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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "figure/",
fig.height = 1
)
```
# Pollen - tools for working with aerobiological data
[](https://github.com/Nowosad/pollen/actions)
[](https://app.codecov.io/gh/Nowosad/pollen?branch=master)
[](https://cran.r-project.org/package=pollen)
[](https://cran.r-project.org/package=pollen)
```{r, echo=FALSE, eval=FALSE}
<!--[](https://codecov.io/github/hadley/lubridate?branch=master)-->
```
The **pollen** package is a set of functions for working with aerobiological data.
It takes care of some of the most widely use aerobiological calculations, including determination of pollen season limits, replacement of outliers (Kasprzyk and Walanus (2014)), and calculation of growing degree days (Baskerville and Emin (1969)).
## Installation
Get the released version from CRAN:
```R
install.packages("pollen")
```
Or the development version from github:
```R
remotes::install_github("nowosad/pollen")
```
## Examples
```{r, lib, eval=TRUE}
library(pollen)
```
```{r, dat, eval=TRUE}
data("pollen_count")
head(pollen_count)
```
### Pollen season calculation
```{r, df, eval=TRUE}
df <- subset(pollen_count, site == "Oz")
pollen_season(value = df$birch, date = df$date, method = "95")
```
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.