Miscellaneous Functions for Environmental Analyses

Small toolbox for data analyses in environmental chemistry and ecotoxicology. Provides, e.g., calibration() to calculate calibration curves and corresponding limits of detection (LODs) and quantification (LOQs) according to German DIN 32645:2008-11. texture() makes it easy to estimate soil particle size distributions from hydrometer measurements (ASTM D422-63(2007)e2).


Project Status: Active - The project has reached a stable, usable state and is being actively developed. Travis-CI Build Status License

envalysis is an R package containing miscellaneous functions for data analyses in environmental chemistry and ecotoxicology. Provides, e.g., calibration() to calculate calibration curves and corresponding limits of detection (LODs) and quantification (LOQs) according to German DIN 32645:2008-11. texture() makes it easy to estimate soil particle size distributions from hydrometer measurements (ASTM D422-63(2007)e2). Some functions of the package require ggplot2 or drc. Currently, the following functions are available:

Data manipulation and analysis

  • Confidence intervals CI()
  • Root mean square errors rmse()
  • Limit of detection (LOD) lod() and limit of quantification (LOQ) loq() as part of the calibration class to make linear calibration curves according to German DIN 32645:2008-11
  • Various sorption isotherms sorption()
  • Determine particle size distributions and soil texture classes (DIN/USDA) measured with a soil hydrometer in accordance with ASTM D422-63(2007)e2 using texture(); see vignette for details

Data presentation

  • Categorize water drop penetration times according to Bisdom et al. (1993) bisdom()
  • Report significant figures, i.e. round means and erros to the least significant digit, using signifig()
  • Clean, black-and-white ggplot2 theme for scientific publications theme_publish(); a preview is available here

Installation

envalysis is available on github. To install the package, paste the following code into your R console (requires devtools):

if (!'devtools' %in% installed.packages()[,'Package']) install.packages('devtools')
devtools::install_github('zsteinmetz/envalysis')
require(envalysis)

News

envalysis 0.3.2

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

  • Reimplementation of drc's mselect() for texture() to get rid of global variables

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

envalysis 0.3.1

NEW FEATURES

MINOR IMPROVEMENTS

  • loq() now uses iterations instead of estimating the value from lod()

BUG FIXES

  • Better handling of unbalanced designs in calibration()

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

  • make.raw(), use rep() instead ;-)

envalysis 0.3.0

NEW FEATURES

  • Starting with testthat

MINOR IMPROVEMENTS

  • signifig() supports 'siunitx' LaTeX output
  • Better data handling in calibration()
  • Updated man pages

BUG FIXES

  • theme_publish() updated to work with current ggplot2 versions
  • signifig() can handle zeros better

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

  • puri.test(), use lmer on ranks (lme4) with Type II-ANOVA (car) instead

envalysis 0.2.2

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

  • Temporary fix to make mselect() work
  • TODO: Get rid of assignment to .GlobalEnv

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

envalysis 0.2.1

NEW FEATURES

MINOR IMPROVEMENTS

  • Switch to drc package for texture curve fitting

BUG FIXES

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

envalysis 0.2.0

NEW FEATURES

  • texture class for automatic determination of particle size distribution using a hydrometer in accordance with ASTM D422-63(2007)e2

MINOR IMPROVEMENTS

  • updated theme_publish()
  • demo file added

BUG FIXES

DEPRECATED FUNCTIONS

DEFUNCT FUNCTIONS

envalysis 0.1.0

INITIAL FEATURE SET

  • Confidence intervals CI()

  • Root mean square errors rmse()

  • Limit of detection (LOD) lod()

  • Limit of quantification (LOQ) loq()

  • Various sorption isotherms sorption()

  • Convert frequency data back to raw data make.raw()

  • ANOVA on ranks according to Sen and Puri (also known as Scheirer-Ray-Hare-Test) puri.test()

  • Categorize water drop penetration times according to Bisdom et al. (1993) bisdom()

  • Report significant figures, i.e. round means and erros to the least significant digit, using signifig()

  • Clean, black-and-white ggplot2 theme for scientific publications theme_publish()

Reference manual

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install.packages("envalysis")

0.3.3 by Zacharias Steinmetz, a year ago


https://github.com/zsteinmetz/envalysis


Report a bug at https://github.com/zsteinmetz/envalysis/issues


Browse source code at https://github.com/cran/envalysis


Authors: Zacharias Steinmetz [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports drc, ggplot2

Suggests knitr, rmarkdown, MASS, testthat


See at CRAN