My new book was published on 28 July. Within the next few days I will make available on-line supplementary material, and explain how I created in R the word cloud in the front cover of the book. The word list I used is that for the R index from the book. I typeset the book using LaTeX. It is currently available from the publisher through the book’s web page.
This release includes fixes to several minor bugs that were reported during the last seven months. In addition to these fixes new specializations of existing methods were added to improve the consistency across the different methods and classes. The Git repository was recently moved from Bitbucket to GitHub and continuous integration using Git actions set up.
Changes from version 0.10.5 the most recent CRAN release, are:
- Fix boundary-condition bug in
- Fix handling of
na.rm = TRUEin
- Revise the computation of the default for
cps2Rfr()so that it takes into account the relative signal in
the reference spectrum.
- Add parameter
cps2irrad()so that corrupted too-short spectra can be converted if the location of missing pixels
- Add row-wise summaries for
- Add support of multiple spectra in long form to
- Add warning for handling of multiple spectra in long form to
NOTE: The updated package is on its way to CRAN.
Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/photobiology/issues
Package ‘ggpmisc’ focuses mainly on plot annotations. The new version fixes minor bugs and adds a major new feature: position functions for data aware nudging. These nudge functions were born out of an exchange of ideas with Kamil Slowikowski, the author and maintainer of the very popular package ‘ggrepel’. We are currently considering how to make them compatible with
Changes from version 0.3.8, the most recent CRAN release, are:
- Update the documentation of
- [Under development!] Link repositioned text to its original position with a segment or arrow:
geom_linked_text(). Except for
the drawing of segments or arrows this new geometry behaves as
ggplot2::geom_text(). Note: Segments and arrows are drawn only
if the position function used returns both the repositioned and original coordinates.
- Add support for advanced nudging:
position_nudge_line()compute the direction of nudging and return
both the nudged and original positions.
- Add support for simple nudging:
position_nudge_to()nudges to new user-supplied position(s);
position(s) based on user-supplies position shift. These functions return both nudged and original position(s).
Example: Nudging text labels away from a curve.
library(ggpmisc) set.seed(16532) df <- data.frame( x = -10:10, y = (-10:10)^2 + rnorm(21, 0, 4), l = letters[1:21] ) ggplot(df, aes(x, y, label = l)) + geom_point() + stat_smooth(method = "lm", formula = y ~ poly(x, 2, raw = TRUE)) + geom_text(aes(y = y, label = l), position = position_nudge_line(method = "lm", x = 0.4, y = 4, formula = y ~ poly(x, 2, raw = TRUE), direction = "split"))
Roadmap: A split of the ‘ggpmisc’ package into two packages, one including the extensions to the grammar of graphics and another one including the functions related to plot annotations based on model fitting and statistical summaries seems necessary as the package has grown to include several extensions to the grammar of graphics that are generally useful. We are also working on improved inter-operation between ‘ggpmisc’ and ‘ggrepel’.
Acknowlegement: I thank Kamil Slowikowski for his contributions of ideas and for his willingness to keep the development of our packages coordinated. This update was done in part to address questions raised and reports of bugs by users, which I thank. The tag
[ggpmisc] is in use at stackoverflow for questions related to the use this package. Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/ggpmisc/issues. Pull requests are also welcome.
Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, and vignettes in HTML format. The online vignettes include the output of all code examples, while the vignettes as included in the package, contain the output of only a subset of the code examples so as to keep the documentation at a reasonable size for package distribution.
NOTE: The new version of the package is on its way to CRAN.
Main changes since version 0.2.2 are:
- Implement support for on-the-fly retrieval of instrument descriptor and calibration data from EEPROM when calibration is not available as R objects: update
acq_irrad_interactive()and the functions it uses to retrieve and save calibration data. (Similar updates are pending for the other data acquisition functions).
- Update calibration data for MAYP11278 and MAYP112785.
- Test with old USB2000 spectrometer.
Full change history is available at: https://docs.r4photobiology.info/ooacquire/news/index.html
NOTE: This package is NOT available through CRAN.
This package is available through the r4photobiology repository and through GitHub.
Note: this version needs the recently released ‘rOmniDriver’ version 0.1.14 or later, so if this package is already installed it may need to be updated before updating or installing ‘ooacquire’ 0.2.3.
- From the binary or source packages of the released version from the CRAN-compatible repository at http://r.r4photobiology.info/.
- From sources of the under development version retrieved from the Git repository at GitHub.
Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/ooacquire/issues
This update includes several rather minor changes compared to ‘rOmniDriver’ 0.1.13:
is_timeout()as ‘OmniDriver’ does not always/any longer provide the Java methods
- Add function
- Add check for success of API initialization to function
- Add preliminary (untested) support for I2C and SPI bus.
- Move repository from BitBucket to GitHub.
- Test with USB2000 (under Windows 10, FX/2 firmware updated to 2.51.0).
- Test good with OmniDriver 2.56.
- Update README to better explain all the steps needed to install this package as well as OmniDriver.
- Update documentation to reflect that the company Ocean Optics has been renamed Ocean Insight.
‘rOmniDriver’ 0.1.13 included minor changes compared to ‘rOmniDriver’ 0.1.12:
- Add brief installation instructions to README.
- Fix bug affecting OS X and Linux.
- Improve on-load diagnosis and messages.
- Test good with OmniDriver 2.46.
The latest version source is kept in a Git repository at GitHub: https://github.com/aphalo/romnidriver/
Please, report bugs and suggest enhancements at https://github.com/aphalo/romnidriver/issues
Pull requests and reports of tests with various models of spectrometers from Ocean Insight are very welcome.