Pollen - tools for working with aerobiological data

The pollen package is a set of functions for working with aerobiological data. It takes care of some of the most widely use aerobiological calculations, including determination of pollen season limits, replacement of outliers (Kasprzyk and Walanus (2014)), and calculation of growing degree days (Baskerville and Emin (1969)).

Installation

Get the released version from CRAN:

install.packages("pollen")

Or the development version from github:

remotes::install_github("nowosad/pollen")

Examples

library(pollen)

data("pollen_count")
head(pollen_count)
#>   site       date alder birch hazel
#> 1   Oz 2007-01-01     0     0     0
#> 2   Oz 2007-01-02     0     0     0
#> 3   Oz 2007-01-03     0     0     0
#> 4   Oz 2007-01-04     0     0     0
#> 5   Oz 2007-01-05     0     0     0
#> 6   Oz 2007-01-06     0     0     0

Pollen season calculation

df <- subset(pollen_count, site == "Oz")
pollen_season(value = df$birch, date = df$date, method = "95")
#> Warning: `arrange_()` was deprecated in dplyr 0.7.0.
#> Please use `arrange()` instead.
#> See vignette('programming') for more help
#>    year      start        end
#> 1  2007 2007-03-31 2007-05-03
#> 2  2008 2008-04-19 2008-05-07
#> 3  2009 2009-04-09 2009-05-09
#> 4  2010 2010-04-14 2010-05-07
#> 5  2011 2011-04-20 2011-05-17
#> 6  2012 2012-04-09 2012-05-14
#> 7  2013 2013-04-09 2013-05-09
#> 8  2014 2014-04-08 2014-05-10
#> 9  2015 2015-04-08 2015-04-30
#> 10 2016 2016-04-06 2016-05-09

More examples of pollen seasons’ calculations can be found in the first package vignette.

Growing degree days (GDD) calculation

Examples of Growing degree days (GDD) calculations can be found in the second package vignette.

Contributions

Feel free to submit issues and enhancement requests.

References

• Baskerville, G., & Emin, P.: 1969. Rapid Estimation of Heat Accumulation from Maximum and Minimum Temperatures. Ecology, 50(3), 514-517. https://doi.org/10.2307/1933912
• Kasprzyk, I. and A. Walanus.: 2014. Gamma, Gaussian and Logistic Distribution Models for Airborne Pollen Grains and Fungal Spore Season Dynamics, Aerobiologia 30(4), 369-83.