bumbl
implements a model for bumblebee colony growth described in
Crone and Williams 20191. The brkpt
function models colony
growth as having a change point at some time, tau, where the colony
switches from growth and worker production to gyne production. The
bumbl
function applies this model to a data frame of data from
multiple colonies, allowing for each colony to have it’s own tau and
returns the original data augmented with coefficients from the
changepoint model.
This is still in very early development, so use at your own risk.
More bumblebee related functions to come…
You can install this development version of bumbl
with:
devtools::install_github("Aariq/bumbl", build_vignettes = TRUE)
View the package vignette with:
library(bumbl)
vignette("bumbl")
View the bomubs
dataset
head(bombus)
#> # A tibble: 6 x 10
#> site colony wild habitat date week mass d.mass floral_resources
#> <fct> <fct> <dbl> <fct> <date> <int> <dbl> <dbl> <dbl>
#> 1 PUT2 9 0.98 W 2003-04-03 0 1910. 0.1 27.8
#> 2 PUT2 9 0.98 W 2003-04-09 1 1940 30.6 27.8
#> 3 PUT2 9 0.98 W 2003-04-15 2 1938 28.6 27.8
#> 4 PUT2 9 0.98 W 2003-04-22 3 1976. 67.1 27.8
#> 5 PUT2 9 0.98 W 2003-05-01 4 2010. 101. 7.96
#> 6 PUT2 9 0.98 W 2003-05-07 5 2143 234. 7.96
#> # … with 1 more variable: cum_floral <dbl>
Using a subset of the bombus
dataframe to estimate the week (tau) that
colonies switch to reproduction
bombus2 <- bombus[bombus$colony %in% c(9, 82, 98, 35), ]
bumbl(bombus2, colonyID = colony, t = week, formula = d.mass ~ week)
#> Warning: glm.fit: algorithm did not converge
#> Warning: glm.fit: algorithm did not converge
#> # A tibble: 4 x 6
#> colony tau logN0 logLam decay logNmax
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 35 9.49 3.68 0.209 -0.295 5.61
#> 2 82 7.43 2.97 0.394 -0.503 5.83
#> 3 9 6.43 2.30 0.610 -0.690 6.18
#> 4 98 6.37 1.27 0.570 -0.578 4.90
Keep the original data and plot the results
results <- bumbl(bombus2, colonyID = colony, t = week, formula = d.mass ~ week, augment = TRUE)
#> Warning: glm.fit: algorithm did not converge
#> Warning: glm.fit: algorithm did not converge
par(mfrow = c(2, 2))
bumbl_plot(results)
par(mfrow = c(1, 1))
1Crone, E. E., and Williams, N. M. (2016). Bumble bee colony dynamics: quantifying the importance of land use and floral resources for colony growth and queen production. Ecol. Lett. 19, 460–468. https://doi.org/10.1111/ele.12581