| Title: | Estimate Pollinator Body Size and Co-Varying Ecological Traits |
|---|---|
| Description: | 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) and bee foraging range, as well as preexisting predictive models for pollinator body size (currently implemented for ants, bees, butterflies, flies, moths and wasps), bee tongue length, foraging range, total field nectar loads and wing loading. An additional GitHub repository <https://github.com/liamkendall/pollimetrydata> provides model objects to use the bodysize and foraging.range functions internally. All models are described in Kendall et al. (2019) <doi:10.1002/ece3.4835> & Kendall et al. (2022) <doi:TBC>. |
| Authors: | Liam Kendall [aut, cre], Ignasi Bartomeus [aut] |
| Maintainer: | Liam Kendall <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.1.0 |
| Built: | 2024-11-12 04:11:34 UTC |
| Source: | https://github.com/liamkendall/pollimetry |
Calculates body size in dry weight (mg) from Kendall et al. (2018) using ITD (and co-variate) values.
bodysize(x, taxa, type)bodysize(x, taxa, type)
x |
A data frame with columns containing 'ITD' values and Sex ('Male' or 'Female'). Optional attributes depending on model choice: Taxonomy ('Family' for bees or 'Subfamily for hoverflies), 'Region' (Currently only "NorthAmerica", "SouthAmerica", "Australasia" and "Europe" implemented) and 'Species' ("Genus_species" format). Non-implemented regions and/or species are acceptable. See details. |
taxa |
A vector specifying insect taxa of interest, can be either "bee" for bee models and "hov" for hoverfly models |
type |
A vector specifying model type to be used: for bees this can be either "taxo" for the full taxonomic model, "phy" for the full phylogenetic model, "sex" for the reduced sexual dimorphic model or "ITD" for the ITD-only model. In hoverflies: this can either be "taxo" for the full taxonomic model, "sex" for the reduced sexual dimorphic model or "ITD" for the ITD-only model. |
For bees, type option 'taxo' requires ITD, sex and taxonomic family. Type option 'phylo' only requires ITD and Sex to run but should be only be used for with Species (and Region) included in model formulation n.b. the function checks for contained species.
For hoverflies, type 'taxo' requires ITD, Subfamily and Sex for each specimen. Type "ITD" for both taxa only requires ITD values (Optional: region and species but check 'setdiff'). If specimens are from included regions or species (see above) we recommend including these as additional columns. Estimates (and variance components) are returned as four additional columns bound to the original dataframe. In the likely case that non-represented taxa and regions are included in inputted datasets, 'allow_new_levels' is set to true for all models. Estimates will then be modelled with group-level uncertainty in the predictions based on the variation of the existing levels. This function makes use of external model objects hosted on GitHub. In the case of slow loading, we recommend you download the pollimetrydata package from https://github.com/liamkendall/pollimetrydata.
The original dataframe (x) along with additional columns of body size, and 90
Kendall et al. (2019) Pollinator size and its consequences: Robust estimates of body size in pollinating insects. Ecology and Evolution, 9(4), 1702-1714. doi:10.1002/ece3.4835.
ITD=c(1.3,2.3) Sex=c("Female","Male") Subfamily=c("Syrphinae","Eristalinae") Region=c("Australasia","Europe") Species=c("Sphaerophoria_macrogaster","Myathropa_florea") example.data <- data.frame(ITD,Sex,Subfamily,Region,Species) bodysize(x=example.data,taxa="hov",type="taxo")ITD=c(1.3,2.3) Sex=c("Female","Male") Subfamily=c("Syrphinae","Eristalinae") Region=c("Australasia","Europe") Species=c("Sphaerophoria_macrogaster","Myathropa_florea") example.data <- data.frame(ITD,Sex,Subfamily,Region,Species) bodysize(x=example.data,taxa="hov",type="taxo")
A dataset containing measurements of foraging range (m), intertegular distance (mm), sociality and metadata for 101 bee species (425 estimates).
forage_datasetforage_dataset
An object of class data.frame with 425 rows and 20 columns.
Kendall et al. (2022). Sociality and body size determine the potential and realized foraging ranges of bees. TBC.#'
'r lifecycle::badge("deprecated")' This function is now deprecated and has been superceded by 'foraging.range'
Calculates foraging range from Greenleaf et al. (2007) using intertegular distance (ITD) values, van Nieuwstadt and Iraheta (1996) using head width (HW) values for Meliponini (stingless bees) and Guedot et al. (2009) using dry weight (mg) values for Osmia species.
foragedist(x, type = "GreenleafAll")foragedist(x, type = "GreenleafAll")
x |
A vector of either bee intertegular spans (IT) measurements in mm, head width values in mm or dry weight values (mg). |
type |
The type of foraging range desired. Options are "GreenleafAll", GrMhd ("Maximum homing distance"), GrThd ("Typical homing distance"), GrMfd ("Maximum feeder training distance"), GrMcd("Maximum communication distance"),"Osmia", "MeliMR" , "MeliFT" or "MeliAll". See details in Greenleaf et al. (2007), Guedot et al. (2009) and van Nieuwstadt and Iraheta (1996). |
A dataframe with bee and foraging range (km) is returned for each bee species.
