photobiologyWavebands 0.4.5

Package documentation web site at: https://docs.r4photobiology.info/photobiologyWavebands/

The main changes from version 0.4.4 the previous CRAN release, are:

  • Major bug fixed! The definitions of UVA1() and UVA2()  were swapped.
  • Git repository moved to GitHub

NOTE: The updated package is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://github.com/aphalo/photobiologyWavebands/issues/

 

ggpp 0.4.3

Functions included in this update provide enhamcements on existing ones. Combining nudging with stack, jitter and dodge positions was not possible within the grammar of graphics as implemented in package ‘ggplot2’. This made it difficult to add data labels to some types of plots. Which for example, can be important in plots aimed at audiences outside academia. These functions are based, with permission, on code written by M. Krassowski in the GitHub repository for ‘ggrepel’.

Other new position functions with names ending in _keep, for which normal counterparts exist, keep the original position in data, allowing the drawing of connecting segments with the geometries from package ‘ggrepel’ and with the updated geometries in ‘ggpp’.

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ggpmisc 0.4.5

Version 0.4.5 includes a minor bugfix and an edit in vignette examples, to ensure compatibility with the upcoming version of package ‘ggpp’.

Changes compared to version 0.4.4, the previous version in CRAN are:

  • Decrease version of ‘gginnards’ in suggests.
  • Edit vignette examples to allow renaming a geom exported by ‘ggpp’ (retaining backwards compatibility).

Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.

NOTE: Version 0.4.5 is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/ggpmisc/issues

photobiology 0.10.8

The package documentation web site at https://docs.r4photobiology.info/photobiology/ includes a changelog with information for each release since version 0.1.0.

This release includes bug fixes and a minor enhancement:

Changes from version 0.10.7 the most recent CRAN release, are:

  • Update functions normalize(), setNormalized() and getNormalized(), and add new function getNormalization(). These changes implement the storage in attribute normalization of the operation done.
  • Fix bug in mat2mspct() affecting matrices with more than 26 columns and without colnames set.
  • Fix a major bug in rowwise methods for collections of spectra.

NOTE: Version 0.10.8 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

ggpmisc 0.4.4

Version 0.4.4 includes enhancements. An issue raised in GitHub and a question in StackOverflow asked for the possibility of changing how fitted lines are plotted based on the “goodness” of the fit. In addition an old question in StackOverflow highlighted the need of more intuitive support for annotations based on stats::cor.test(). In addition to implementing these enhancements we continued adding support for flipping of statistics controlled through formal parameter orientation as implemented in ‘ggplot2’ since version 3.3.0.

Changes compared to version 0.4.3, the previous version in CRAN are:

  • Add new function stat_correlation() to annotate plots with correlation estimates, their P-value, a test statistic and n computed with stats::cor.test(). In addition to formatted character strings, numeric values are included in the returned data frame to facilitate conditional display.
  • Update stat_poly_line() to optionally add columns n, p.value, r.squared , adj.r.squared and method to the returned data frame. Code breaking: This statistic no longer supports fitting of splines with methods such as loess . This could potentially break user code, in which case the solution is to use stat_smooth().
  • Update stat_ma_line() to optionally add columns n, p.value, r.squared and method to the returned data frame. (As only a slope can be fitted, adj.r.squared is irrelevant.)
  • Update stat_quant_line() and stat_quant_band() to optionally add n and method columns to the returned data frame. (No exact equivalent of r.squared exists for quantile regression.)
  • Update stat_fit_residuals() to optionally return weighted
    residuals.
  • Update stat_peaks() and stat_valleys() to allow flipping with new parameter orientation.

Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.

NOTE: Version 0.4.4 is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/ggpmisc/issues

photobiologyInOut 0.4.23

Fifteen months since the previous release, this update adds support for one new spectrometer from LI-COR and multiple spectrometers from Wasatch Photonics. Updates to the tidyverse were triggering deprecation notices which are now avoided. Updates to package ‘photobiology’ revealed some minor bugs that are also fixed. Unnecessary progress messages during file realing and text scanning have been silenced.

The main changes from version 0.4.22 the previous CRAN release, are:

  • Add parameters na and ... to read_csi_data().
  • Add function read_wasatch_csv() supporting data import from long form CSV spectrum files saved by Wasatch’s Enlighten program.
  • Add function read_li180_txt() supporting data import from files saved by the LI-180 handheld array spectrometer from LI-COR.
  • Avoid spurious progress messages when reading files.
  • Track various changes in the tidyverse that deprecated functions used in this package.
  • Fix bugs in some imports from ‘photobiology’.
  • Move git repository from Bitbucket to Github.
  • Set up Github action for CRAN-checks on Windows, OS X and Ubuntu.
  • Documentation web site at http://docs.r4photobiology.info/photobiologyInOut/.

