pollimetry v1.0.1

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Estimate Pollinator Body Size and Co-Varying Ecological Traits

Tools to estimate pollinator body size and co-varying traits. This package contains novel Bayesian predictive models of pollinator body size (for bees and hoverflies) as well as preexisting predictive models for pollinator body size (currently implemented for ants, bees, butterflies, flies, moths and wasps) as well as bee tongue length and foraging distance, total field nectar loads and wing loading. An additional GitHub repository <https://github.com/liamkendall/pollimetrydata> provides model objects to use the bodysize function internally. All models are described in Kendall et al (2018) <doi:10.1101/397604>.

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DOI Travis build status CRAN status

Pollimetry: Predictive allometry for pollinating insects

Tools to estimate pollinator body size as well as bee tongue length and foraging distances.

To install

if (!requireNamespace("devtools")) {
  install.packages("devtools")
}
devtools::install_github("liamkendall/pollimetry")
library(pollimetry)

We also recommend downloading the data package so the bodysize function runs faster

#Loading is slow (~ up to 26 Mb per model file)
if (!requireNamespace("devtools")) {
  install.packages("devtools")
}
devtools::install_github("liamkendall/pollimetrydata")
library(pollimetrydata)

Estimating body size

The bodysize function uses Bayesian generalised linear mixed models (BGLMMs) to provide posterior estimates (along with S.E. and 95% credible intervals) of pollinator body size (i.e. dry body weight (mg)) using the intertegular distance (ITD), species taxonomy or phylogeny (bees only type="phylo"), sex and biogeography (at present only Australia, Europe, North America and South America). Estimates (and variance components) are returned as four additional columns bound to the original dataframe. These models will be periodically updated using novel data as and when it becomes available. See bodysize details for more information.

Pre-existing equations for Diptera, Hymenoptera and Lepidopteran taxa using body length (lengthsize), body length * width (lengthwidthsize) and head width (headwidthsize) are also provided.

Allometric traits

Users can predict bee tongue length (tonguelength) from Cariveau et al. (2015) and bee foraging distances (foragedist) from equations described in van Nieuwstadt and Iraheta (1996) for Meliponini, Greenleaf et al. (2007) and Guedot et al. (2009) for Osmia spp.

Future traits of interest

Many other ecological traits crucial to pollination are likely to be allometric. Therefore, we hope to examine these unexplored body size - trait relationships with the aim of including new predictive models in the future.

Example

Install and call the pollimetry library as follows:

devtools::install_github("liamkendall/pollimetry")
library(pollimetry)

This will install pollimetry and it's dependency brms. You can check the raw data used in the paper as follows:

load("data/pollimetry_dataset.rdata")
head(pollimetry_dataset)
?pollimetry_dataset #for metadata.

Let's predict some body sizes from a dataframe using taxonomy:

(example <- cbind.data.frame(IT = c(1.2, 2.3), 
                            Sex = c("Female","Male"), 
                            Family = c("Apidae","Andrenidae"),
                            Region = c("NorthAmerica","Europe"),
                            Species = c("Ceratina_dupla","Andrena_flavipes")))

bodysize(x = example, taxa = "bee", type = "taxo")
?bodysize

Now let's calculate some foraging distances based only in ITDs:

foragedist(c(10,5,2), type = "GreenleafAll")

Other functions included are tonguelength() for estimating tongue length and older allometric equations: headwidthsize(), lengthwidthsize(), and lengthsize().

Functions in pollimetry

Name Description
nectarload Converts bee body length (mm) to total field nectar load (ul).
wingloading Converts intertegular distance (mm) to wing loading (mg mm2).
pollimetry_dataset Body size and intertegular distance measurements of ~4500 pollinating insect specimens.
tonguelength Converts ITD (cm) to tongue length for bees.
bodysize Converts the intertegular distance (IT) and co-variates to body size in dry weight (mg) for bees or hoverflies.
foragedist Converts body weight to measures of foraging distance for bees.
lengthwidthsize Converts pollinator body length*body width to body size (dry weight (mg)).
headwidthsize Converts pollinator (Diptera, Hymenoptera and Lepidoptera) head width (mm) to body size (dry weight (mg)).
lengthsize Converts body length to body size (body weight (mg)) for three pollinating insect groups (Diptera, Hymenoptera and Lepidoptera).
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Details

Type Package
Date 2018-11-19
License GPL (>= 2)
LazyData true
RoxygenNote 6.1.1
NeedsCompilation no
Packaged 2018-11-19 01:40:57 UTC; liamkendall
Repository CRAN
Date/Publication 2018-11-19 12:20:08 UTC

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