forImage (version 0.1.0)

volume.total: Volumetric calculus of organisms

Description

The function calculates organisms volume based on geometric approximation.

Usage

# S3 method for 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.

Value

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

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'	\(V = ((length * width)/2) * h)/3\)

References

• Hillebrand, H., D<U+00FC>rselen, C.D., Kirschtel, D., Pollingher, U., & Zohary, T. (1999). Biovolume calculation for pelagic and benthic microalgae. Journal of Phycology, 35(2), 403<U+2013>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<U+2013>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<U+2013>102. doi:10.1285/i1825229Xv1n2p83

See Also

measure

bio.volume

Examples

# NOT RUN {
#Ammonia size data
data("ammonia")

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


# }