--- title: "The BSO model" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{The BSO model} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- BSO works structurally differently than the other models in this package. It stochastically simulates a multitude of individuals instead of only returning a result for one representative beetle. Additionally, it requires an hourly onset to function. This is why the BSO-specific phenology function `bso_phenology()` exists. While it is still possible to combine the diapause and the mortality submodels with other models, this is not the case for the onset and development submodels. ``` r library(barrks) library(tidyverse) library(terra) # function to unify the appearance of raster plots my_rst_plot <- function(rst) { plot(rst, mar = c(0.2, 0.1, 2, 5), axes = FALSE, box = TRUE, nr = 1, cex.main = 1.9, plg = list(cex = 1.8)) } pheno_bso <- bso_phenology('bso', barrks_data()) ``` # BSO-specific plots As `bso_phenology()` returns a more detailed result than `phenology()`, a few more functions are available for illustration. The stage diagram illustrates the share of the total individuals at a specific developmental stage. ``` r station <- stations_create('station 1', 234) bso_plot_stage_diagram(pheno_bso, station) ``` <div class="figure"> <img src="figures/bso-stage-diagram-1.png" alt="BSO stage diagram (the different colors represent the respective generation, generation '0' stands for the hibernating beetles)" width="100%" /> <p class="caption">BSO stage diagram (the different colors represent the respective generation, generation '0' stands for the hibernating beetles)</p> </div> The flight diagram shows the relative flight activity at a specific date. ``` r bso_plot_flight_diagram(pheno_bso, station) ``` <div class="figure"> <img src="figures/bso-flight-diagram-1.png" alt="BSO flight diagram (the colors describe which generation flies to establish a new filial generation or a sister brood respectively)" width="100%" /> <p class="caption">BSO flight diagram (the colors describe which generation flies to establish a new filial generation or a sister brood respectively)</p> </div> # Standard outputs With `bso_translate_phenology()` it is possible to translate the BSO-specific phenology to a form that corresponds to the output of `phenology()`. This makes it possible to use functions that are available to analyse phenology objects. ``` r pheno_translated <- bso_translate_phenology(pheno_bso) dates <- c('2015-04-15', '2015-06-15', '2015-08-15', '2015-10-15') get_generations_rst(pheno_translated, dates) %>% my_rst_plot() ``` <div class="figure"> <img src="figures/bso-gens-1.png" alt="Generations calculated by BSO" width="100%" /> <p class="caption">Generations calculated by BSO</p> </div>