NOTE: This version of the package is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://github.com/aphalo/photobiologyinout/issues

photobiology 0.10.7

The package documentation web site at https://docs.r4photobiology.info/photobiology/ includes a changelog with information for each release since version 0.1.0.

This release includes enhancements related to the computations of reference evapotranspiration:

Changes from version 0.10.6 the most recent CRAN release, are:

  • Add function ET_ref() for computation of reference
    evapotranspiration, implementing the original FAO56 formulation of the Penman-Monteith method as well as modified in 2005 for tall and short vegetation according to ASCE-EWRI. The formulation is that for ET expressed in mm/h, but modified to use as input flux rates in W/m2 and pressures expressed in Pa.
  • Add function net_radiation() that computes the long wave net radiation balance if downwelling long wave radiation is available and otherwise estimates it.
  • Add function irrad_extraterrestrial() that computes down-welling solar irradiance on a horizontal plane at the top of the atmosphere based on the Sun to Earth distance.
  • Revise function sun_angles() to also return the Sun to Earth distance.

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

ggpmisc 0.4.3

Version 0.4.3 contain the bug fix implemented in version 0.4.2-2, which did not make it to CRAN. (See bug listed under 1. in the post ggpmisc 0.4.2.)

New

  1. Add stat_ma_line() and stat_ma_eq() implementing support for major axis (MA), standard major axis (SMA), ranged major axis (RMA) and ordinary least squares (OLS) using function lmodel2() from package ‘lmodel2’.

Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.

NOTE: Version 0.4.3 is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/ggpmisc/issues

ggpmisc 0.4.2

During the major updates to 0.4.0 and 0.4.1 some bugs slipped through various tests. Versions 0.4.2, 0.4.2-1 and 0.4.2-2 contain fixes to these bugs. The bug fixed in 0.4.2-2 triggered an error only when R had been built with specific compilers.

Bugs fixed

  1. Error in stat_poly_eq() and stat_quant_eq() under some Linux builds of R, including when used in RStudio Cloud. This bug did not affect Windows.
  2. Failure to find after_stat() when instead of attaching the package with library(ggpmisc) statistics were called using the ggpmisc::<name> notation.
  3. Remove or convert to suggests some dependencies no longer needed after the split of ‘ggpp’.

Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.

NOTE: Version 0.4.2-2 addressing all three bugs was not submitted to CRAN but instead the fix was released in version 0.4.3 now in CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/ggpmisc/issues

ggpmisc 0.4.1

Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.

Overview

This update is special in that it was built with the input of excellent ideas and code contributions from users. I learnt a lot myself and these improvements have made ‘ggpmisc’ more useful in general and for myself. Support for quantile regression is now, I hope, close to its final shape. Support for the new ‘ggplot2’ feature: orientation is implemented in the statistics where it is most useful, and can be also be changed, more intuitively, through the model formula. Of the planned enhancements, implementing support for major axis regression, remains in the to do list. Both stat_poly_eq() and stat_quant_eq() now return additional labels, plus some numeric values to facilitate conditional display. Much of the code used to generate the text labels has been improved, and markdown formatting tested.

The suggestion from Mark Neal of adding support for quantile regression partly addressed in ggpmisc 0.4.0 has lead to additional enhancements in this version. The idea of supporting confidence bands for quantile regression came from Samer Mouksassi who also provided code and examples for different types of quantile regression. Additional suggestions from Mark Neal, Carl and other users have lead to bug fixes as well as to an interface with better defaults for arguments (see issue #1).

