volume: Volumetric calculus of organisms

In forImage: Foraminiferal Image Analysis and Test Measurement

Description

The function calculates organisms volume based on geometric approximation.

Usage

## S3 method for class 'total'
volume(data, model, ...)

Arguments

data	data frame containing size data. Size data parameters may vary according to chosen model, see Details.
model	character informing geometric model to calculate volume, the models options are listed below: '1hl' : sphere '2sl' : half-sphere '3hl' : prolate spheroid '4hl' : cone or double cone '6fs' : paraboloid '7fs' : dome '8hl' : cylinder '10hl' : ellipsoid '11fs' : elliptic cone '12v' : cone + half ellipsoid '13hlsl' : gomphonemoid '14hl' : prism on elliptic base/elliptic cylinder '15hl' : half elliptic prism '17fs' : triangular dypyramid 'ahx' : area x height
...	other parameters.

Details

These geometric models applied in this function are based and adapted from microalgae models developed by Hillebrand et al. (1999) - ('.hl'), Sun and Liu (2003) - ('.sl') and Vadrucci, Cabrini and Basset (2007) - ('.v'), plus other adapted models ('.fs'). The models can be a variable in data if specified as model.The size data parameters should follow the specified measures determined by each model, where d_one is minor diameter, d_two is major diameter and h is height.

'1hl'	V = (pi * (d_one^3))/6
'2sl'	V = (pi * (d_one^3))/12
'3hl'	V = (pi * h * (d_one^2))/6
'4hl'	V = (pi * h * (d_one^2))/12
'6fs'	V = (pi * hx * (d_one^2))/8
	where hx is a function of test height for trochamminids.
'7fs'	V = (pi * h * (4 * (h^2) + 3 * (d_one^2)))/24
'8hl'	V = (pi * h * (d_one^2))/4
'10hl'	V = (pi * h * d_one * d_two)/6
'11fs'	V = (pi * h * d_one * d_two)/12
'12v'	V = (pi * h * d_one * d_two)/12
'13hlsl'	V = ((d_one * d_two)/4) * (d_one + ((pi/4) - 1) * d_two) * asin(h/(2*d_one))
'14hl'	V = (pi * h * d_one * d_two)/4
'15hl'	V = pi * h * d_one * d_two)/4
'17fs'	V = ((length * width)/2) * h)/3

Value

A 'data.frame' or numeric object, consisting of calculated individual volume along with biovolume if the pco is informed.

Author(s)

Thaise R. Freitas [e-mail]

References

• Hillebrand, H., Dürselen, C.D., Kirschtel, D., Pollingher, U., & Zohary, T. (1999). Biovolume calculation for pelagic and benthic microalgae. Journal of Phycology, 35(2), 403–424. doi:10.1046/j.1529-8817.1999.3520403.x

• Sun, J., & Liu, D. (2003). Geometric models for calculating cell biovolume and surface area for phytoplankton. Journal of Plankton Research, 25(11), 1331–1346. doi:10.1093/plankt/fbg096

• Vadrucci, M. R., Cabrini, M., & Basset, A. (2007). Biovolume determination of phytoplankton guilds in transitional water ecosystems of Mediterranean Ecoregion. Transitional Waters Bulletin, 2, 83–102. doi:10.1285/i1825229Xv1n2p83

See Also

measure

bio.volume

Examples

#Ammonia size data
data("ammonia")

#calculate test volume
volume.total(ammonia, model = "10hl")

forImage documentation built on March 3, 2021, 1:13 a.m.