In the introduction to this series of post, I described the Yoctopuce library and told that R package ‘reticulate’ can be used to access the Python version of the yoctopuce library. Here I describe a simple and cheap “micro” spectrometer with a digital interface and its use together with R packages from the 'r4photobiology' suite.
I will use a miniature and low cost spectrometer, type AS7265X from ams. It does not used a grating as monochromator, but instead each of the 18 channels has a different interference filter deposited directly on the silicon chip. The FWHM is 20 nm, and the wavelength range from 410 nm to 940 nm. The spectrometer consists in three separate sensor units working together. The interface is digital, and temperature compensation and analogue to digital conversion takes place in the sensor modules. In spite of the number of channels communication between the spectrometer and a micro-processor requires only two wires. The spectrometer supports two different communication protocols, the specialized I2C and a generic serial communication (UART).
The site has been updated to use encryption. For the web site, old addresses using http: are silently redirected to https:. If you have earlier received warnings from browsers because of the lack of encryption, this upgrade to the server settings should remove them.
The repository at the subdomain https://r.photobiology.info also supports encrypted connections. In addition, because of tightening of security in other ways, if you have been earlier using the address http://www.photobiology.info/R to access the repository, you will need to use https://r.photobiology.info instead from now on. In other words if you are setting this repository address in an .Rprofile file you should edit it to use the new address.
The documentation should be accessed through https://docs.photobiology.info as settings for this subdomain have been changing in the same way.
All these changes should ensure enhanced security for the site and downloads.
R 3.5.0 was released on 23 April. It includes several performance improvements. All packages in the ‘r4photobiology’ suite pass checks on the new version. In CRAN binaries for R 3.5.0 of all packages have been built. In the case of development versions and packages not in CRAN, the repository at http://r.r4photobiology.info/ will soon be updated to include binaries suitable for R 3.5.0. Meanwhile packages will be installed from sources if the require tools are available (e.g. RTools 3.5.0 or 3.4.0 installed in Windows computers).
The update from R 3.4.x to R 3.5.x requires that all packages are reinstalled. For the time being avoid using package ‘installr’ to do the update, at least on Windows, as copying installed packages from an earlier installation is not useful. Please see the page Upgrading Rfor instructions.