with {rhub}
If you sent packages on CRAN, you may have encountered some fails on different operating systems configurations that you never heard about before: Solaris, debian clang, fedora gcc, … Package {rhub} allows to test your package on some of them, prior to sending to CRAN. But, how to debug directly on …
How to debug your package on Win-Builder before sending to CRAN?
CRAN submission can be difficult as your package is checked on multiple OS and R versions that you may not be able to check yourself locally. Thankfully, some services like {rhub} and Win-Builder prevent some unfortunate CRAN errors. But how to debug code that is run on an external server, without …
Date-time Conversion in R with format and strptime
Each time I want to extract or show a specific attribute of a date or a time, I am lost in the documentation. What letter do I need to use in format() to get the name of the day written in full, in my language, from the current date? Is it “%Y %m %d”, “%a %b %d”, …? So let’s keep it short this time! …
Buffer areas for nearest neighbours or national marine areas delineation
A few weeks ago, Christina Buelow asked on Twitter how she could create the polygons of coastal waters using the land polygons, and making sure there is no overlap in buffer areas. This would make it possible to know which land area is closest to any place in the sea. Let’s explore what solution …
Find most retweeted tweets of the #rspatial bot
Bots that retweet #rspatial and #BioImageAnalysis tweets are working well. It is now time to add a little functionnality with the best retweeted tweet of the month, a function added to {tweetrbot} package. […] You can retrieve the updated dataset for all tweets here and the dataset for the …
#30DayMapChallenge: 30 days building maps (3) - Earth is spherical
The #30DayMapChallenge was initiated by Topi Tjukanov on Twitter. This is open to anyone who would like to show a map, whatever the software is. In this blog post, I will show maps made with R. I add constraints to myself for fun. This week, I will create maps that remind map makers that Earth is …
#30DayMapChallenge: 30 days building maps (2) - tmap
The #30DayMapChallenge was initiated by Topi Tjukanov on Twitter. This is open to anyone who would like to show a map, whatever the software is. In this blog post, I will show maps made with R. I add constraints to myself for fun. This week, I will use {tmap} to create maps. This follows previous …
#30DayMapChallenge: 30 days building maps (1) - ggplot2
The #30DayMapChallenge was initiated by Topi Tjukanov on Twitter. This is open to anyone who would like to show a map, whatever the software is. In this blog post, I will show maps made with R. I add constraints to myself for fun. This week, I will use {ggplot2} to create maps. […] […] …
Follow moving particle trajectory over raster with {rayshader}
{rayshader} is a fantastic package for 3D mapping, but it comes with the limitations of {rgl}. I always found it a shame not being able to travel in all directions over my 3D objects. In this blog post, I will show a trick to simulate particle trajectory in 3 dimensions like in a “first person” …
Create a twitter bot on a Raspberry Pi 3 using R
With Marion Louveaux, we decided that we had to build a Twitter bot for our preferred hashtag. We explored different possibilities but truth is I couldn’t resist building it using R and {rtweet}. Here are the steps I used to set up a Twitter bot on my Raspberry Pi. […] I use package {rtweet} …
Keep a github/gitlab fork up-to-date
Developers in the R-community are open to any kind of help in the development of their packages. You can open issues but also propose some pull/merge requests to improve code and/or documentation. But once you have forked the main repository, how can you be sure to work on the last version of the …
Render mesh3d objects with rayshader and rayrender
People like to show 3D images in their presentations because it usually impresses the audience. Does it really ? I do not care ! I am just looking for an opportunity to play with some 3D images… This blog post is a detailed version of some 3D images shown during my presentation “Everything but maps …
Kaggle survey 2018: Maps of programming languages used and repartition of reproducibility issues
Last year I participated to the Kaggle survey data challenge. The challenge objective: tell a data story about a subset of the data science community represented in this survey, through a combination of both narrative text and data exploration. I used this opportunity to build ternary choropleth …
Blogdown Hugo themes to share scripts
I modified two Hugo themes to be able to share R code using blogdown. hugo-future-imperfect and hugo-statnmap-theme are multilingual themes allowing for code folding, syntax highlighting, list of related articles, citation card, SEO graph or contact form. All options listed below are detailed in the …
Play with spatial tools on 3D cells images
Let’s play with mapping tools on non-maps data ! {rayshader} is nice on raster maps, but what about using it on segmentized plant cell? […] I wanted to find a good reason to play with Tyler Morgan-Wall packages for 3D visualisation of raster data: {rayshader} and {rayfocus}. Using cell …
Introduction to mapping with {sf} & Co.
