Title: | Body Mass Estimation Equations for Vertebrates |
---|---|
Description: | Estimation equations are from a variety of sources and associated error estimation. |
Authors: | Nicolas E. Campione |
Maintainer: | Nicolas E. Campione <[email protected]> |
License: | GPL (>= 2) |
Version: | 2.0-1 |
Built: | 2024-12-11 07:00:47 UTC |
Source: | CRAN |
Estimation equations are from a variety of sources and associated error estimation.
Package: | MASSTIMATE |
Type: | Package |
Version: | 2.0 |
Date: | 2020-09-01 |
License: | GPL(>= 2) |
Nicolas E. Campione
Maintainer: Nicolas E. Campione <[email protected]>
Anderson, J. F., Hall-Martin, A. and Russell, D.A. (1985) Long-bone circumference and weight in mammals, birds and dinosaurs. Journal of the Zoological Society of London A, 207, 53-61.
Campbell Jr., K.E. and Marcus, L. (1992) The relationships of hindlimb bone dimensions to body weight in birds. Natural History Museum of Los Angeles County Science Series, 36, 395-412.
Campione, N. E. and Evans, D. C. (2012) A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biology, 10, 60.
Campione, N. E., Evans, D. C., Brown, C. M. and Carrano, M. T. (2014) Body mass estimation in non-avian bipeds using a theoretical conversion to quadruped stylopodial proportions. Methods in Ecology and Evolution, 5(9), 913-923.
Campione, N. E. (2017) Extrapolation of a universal scaling relationship for estimating body masses in extinct terrestrial vertebrates. Paleobiology, 43, 693-699.
Campione, N. E. and Evans, D. C. (2020) The accuracy and precision of body mass estimation in non-avian dinosaurs. Biological Reviews.
Christiansen, P. and Farina, R. A. (2004) Mass prediction in theropod dinosaurs. Historical Biology, 16, 85-92.
Erickson G. M. and Tumanova, T. A. (2000). Growth curve of Psittacosaurus mongoliensis Orborn (Ceratopsia; Psittacosauridae) inferred from long bone histology. Zoological Journal of the Linnean Society, 130, 551-566.
Mazzetta, G. V., Christiansen, P. and Farina, R. A. (2004) Giants and bizzares: body size of some southern South American Cretaceous dinosaurs. Historical Biology, 16, 71-83.
This function estimates body mass based on humeral and/or femoral circumferences using the quadrupedal and bipedal equations of Anderson et al. (1985)
AHR1985(HC = NULL, FC, equation = c("bip", "quad"), data=NULL)
AHR1985(HC = NULL, FC, equation = c("bip", "quad"), data=NULL)
HC |
an optional value or vector representing humeral circumference (in mm) |
FC |
a value or vector representing femoral circumference (in mm) |
equation |
desired estimation equation. Two possible choices: |
data |
an optional object of |
If equation = "bip"
then only femoral circumference is needed. Both humeral and femoral circumference are needed to estimate body mass of a quadruped (equation = "quad"
). If a data object is specified, the mass estiamtes will be added as a column to the data.frame or matrix within that object.
AHR1985 |
A numeric value or vector representing the mass estimate(s) in grams |
Nicolas E. Campione
Anderson, J. F., Hall-Martin, A. and Russell, D.A. (1985) Long-bone circumference and weight in mammals, birds and dinosaurs. Journal of the Zoological Society of London A, 207, 53-61.