Kendall et al. (2019) Pollinator size and its consequences: Robust estimates of body size in pollinating insects. Ecology and Evolution, 9(4), 1702-1714. doi:10.1002/ece3.4835.
Greenleaf et al. (2007) Bee foraging ranges and their relationship to body size. Oecologia, 153, 589-596. doi:10.1007/s00442-007-0752-9.
Guedot et al. (2009). Relationship between body size and homing ability in the genus Osmia (Hymenoptera; Megachilidae). Ecological Entomology, 34(1), 158-161. doi:10.1111/j.1365-2311.2008.01054.x.
van Nieuwstadt, M. G. L., & Iraheta, C. R. (1996). Relation between size and foraging range in stingless bees (Apidae, Meliponinae). Apidologie, 27(4), 219-228.
foragedist(c(10,5,2), type = "MeliMR")foragedist(c(10,5,2), type = "MeliMR")
Calculates realized (or potential) foraging range from Kendall et al. (2022) using intertegular distance (ITD) values and degree of sociality (highly eusocial, primitively eusocial or solitary).
foraging.range( data, model.type = "social", random.effects = "reduced", measure.type = "realized" )foraging.range( data, model.type = "social", random.effects = "reduced", measure.type = "realized" )
data |
A dataframe containing between two to four columns: bee intertegular distance (ITD) measurements in mm, species (Format: "Genus_species") and sociality (Format: "Highly Eusocial","Primitively Eusocial", "Solitary"). |
model.type |
A string stating which model should be used: "social", for the model that includes sociality, body size (ITD) and measurement type, or "ITD", for the reduced model that only includes body size and measurement type. |
random.effects |
A sting stating if random effects are to be used using predictive purposes. Options are 1) phylogenetic effect and species effects "full", 2) only phylogenetic effect ("phylo"), or 3) fixed effects only ("reduced"). Default is "reduced". |
measure.type |
A string stating whether to return realized ("realized") or potential ("potential") estimates. |
A dataframe with bee foraging range (km) is returned for each bee species (row).
Kendall et al. (2022) The potential and realized foraging movements of bees are differentially determined by body size and sociality Ecology TBC.
ITD=c(2.9,2.9,2.9) species=c("Apis_mellifera","Osmia_cornifrons","Bombus_bifarius") sociality=c("Highly Eusocial","Solitary","Primitively Eusocial") example.data <- data.frame(ITD,species,sociality) foraging.range(example.data,random.effects = "full",measure.type = "realized")ITD=c(2.9,2.9,2.9) species=c("Apis_mellifera","Osmia_cornifrons","Bombus_bifarius") sociality=c("Highly Eusocial","Solitary","Primitively Eusocial") example.data <- data.frame(ITD,species,sociality) foraging.range(example.data,random.effects = "full",measure.type = "realized")
Calculates dry body weight (mg) using head width (mm) from Hodar (1997).
headwidthsize(HW, Eq = "H97DB")headwidthsize(HW, Eq = "H97DB")
HW |
A vector of head width measurements (mm). |
Eq |
a vector of predictive allometries for insect taxa from Hodar (1997). Options implemented are: H97DB (Brachycera), H97DN (Nematocera), H97HA (Hymenoptera), H97LH (Heterocera) and H97LR (Rhopalocera). |
A dataframe with pollinator body size as dry weight (mg) is returned for each specimen from selected equation.
Kendall et al. (2019) Pollinator size and its consequences: Robust estimates of body size in pollinating insects. Ecology and Evolution, 9(4), 1702-1714. doi:10.1002/ece3.4835.
Hodar, J. A. (1997). The use of regresion equations for the estimation of prey length and biomass in diet studies of insectivore vertebrates. Miscellania Zoologica, 20(2), 1-10.
headwidthsize(HW=c(10,5,2), Eq = c("H97DB"))headwidthsize(HW=c(10,5,2), Eq = c("H97DB"))
Calculates body size as dry weight (mg) from existing allometries (See 'Details') using body length values (mm).
lengthsize(BL, Eq = "DIP")lengthsize(BL, Eq = "DIP")
BL |
A vector of pollinator body length (BL) measurements (mm). |
Eq |
A vector specificing which predictive allometry to use. Acronyms denote first (and second author), publication date and taxon. DIP, HYM and LEP options are cases where authors modelled body size across all specimens within each order.
Options implemented are:
Hymenoptera
Lepidoptera
|
A dataframe with pollinator body size (mg) is returned for each species from selected equation/s.