Changes compared to ‘ggpmisc’ 0.4.0

Enhancements

  • Support robust regression using rlm and the use of function objects as argument to method in stat_poly_eq().
  • Support in stat_poly_eq() and stat_quant_eq() formula = x ~ y and other models in which the explanatory variable is y in addition to models with x as explanatory variable.
  • stat_poly_eq() and stat_quant_eq() now pass to the geom by default a suitable value as argument to parse depending on output.type (enhancement suggested by Mark Neal in issue #11).
  • stat_poly_eq() and stat_quant_eq() return the coefficient estimates as numeric columns in data when output.type = "numeric"  (problem with coefs.ls reported by cgnolte in issue #12).
  • stat_poly_eq() now supports optional use of lower case for r2 and p-value.
  • Revise stat_poly_eq() and stat_quant_eq() so that by default they keep trailing zeros according to the numbers of significant digits given by coef.digits. A new parameter coef.keep.zeros can be set to FALSE to restore the deletion of trailing zeros. Trailing zeros in the equation will be rendered to the plot only if output.type is other than "expression".
  • Add stat_poly_line(),  a new interface to ggplot2::stat_smooth() accepting formula = x ~ y and other models in which the explanatory variable is y rather than x or setting orientation = "y". In contrast to ggplot2::stat_smooth(), stat_poly_line() has always "lm" as default method.
  • Add stat_quant_line() which is an adaptation of ggplot2::stat_smooth() and ggplot2::stat_quantile() accepting formula = x ~ y and other models in which the explanatory variable is y rather than x or setting orientation = "y" to fit models with x as explanatory variable. This change makes it possible to add to a plot a double quantile regression. stat_quant_line() supports plotting of confidence bands for quantile regression using ggplot2::geom_smooth() to create the plot layer.
  • Add stat_quant_band() which plots quantile regressions for three quantiles as a band plus a line, accepting formula = x ~ y and other models in which the explanatory variable is y rather than x or setting orientation = "y" to fit models with x as explanatory variable.
  • Add support for quantile regression rq, robust regression rlm, and resistant regression lqs and function objects to stat_fit_residuals() and stat_fit_deviations().
  • Support use of stat_fit_residuals() and stat_fit_deviations() with formula = x ~ y and other models in which the explanatory variable is y in addition to models with x as explanatory variable.
  • Add weights to returned values by stat_fit_residuals() and stat_fit_deviations() and add support for the weight aesthetic as input for parameter weights of  model fit functions.

Bugs fixed

  • Fix bug in stat_poly_eq() and stat_quant_eq() resulting in mishandling of formulas using the + 0 notation (reported by orgadish in issue #10).
  • Fix bug in stat_poly_eq() and stat_quant_eq() resulting in bad/non-syntactical character strings for eq.label when output.type was different from its default of "expression".

Documentation web site at http://docs.r4photobiology.info/gginnards/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.

NOTE: The new version of the package is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/gginnards/issues

ggpp 0.4.2

Documentation web site at http://docs.r4photobiology.info/ggpp/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.

Overview

The initial implementation and user interface of three apply statistics first introduced in ‘ggpmisc’ 0.3.6 has been revised to expand their usefulness and to make them less error-prone, while the
fourth one is now defunct.

Changes compared to ‘ggpp’ 0.4.1

Enhancements

  • Update stat_apply_group() to support summary functions like quantile() that return vectors with more than one value but shorter than the original number of observations.
  • Update stat_summary_xy() and stat_apply_group() to return NA x and/or y when .fun.x or .fun.y are not passed anargument. This is a code breaking change with respect to the previous (unstable) version.
  • Update stat_summary_xy() and stat_centroid() to support functions that return a one row data frame, like those defined in ‘ggplot2’ to be passed as argument to parameter fun.data of ggplot2::stat_summary(), such as mean_se, mean_cl_boot, etc.

Bugs fixed

  • Fix bug in stat_centroid(), stat_summary_xy() and stat_apply_group() resulting in the return of a long data frame with NA values instead of a data frame with fewer rows.
  • Remove stat_apply_panel() , as it was redundant. (Grouping can be modified per layer when needed.)

Warning

The default argument for geom in stat_centroid() is likely to change in the near future. Otherwise, the three statistics can be considered now stable.

Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/ggpp/issues. Pull requests are also welcome.

NOTE: The updated ‘ggpp’ (0.4.2) is on its way to CRAN. The latest development version of the package can be installed from GitHub.

remotes::install_github("aphalo/ggpp")

ggpp 0.4.1

The package documentation web site at: https://docs.r4photobiology.info/ggpp/ includes a changelog.

Compared to ‘ggpp’ 0.4.0, the following changes have been introduced.

  • Update compute_just2D() and compute_just() to work with any value for the angle aesthetic, as in ‘ggplot2’ (>= 3.3.5).
  • Fix bug in geom_table() that would cause text left or right justified to be clipped when the text in a cell was very long (reported by dryguy). (Cell padding still needs improvement.)

Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/ggpp/issues. Pull requests are also welcome.

NOTE: The updated ‘ggpp’ (0.4.1) is on its way to CRAN. The latest development version of the package can be installed from GitHub.

remotes::install_github("aphalo/ggpp")