QE
cQE
quadrupeds
bipeds
CM1992
CF2004
MCF2004
##Quadrupedal dinosaurs data(dinos) AHR1985(dinos$HC, dinos$FC, equation = "quad", data = dinos) ##Bipedal dinosaurs data(dinosbip) AHR1985(HC=NULL, dinosbip$FC, equation = "bip", data = dinosbip)
##Quadrupedal dinosaurs data(dinos) AHR1985(dinos$HC, dinos$FC, equation = "quad", data = dinos) ##Bipedal dinosaurs data(dinosbip) AHR1985(HC=NULL, dinosbip$FC, equation = "bip", data = dinosbip)
This function returns body mass estimates for bipeds based on minimum femoral circumference using a set of five equations (intended for non-avian dinosaurs)
bipeds(FC, cQE.eq = "raw", cQE.cor = 2, data = NULL)
bipeds(FC, cQE.eq = "raw", cQE.cor = 2, data = NULL)
FC |
a value or vector representing femoral circumference (should be in mm) |
cQE.eq |
desired estimation equation for the cQE. Two possible choices (See |
cQE.cor |
correction factor to be used ( |
data |
an optional object of |
This function returns estimates from five equations intented for terrestrial bipeds (in particular non-avian dinosaurs): Campione et al. (2014); Campione (in review); Anderson et al. (1985); Christiansen and Farina (2004); Campbell and Marcus (1992). For more details please see the specific functions.
If a data object is specified, the mass estiamtes and additional results will be added as columns to the data.frame or matrix within that object.
Nine numeric values or columns are returned (all masses are in grams):
cQE |
A numeric value or vector of mass estimates using cQE |
upper.cQE |
A numeric value or vector representing the upper prediction error of the cQE based on that derived for the specific equation in Campione and Evans (2012) |
lower.cQE |
A numeric value or vector representing the lower prediction error of the cQE |
qcQE |
A numeric value or vector of mass estimates using qcQE (quadratic equation) |
upper.qcQE |
A numeric value or vector representing the upper prediction error of qcQE derived for the specific equation in Campione (in review) |
lower.qcQE |
A numeric value or vector representing the lower prediction error of qcQE |
AHR1985 |
A numeric value or vector of mass estimates using Anderson et al. (1985) |
CF2004 |
A numeric value or vector of mass estimates using Christiansen and Farina (2004) |
CM1992 |
A numeric value or vector of mass estimates using Campbell and Marcus (1992) |
Nicolas E. Campione
Anderson, J. F., Hall-Martin, A. and Russell, D.A. (1985) Long-bone circumference and weight in mammals, birds and dinosaurs. Journal of the Zoological Society of London A, 207, 53-61.
Campbell Jr., K.E. and Marcus, L. (1992) The relationships of hindlimb bone dimensions to body weight in birds. Natural History Museum of Los Angeles County Science Series, 36, 395-412.
Campione, N. E., Evans, D. C., Brown, C. M. and Carrano, M. T. (2014) Body mass estimation in non-avian bipeds using a theoretical conversion to quadruped stylopodial proportions. Methods in Ecology and Evolution, 5(9), 913-923.
Campione, N. E. (2017) Extrapolation of a universal scaling relationship for estimating body masses in extinct terrestrial vertebrates. Paleobiology, 43, 693-699.
Christiansen, P. and Farina, R. A. (2004) Mass prediction in theropod dinosaurs. Historical Biology, 16, 85-92.
This function is meant for bipedal mass estimate (in particular theropod dinosaurs) and offers some of the body mass prediction equations published by Christiansen and Farina (2004) derived from volumetric reconstructions of theropod dinosaurs
CF2004(X, X2 = NULL, eqn, data = NULL)
CF2004(X, X2 = NULL, eqn, data = NULL)
X |
a value or vector representing the first variable in the equation (in mm) |
X2 |
an optional second variable with same length as |
eqn |
a character specifying the desired prediction equation (see Details) |
data |
an optional object of |
Possible bivariate regression equations (eqn =
) include: femur length ("FL"
), femur circumference ("FC"
), femur anteroposterior diameter ("FAP"
), femur mediolateral diameter ("FML"
), tibia circumference ("TC"
), tibia distal mediolateral diameter ("TdistML"
), fibula distal anteroposterior diameter ("FidistAP"
). Multiple regression equations include femur circumference + length ("FC+FL"
), femur mediolateral diameter + femur length ("FML+FL"
), tibia circumference + femur length ("TC+FL"
), tibia length + femur circumference ("TL+FC"
), and tibia circumference + femur anteroposterior diameter ("TC+FAP"
). If a multiple regression equation is chosen, X2 != NULL
. See Christiansen & Farina (2004) for specific details and Campione & Evans (2020) for evaluations of the models.
