bumbl

R package for modeling bumblebee colony growth.

https://github.com/aariq/bumbl

Keywords

Repository

R package for modeling bumblebee colony growth.

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# Tools for modeling bumblebee colony growth



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`bumbl` implements a model for bumblebee colony growth described in Crone and Williams 2016^1^.
It models colony growth as having a switchpoint at some time, *tau*, where the colony switches from growth and worker production to gyne production and decline.
Currently `bumbl()` works by fitting a separate switchpoint model to each colony, optimizing the switchpoint, *tau*.
It returns the optimal switchpoint, growth, and decline rates for each colony.
Because the current version of `bumbl()` works by fitting a separate GLM to each colony, if covariates are included, their estimates could vary significantly among colonies.
Stay tuned for future developments that may allow estimating a single value of a covariate but different values of growth and decline rates and *tau* for each colony.

## Contributing

I'm looking for collaborators who know (or are willing to let me teach them) how to use git and GitHub and who have an interest in taking over as maintainer of this package.
I'm not a bumblebee biologist, so I would especially love a collaborator who works on bumblebees or other organisms with a similar growth, switch, decline lifecycle.

I also welcome contributions including bug-fixes, improvement of documentation, additional features, or new functions relating to bumblebee ecology and demography from anyone!

### Roadmap

-   [x] Write `bumbl()` function to model colony growth with switchpoint
-   [x] Finish documentation and vignette(s)
-   [x] [rOpenSci review]()
-   [x] Regroup with Elizabeth Crone to discuss current behavior of `bumbl()`
-   [x] Release v0.1.0 and archive on Zenodo
-   [x] Bug fixes
-   [x] Submit v1.0.0 of package to CRAN
-   [x] Write a manuscript for JOSS ([desk-reject](https://github.com/openjournals/joss-reviews/issues/3532), out of scope)
-   [x] Release minor version to CRAN to update citation
-   [ ] Possibly re-work internals of `bumbl()`? (see [\#58](https://github.com/Aariq/bumbl/issues/58) and [notes](https://github.com/Aariq/bumbl/blob/master/notes/single-model-rework-notes.Rmd))
-   [ ] Submit v2.0.0 of package to CRAN

Other possible areas of improvement:

-   Extend `bumbl()` to work with GLMMs
-   Test significance of switchpoint (see [\#62](https://github.com/Aariq/bumbl/issues/62))
-   Extend `bumbl()` to work with dates, datetimes, or other timeseries classes (see [\#46](https://github.com/Aariq/bumbl/issues/46))

## Installation

You can install `bumbl` with:

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

Or install the development version with:

``` r
devtools::install_github("Aariq/bumbl", build_vignettes = TRUE)
```

## Getting started

View the package vignette with:

``` r
library(bumbl)
vignette("bumbl")
```

```{r include=FALSE}
# library(bumbl)
devtools::load_all()
```

View the `bomubs` dataset

```{r}
head(bombus)
```

### Example use

Using a subset of the `bombus` dataframe to estimate the week (tau) that colonies switch to reproduction

```{r}
bombus2 <- bombus[bombus$colony %in% c(9, 82, 98, 35), ]
results <- bumbl(bombus2, colonyID = colony, t = week, formula = d.mass ~ week)
results
```

Plot the results

```{r}
par(mfrow = c(2, 2))
plot(results)
par(mfrow = c(1, 1))
```

# References

^1^Crone, 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.


------------------------------------------------------------------------

Please note that the `bumbl` project is released with a [Contributor Code of Conduct](https://github.com/Aariq/bumbl/blob/master/CODE_OF_CONDUCT.md).
By contributing to this project you agree to abide by its terms.

Owner

Citation (CITATION.cff)

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.4.1
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------

cff-version: 1.2.0
message: 'To cite package "bumbl" in publications use:'
type: software
license: CC-BY-4.0
title: 'bumbl: Tools for Modeling Bumblebee Colony Growth and Decline'
version: 1.0.4
doi: 10.5281/zenodo.4545782
abstract: Bumblebee colonies grow during worker production, then decline after switching
  to production of reproductive individuals (drones and gynes). This package provides
  tools for modeling and visualizing this pattern by identifying a switchpoint with
  a growth rate before and a decline rate after the switchpoint. The mathematical
  models fit by bumbl are described in Crone and Williams (2016) <doi:10.1111/ele.12581>.
authors:
- family-names: Scott
  given-names: Eric R.
  email: scottericr@gmail.com
  orcid: https://orcid.org/0000-0002-7430-7879
preferred-citation:
  type: generic
  title: 'bumbl: Tools for modeling bumblebee colony growth and decline'
  authors:
  - family-names: Scott
    given-names: Eric R.
    email: scottericr@gmail.com
    orcid: https://orcid.org/0000-0002-7430-7879
  year: '2021'
  publisher:
    name: Zenodo
  version: 1.0.4
  doi: 10.5281/zenodo.4545782
  url: https://doi.org/10.5281/zenodo.4545782
repository: https://CRAN.R-project.org/package=bumbl
repository-code: https://github.com/Aariq/bumbl
url: https://github.com/Aariq/bumbl
contact:
- family-names: Scott
  given-names: Eric R.
  email: scottericr@gmail.com
  orcid: https://orcid.org/0000-0002-7430-7879
keywords:
- bumblebee
- demography
- glm
- switchpoint
references:
- type: article
  title: 'Bumble bee colony dynamics: quantifying the importance of land use and floral
    resources for colony growth and queen production'
  authors:
  - family-names: Crone
    given-names: Elizabeth E.
    email: elizabeth.crone@tufts.edu
  - family-names: Williams
    given-names: Neal M.
  journal: Ecology Letters
  year: '2016'
  volume: '19'
  issue: '4'
  doi: 10.1111/ele.12581
  start: 460-468

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