added functions:
add_wavelet adds a wavelet plot to a larger plot
add_wavelet_avg adds the average wavelet power to a larger plot
curve2time_unc converts a tracked period curve to time taking the uncertainty of the curve into account
curve2time_unc_anchor converts a tracked period curve to time by taking the uncertainty of the curve and anchored radiometric date into account
dur_gaps calculates the duration off a hiatus based on the missing part of an astronomical cycle
geo_col generate standard color codes for the Geological Time Scale
geo_loc generates ages for the boundaries of a geochronological subdivision
geo_mid generate the mean age of a geological subdivision
lithlog_disc discriticizes lithologs from a block pattern to a continous signal which allows it to analyzed using spectral analysis techniques
minimal_tuning Creates an age model using the minimal tuning technique. This means that the distance between 2 peaks of an extracted cycle is set to duration of the interpreted astronomical cycle
retrack_wt_MC Re-track cycles using a Monte-Carlo simulation Then input is an already tracked period of an astronomical cycle and the wavelet in which it was tracked. the already tracked periods are combined to create a pseudo-curve which is then re-tracked in one of the wavelets (randomly selected) the result is a bunch of retracked curves
sedrate2tune converts a data set using the sedimentation rate to a tuned age-model
updated functions:
Hilbert_transform added side padding to avoid edge effects
plot_wavelet added additional color plotting option
plot_win_fft added additional color plotting option
track_period_wavelet added additional color plotting option added the option to select any point within the plot
since submission: ## CRAN package check Kurt Hornik writes:
Still open …
Please fix before 2023-09-10 to safely retain your package on CRAN.
Dear maintainer,
R-devel will soon find
Found the following (possibly) invalid DOIs: DOI: 1016/j.epsl.2018.02.010 From: man/mag.Rd Status: 404 Message: Not Found DOI: doi:10.1190/1.1441328 From: man/analyze_wavelet.Rd man/plot_wavelet.Rd Status: 404 Message: Not Found DOI: doi:10.1190/1.1441329 From: man/analyze_wavelet.Rd Status: 404 Message: Not Found DOI: doi.org/10.1051/0004-6361/201117504 From: man/astro_anchor.Rd Status: 404 Message: Not Found
for you package: previously DOIs in Rd files were missed in the CRAN submission checks.
Please fix.
When doing so, please note that for the valid DOIs you do things like
win_fft.Rd:time series analysis <>
where you enclose the inside <…>: please don’t do this (and drop the extra doi:). One needs to do e.g.
doi:10.1016/j.earscirev.2018.11.015
in the package DESCRIPTION Description, but should do
in Rd.
Please fix before 2023-08-23.
Best -k
The (possibly) invalid links were fixed The way links should be written in the documentation and documentation is also adjusted to be inline with CRAN guidelines
Examples contained dontrun{} which were replaced with donttest{} when examples are executed in >5 seconds otherwise dontrun{} is removed completely. Searched all files using CTR:+SHIFT+F to see if dontrun{} was still present and dontrun{} was not found after replacement
Checked and can now confirm that only 1 core is used by default in functions which can run using multiple cores by default the parameter to run multiple cores is set to (run_multicore = FALSE). In examples run_multicore is set to; (run_multicore = FALSE).
Information messages were still written to the console which is replaced with the if(verbose)cat(..) option for interactive scripts where printing text to the console is important text is added to the examples and arguments of text indicating that functionality is reduced if verbose is set to FALSE meaning that only basic functionality is maintained
package names, software names and API are now written in quotes e.g. ‘—-’.
some plotting functions opened new windows for new plots, these plot would not show up in Rmarkdown documents. An option was added to turn off the open plots in new windows.
added support for more color palette options. added support to switch the x and y-axis when plotting.
Please always write package names, software names and API (application programming interface) names in single quotes in title and description. e.g: –> ‘WaverideR’ Please note that package names are case sensitive.
You still have example wrapped within dontrun{} which I think is not necessary. Please unwrap the examples if they are executable in < 5 sec, or replace dontrun{} with donttest{} or explain why dontrun{} is necessary for these examples.
You still write information messages to the console that cannot be easily suppressed. It is more R like to generate objects that can be used to extract the information a user is interested in, and then print() that object. Instead of print()/cat() rather use message()/warning() or if(verbose)cat(..) (or maybe stop()) if you really have to write text to the console. (except for print, summary, interactive functions)
Please confirm that you do not use more than 2 cores in your examples, vignettes, etc.
General changes:
Added References both in the description file of the package and the description texts of individual functions.
Changed print() statements to if(verbose)cat(..) to allow suppression of messages in the console An exception was made for the astro_anchor function where cat() is used instead because because “feedback” needs to entered into the console
spell-checked code and removed misspelled words
Removed dontrun from examples and replaced with donttest when examples are executed in >5 seconds otherwise dontrun is removed and extra code is added. Many examples still have donttest added to them as the examples of functions use real-world examples of already published records. Using real-world example data-sets is preferred over synthetic data sets as
Previous iterations of functions often contained code which changed the user’s options. by adding oldpar <- par(no.readonly = TRUE) followed by on.exit(par(oldpar)) to functions this issue is avoided. This however makes images/plots uneditable after plotting. To keep images/plot editable the parameter “keep_editable” is added to functions which generate images/plots, If keep_editable is set to TRUE plot/images remain editable but by default keep_editable is set to FALSE to avoid changing the user’s options.
Functions which have the option to run on multiple cores have the parameter “run_multicore” added to them. On default run_multicore is set to FALSE to avoid running the process on multiple cores overloading the user’s computer. In all examples run_multicore is set to FALSE meaning that only 1 core is used when a function is executed.
Function specific changes:
NEWS.md file to track changes to the
package.