At the “Rencontres R 2018” in Rennes, I proposed a brief introduction to mapping using the recent {sf} package and some other interesting packages. This blog post is an extended version of my presentation allowing me to share the code of the different maps that appeared on it. It’s still a brief …
Draw maps like paintings
On the Grrr Slack, a mutual-aid Slack on R for French speaking people, Thomas Vroylandt showed the following maps asking how this could be done using {ggplot2} : EDIT : This maps was originally presented on visionscarto.net with drawings by Agnès Stienne […] As of today (2018-04-18): …
Spatial correlation between rasters
In this blog article, I propose a way to look at the spatial repartition of correlation between two rasters. For your own reason, you may want to know the correlation between rasters, but a unique value issued from fonction cor is not enough. You would like to know if there are variations of …
Enable code folding in bookdown and blogdown
Code folding is an interesting feature in Rmarkdown documents. Find out how to realise it in bookdown documents and blogdown websites. […] I modified Hugo themes with code folding, find out the list here. […] Some time ago, I answered a question on stackoverflow to make code folding …
Spatial interpolation on Earth as a 3D sphere
Earth map is usually presented flat. Geographical coordinates usually go from -180° to +180°. Spatial interpolations using coordinates may be tricky as -180° is equal to +180°. Here I propose a way to realize spatial interpolations on Earth as a sphere and then map the outputs in 3D using rgl. The …
Migration from wordpress to Hugo with Blogdown
I used the nice hugo-icarus-theme from digitalcraftsman as a basis and moved different things. I also added a few things to have a blog along with the freelance presentation. Feel free to fork it or propose your pull requests. The hugo-statnmap-theme has the following functionnalities: […] …
Translation of rmarkdown documents using a data frame
In my post “Rmarkdown conditional chunks to create multilingual pdf and html with images”, I proposed a way to create a rmarkdown document to be printed in two different languages. If you deal with more than two languages, your document may become difficult to read. Moreover, if you work with …
SDMSelect: Cross-validation model selection and species distribution mapping
This library has originally been created for covariates selection to predict species distribution (biomass, density or presence/absence). Its final aim is thus to produce maps of predicted distributions (Look at vignette SDM_Selection). However, the core of the library is a N-times k-fold …
Polygons tint band with leaflet and simple feature (library sf)
Let’s use some French regions polygons and attribute one colour to each region. I like piratepal colours of library yarrr. […] To create the doughnuts using original and buffer polygons, I used st_difference. However as discussed with edzer in the sf github repository, I had to transform the …
How to fill a hatched area polygon with holes in leaflet with R
I built a R package, available on my statnmap github, to provide the function hatched.SpatialPolygons. This function is based on the plot method for SpatialPolygons of library sp. I modified the functions and sub-functions to remove all code for direct drawing and allow to output a …
Format text conditionally with rmarkdown chunks - Complete iframed article
The following of this article is an embed iframe. As it was built for my previous website, the links inside may not work, in particular the summary. Sorry for that. Related article in the blog is here
Rmarkdown conditional chunks to create multilingual pdf and html with images
In the upper output files, I list some of the tips I have to use to make this work and some bonus: […] I will modify this list if I face new difficulties or I find better ways to do things. […] The complete list of tips can be seen on the following web pages (embedded in iframes). Rmd …
Add multiple layers in leaflet widget with R
Library leaflet with R is well integrated with pipe writing (%>%). Thus, it is really easy to add multiple layers and options in a leaflet widget. If you want to add a lot of layers in your widget, it is not necessary to provide a “addPolygons” for each of these layers, you can simply use a loop. …
Rshiny expert image comparison app
The expert image comparison was long: 40min for the small analysis and 3h for the complete one. As the shinyapp is freely hosted on the Rstudio shinyapps.io servers, it was not possible to save outputs of a specific session on the server. Thus, the web application has been built such that the …
A nice RShiny On/Off switch button
[…] This Rshiny ‘SwitchButton’ function allows to use nice on/off (or True/False) switch buttons instead of the default Rshiny ‘checkboxInput’ function. This only uses CSS code and does not make use of javascript. The ‘switchButton’ function includes two options: […] Steps to include …
Bayesian life cycle model: OpenBUGS code
The OpenBUGS code presented below is the additional material of a publication. This is the life cycle model of a marine species (the sole in the Eastern Channel). The Bayesian hierarchical model incorporates indices of juvenile spatialized abundance, larval dispersion, adult abundance indices and …
Mapping, spatial analyses and GIS with R
If you download the following presentation, you will find a presentation of different functions in the R-software useful for spatial data manipulations. Choosing the right libraries allows to create, import, modify, manipulate and map vector (shapefiles) or matrix (raster) spatial data. Your spatial …
Sensitivity of Inverse Community matrix
This script is the supplemental material of two publications on trophic network analyses. This allows to test for uncertainties of direct and indirect effects of small variation in biomass of a trophic network compartment on the rest of the ecosystem. […] Lassalle Geraldine, Bourdaud Pierre, …