Full reference list provided within Kendall et al. (2019) Pollinator size and its consequences: Robust estimates of body size in pollinating insects. Ecology and Evolution, 9(4), 1702-1714. doi:10.1002/ece3.4835.
lengthsize(BL=c(10,5,2), Eq = c("S80DCR"))lengthsize(BL=c(10,5,2), Eq = c("S80DCR"))
Calculates body size as dry weight (mg) from the equations described by Sample (1993) and others using body length*body width values (mm).
lengthwidthsize(BLW, Eq = "DIP")lengthwidthsize(BLW, Eq = "DIP")
BLW |
A vector of fly body length*body width measurments (mm). |
Eq |
a vector of a predictive allometry for Diptera, Hymenoptera or Lepidoptera. Options implemented are: |
A dataframe with body size, as dry weight (mg) is returned for each specimen from selected equation.
Kendall et al. (2019) Pollinator size and its consequences: Robust estimates of body size in pollinating insects. Ecology and Evolution, 9(4), 1702-1714. doi:10.1002/ece3.4835.
Sample et al. (1993) Estimation of insect biomass by length and width. American Midland Naturalist, 234-240.
lengthwidthsize(BLW=c(3,5,2), Eq = c("Brachycera"))lengthwidthsize(BLW=c(3,5,2), Eq = c("Brachycera"))
A dataset containing glossa (mm), prementum (mm) and proboscis (mm) and taxonomic information for 179 measured bee specimens.
Melin_et_al_2019Melin_et_al_2019
An object of class data.frame with 179 rows and 7 columns.
@references
Melin et al. (2019) The allometry of proboscis length in Melittidae (Hymenoptera: Apoidae) and an estimate of their foraging distance using museum specimens. PloS one, 14(6), e0217839. doi:10.1371/journal.pone.0217839.
Calculates total field nectar load (ul) using body length (mm) from Henry & Rodet (2008).
nectarload(BL)nectarload(BL)
BL |
vector of body length measurements (mm). |
A dataframe with bee total field nectar load (ul) is returned for each specimen.
Kendall et al. (2019) Pollinator size and its consequences: Robust estimates of body size in pollinating insects. Ecology and Evolution, 9(4), 1702-1714. doi:10.1002/ece3.4835.
Henry, M., & Rodet, G. (2018). Controlling the impact of the managed honeybee on wild bees in protected areas. Scientific reports, 8(1), 9308. doi:10.1038/s41598-018-27591-y.
nectarload(BL=c(10,5,2))nectarload(BL=c(10,5,2))
A dataset containing the body size in dry weight (mg), intertegular distance (mm), body length (mg) and metadata for 4438 measured bee and hoverfly specimens.
pollimetry_datasetpollimetry_dataset
An object of class data.frame with 4434 rows and 23 columns.
@references
Kendall et al. (2019) Pollinator size and its consequences: Robust estimates of body size in pollinating insects. Ecology and Evolution, 9(4), 1702-1714. doi:10.1002/ece3.4835.
Calculates tongue length (mm) from Cariveau et al. (2015) and Melin et al. (2019) using intertegular distance (ITD) values (mm).
tonguelength(x, mouthpart = "all")tonguelength(x, mouthpart = "all")
x |
A dataframe with the following two columns: bee intertegular distance (IT) measurements in mm and family, a vector of bee families. Only six out of the extant seven families are implemented: "Andrenidae", "Apidae", "Colletidae", "Halictidae", "Melittidae" and "Megachilidae". |
mouthpart |
The mouthpart you are interested in. Options are: "all", "glossa", "prementum" and "tongue" (i.e. gloss + prementum) |
A dataframe with bee tongue length (mm) and 95
Kendall et al. (2019) Pollinator size and its consequences: Robust estimates of body size in pollinating insects. Ecology and Evolution, 9(4), 1702-1714. doi:10.1002/ece3.4835.
Cariveau et al. (2016) The allometry of bee tongue length an its uses in ecology and evolution. PloS one, 11(3): e0151482. doi:10.1371/journal.pone.0151482.
Melin et al. (2019) The allometry of proboscis length in Melittidae (Hymenoptera: Apoidae) and an estimate of their foraging distance using museum specimens. PloS one, 14(6), e0217839. doi:10.1371/journal.pone.0217839.
example=cbind.data.frame(IT=c(1.3,2.3), Family=c("Andrenidae","Apidae")) tonguelength(example,mouthpart="all")example=cbind.data.frame(IT=c(1.3,2.3), Family=c("Andrenidae","Apidae")) tonguelength(example,mouthpart="all")
Calculates wing loading (mg mm2) expressed as dry weight per total wing area using intertegular distance (mm) from Bullock (1999).
wingloading(IT)wingloading(IT)
IT |
vector of intertegular distance measurements (mm). |
A dataframe with wing loading (mg mm2) is returned for each specimen.
Kendall et al. (2019) Pollinator size and its consequences: Robust estimates of body size in pollinating insects. Ecology and Evolution, 9(4), 1702-1714. doi:10.1002/ece3.4835.
Bullock, S. H. (1999). Relationships among body size, wing size and mass in bees from a tropical dry forest in Mexico. Journal of the Kansas Entomological Society, 426-439.
wingloading(IT=c(10,5,2))wingloading(IT=c(10,5,2))