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# Pollen - tools for working with aerobiological data

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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:

``` r
install.packages("pollen")
```

Or the development version from github:

``` r
remotes::install_github("nowosad/pollen")
```

## Examples

``` r
library(pollen)
```

``` r
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

``` r
df <- subset(pollen_count, site == "Oz")
pollen_season(value = df$birch, date = df$date, method = "95")
#>    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](https://jakubnowosad.com/pollen/articles/intro.html).

### Growing degree days (GDD) calculation

Examples of Growing degree days (GDD) calculations can be found in [the
second package
vignette](https://jakubnowosad.com/pollen/articles/gdd.html).

## Citation

To cite the `pollen` package in publications, please use:

Nowosad, Jakub (2019). pollen: Analysis of Aerobiological Data. R
package version 0.71.0. <https://github.com/Nowosad/pollen>

LaTeX/BibTeX version can be obtained with:

    library(pollen)
    citation("pollen")

## Contributions

[Feel free to submit issues and enhancement
requests.](https://github.com/Nowosad/pollen/issues)

## 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.
