As the latest version (0.4.15) of our package ‘photobiologyInOut’ supports the automatic import of the files returned by the Quick TUV Calculator we show here how to produce such files, and link to an example of their import and plotting in R.
The TUV model is a well known model of atmospheric chemistry that also simulates the solar spectrum within the atmosphere or at ground level using a radiation transfer approach. The model is written in FORTRAN and available for local use. When one needs just to compute a few spectra with no special conditions, it is possible to use the on-line interface provided by the National Centre of Atmospheric Research (NCAR) under the name of Quick TUV Calculator.
This interface is easy to use once one understands the different options and required input data. (This video, authored by Pedro J. Aphalo is published with the express permission of Sasha Madronich, creator of the TUV model.)
An R notebook demonstrating how the solar spectrum is affected by variation in the atmospheric composition, solar elevation and observer elevation is available for reading and/or download. The R code used in embedded in this HTML file. Click on the image below to access the article. (The article is still a draft. Corrections and suggestions for improving it are most welcome.)
Functions earlier included in ‘ggpmisc’ (< 0.3.0) related to debugging and low level manipulation of ggplot objects have been moved to package ‘gginnards’. The functions that remain in ‘ggpmisc’ (>= 0.3.0) are related to annotation of plots with fitted-model equations, fit diagnosis, ANOVA and summary tables, highlighting and labelling of peaks and valleys in curves, and local density-based highlighting or labelling in scatter plots. Additionally specializations of the ggplot() constructor allow on-the-fly conversion of time-series and geom_table() makes it possible to add tables to plots respecting the the Grammar of Graphics paradigm.
The enhancements in this update to ‘ggpmisc’ are made possible by changes to ‘ggplot2’ (>= 3.0.0) made while adding support for sf (simple features). Not all extensions to ‘ggplot2’ have been updated yet to be compatible with the new version of ‘ggplot2’ so if you need them, you may need to wait before updating to ‘ggplot2’ (3.0.0) and consequently also before updating to this version of ‘ggpmisc’.
This time I include some example plots taken from the documentation of the package. In all cases annotations are generated automatically, but formatting is flexible. Larger plots are linked to the thumbnails.
Main changes since ‘ggpmisc’ (0.2.17) the previous CRAN release.
Add geom_table() a geom for adding a layer containing one or more tables to a plot panel.
Add stat_fit_tb() a stat that computes a tidy tabular version of the summary table or ANOVA table from a model fit.
Add support for "weight" aesthetic in stat_poly_eq() so that weights can be passed to lm() (fixing bug reported by S.Al-Khalidi).
Add support for column selection and renaming to stat_fit_tb().
Add new statistic stat_fmt_tb() for formatting of tibbles for addition to plots as tables.
Rename stat_quadrat_count() into stat_quadrant_count() (fix miss-spelling).
Move debug stats and geoms to package ‘gginnards’.
Move plot layer manipulation functions to package ‘gginnards’.
NOTE: The new version of ‘ggpmisc’ is on its way to CRAN and should be available for download later in the week.