If a data object is specified, the mass estiamtes will be added as a column to the data.frame or matrix within that object.
CF2004 |
A vector representing the mass estimate(s) in log grams and grams |
Nicolas E. Campione
Christiansen, P. and Farina, R. A. (2004) Mass prediction in theropod dinosaurs. Historical Biology, 16, 85-92.
Campione, N. E. and Evans, D. C. (2020) The accuracy and precisions of body mass estimation in non-avian dinosaurs. Biological Reviews.
##Bipedal dinosaurs data(dinosbip) CF2004(dinosbip$FC, eqn = "FC", data = dinosbip)
##Bipedal dinosaurs data(dinosbip) CF2004(dinosbip$FC, eqn = "FC", data = dinosbip)
This function estimates body mass based on femoral circumference using the avian equation of Campbell and Marcus (1992)
CM1992(FC, data = NULL)
CM1992(FC, data = NULL)
FC |
a value of vector representing femoral circumference (in mm) |
data |
an optional object of |
If a data object is specified, the mass estiamtes will be added as a column to the data.frame or matrix within that object.
CM1992 |
A numeric value or vector representing the mass estimate(s) in grams |
Nicolas E. Campione
Campbell Jr., K.E. and Marcus, L. (1992) The relationships of hindlimb bone dimensions to body weight in birds. Natural History Museum of Los Angeles County Science Series, 36, 395-412.
##Bipedal dinosaurs data(dinosbip) CM1992(dinosbip$FC, data = dinosbip)
##Bipedal dinosaurs data(dinosbip) CM1992(dinosbip$FC, data = dinosbip)
This function presents equations from Campione et al. (2014) for esimating body mass in bipeds using minimum femoral circumference and based on a correction of the quadrupedal equations from Campione and Evans (2012)
cQE(FC, equation = "raw", cor = 2, quadratic = FALSE, data = NULL, return_PI = FALSE)
cQE(FC, equation = "raw", cor = 2, quadratic = FALSE, data = NULL, return_PI = FALSE)
FC |
a value or vector representing femoral circumference (in mm) |
equation |
desired estimation equation. Two possible choices (See Details) |
cor |
correction factor to be used ( |
quadratic |
a logical indicating whether estimates based on the quadratic equation should be used (See Details) |
data |
an optional object of |
return_PI |
an optional logical value to also provide the wider prediction intervals on the estimate, currenly only works if |
The function includes two different equations. equation = "raw"
(default) applies the correction factor derived in Campione et al. (2014) to the raw (non-phylogenetically corrected) bivariate regression equation from Campione and Evans (2012). equation = "phylocor"
applies the same correction factor to the phylogenetically corrected equation presented in the same study.
cor = 2
refers to the correction factor () to be used. The default (
cor = 2
) refers the initial derivation in Campione et al. (2014), however, this value can be modified based on the level of eccentricity of the femur. A set of values for cor
corresponding to set eccentricities can be found in table S2 of Campione et al. (2014).
If quadratic = TRUE
, then a second set of estimates will be returned based on a quadratic estimation equation (Campione, 2017).
If a data object is specified, the mass estiamtes and additional results will be added as columns to the data.frame or matrix within that object.
