The goal of barrks (bark beetle raster kit for seasonal development) is to calculate the phenological development of bark beetles. Rather than implementing one specific model, the package provides a collection of different models that can be chosen. Additionally, the models can be customized and combined to create an individual model. The calculations can be done spatially explicit by using raster inputs, or based on station inputs that are available as data frames. Even though most of the implemented models describe the phenology of Ips typographus, the package is not limited to particular bark beetle species. For instance, CHAPY models the phenology of Pityogenes chalcographus and the package may be extended by models for additional bark beetle species. The full documentation of barrks can be found here.
The following table lists the models that are implemented in the package.
| Model | Publication | Species | Help |
|---|---|---|---|
| BSO | Jakoby, Lischke, and Wermelinger (2019) | I. typographus |
?model.bso.apply ?model.bso.customize
|
| Lange | Lange, Økland, and Krokene (2008) | I. typographus |
?model.lange.apply ?model.lange.customize
|
| Jönsson | Jönsson et al. (2011) | I. typographus |
?model.joensson.apply ?model.joensson.customize
|
| PHENIPS | Baier, Pennerstorfer, and Schopf (2007) | I. typographus |
?model.phenips.apply ?model.phenips.customize
|
| PHENIPS‑Clim | - | I. typographus |
?model.phenips_clim.apply ?model.phenips_clim.customize
|
| RITY | Ogris et al. (2019) | I. typographus |
?model.rity.apply ?model.rity.customize
|
| CHAPY | Ogris et al. (2020) | P. chalcographus |
?model.chapy.apply ?model.chapy.customize
|
Installation
The latest released version of barrks can be installed from CRAN from within R:
install.packages('barrks')The development version of barrks can be installed from GitHub:
devtools::install_github("jjentschke/barrks")Basic Example
barrks comes with sample data that will be used below. The phenology is calculated with phenology() which takes all necessary inputs as arguments. Subsequently, the rasters of emerged generations by date can be retrieved with get_generations_rst(). terra::plot() can be used to visualize these rasters.
library(barrks)
library(tidyverse)
library(terra)
# calculate phenology
pheno <- phenology('phenips-clim', barrks_data())
# plot number of prevailing generations on 4 different dates
dates <- c('2015-04-15', '2015-06-15', '2015-08-15', '2015-10-15')
get_generations_rst(pheno, dates) %>% plot(mar = c(0.2, 0.1, 2, 5),
axes = FALSE, box = TRUE, nr = 1,
cex.main = 1.9, plg = list(cex = 1.8))
Generations plot (“1” means that the first generation hatched, “1s” means that the first generations sister brood hatched)
barrks makes it easy to plot the development of the individual generations. To illustrate that, a “shaded” variant of the phenology above is calculated and the development diagram for a specific cell (called “station” in barrks) is plotted for both phenology variants.
pheno_shaded <- phenology('phenips-clim', barrks_data(), exposure = 'shaded')
plot_development_diagram(list(sunny = pheno, shaded = pheno_shaded),
stations_create('Example', 234),
.lty = c(1, 2),
xlim = as.Date(c('2015-04-01', '2015-12-31')))
Development diagram