Eight numeric values or columns are returned if quadratic = TRUE
(identified by q
):
log.cQE |
A numeric value or vector representing the mass estimate(s) in log10 grams |
cQE |
A numeric value or vector representing the mass estimate(s) in grams |
lower.cQE |
A numeric value or vector representing the lower prediction error derived for the specific equation in Campione and Evans (2012) |
upper.cQE |
A numeric value or vector representing the upper prediction error |
log.qcQE |
A numeric value or vector representing the mass estimate(s) in log10 grams using a quadratic equation |
qcQE |
A numeric value or vector representing the mass estimate(s) in grams |
lower.qcQE |
A numeric value or vector representing the lower prediction error derived for the specific equation by Campione (2017) |
upper.qcQE |
A numeric value or vector representing the upper prediction error |
Nicolas E. Campione
Campione, N. E. and Evans, D. C. (2012) A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biology, 10, 60.
Campione, N. E., Evans, D. C., Brown, C. M. and Carrano, M. T. (2014) Body mass estimation in non-avian bipeds using a theoretical conversion to quadruped stylopodial proportions. Methods in Ecology and Evolution, 5(9), 913-923.
Campione, N. E. (2017) Extrapolation of a universal scaling relationship for estimating body masses in extinct terrestrial vertebrates. Paleobiology, 43 (4), 693-699.
QE
bipeds
AHR1985
CF2004
CM1992
##Bipedal dinosaurs data(dinosbip) #Estimates for Tyrannosaurus (FMNH PR 2081 "Sue") sue<-which(dinosbip$Taxon=="TyrannosaurusFMNH2081") cQE(dinosbip$FC[sue]) #default correction factor cQE(dinosbip$FC[sue], cor = 1.815) #based on eccentricity of the femur ##Estimates of bipedal dinosaurs using phylogeneteically corrected linear and quadratic equations cQE(dinosbip$FC, equation = "phylocor", cor = dinosbip$cor, quadratic = TRUE, data = dinosbip)
##Bipedal dinosaurs data(dinosbip) #Estimates for Tyrannosaurus (FMNH PR 2081 "Sue") sue<-which(dinosbip$Taxon=="TyrannosaurusFMNH2081") cQE(dinosbip$FC[sue]) #default correction factor cQE(dinosbip$FC[sue], cor = 1.815) #based on eccentricity of the femur ##Estimates of bipedal dinosaurs using phylogeneteically corrected linear and quadratic equations cQE(dinosbip$FC, equation = "phylocor", cor = dinosbip$cor, quadratic = TRUE, data = dinosbip)
Metadata combining volumetric-density reconstruction mass estimates with their associated limb circumference measurements.
data("dino_comparisons")
data("dino_comparisons")
A data frame with 447 observations on the following 8 variables.
Clade
a character vector specifying the clade to which the Taxon
belongs.
Taxon
a character vector specifying the genus or species name.
Recon.Method
a character vector specifying the reconstruction method used to generate Recon.BM
.
Recon.BM
a numeric vector of the reconstruction body mass, in g.
Gait
a character vector specifying whether the Taxon
is bipedal or quadrupedal.
HCFC
a numeric vector of the combined humeral and femoral circumferences, in mm (if Gait = "quad"
).
HC
a numeric vector of the humeral circumferences, in mm (if Gait = "quad"
).
FC
a numeric vector of the femoral circumferences, in mm.
Campione, N. E. and Evans, D. C. (2020) The accuracy and precisions of body mass estimation in non-avian dinosaurs. Biological Reviews.
Humeral and Femoral circumference data for eight quadrupedal dinosaurs
data(dinos)
data(dinos)
A data frame with 8 observations and the following 3 variables.
Taxon
a factor with levels Brachiosaurs
Corythosaurus
Diplodocus
Iguanodon
Protoceratops
Stegosaurus
Styracosaurus
Triceratops
HC
a numeric vector of humeral circumferences
FC
a numeric vector of femoral circumferences
Campione, N. E. and Evans, D. C. (2012) A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biology, 10, 60.
Femoral circumference data for 34 bipedal dinosaurs
data(dinosbip)
data(dinosbip)
A data frame with 34 observations and the following 3 variables.
Taxon
a factor with the taxon names
FC
a numeric vector of femoral circumferences
cor
a numeric vector with the correction factor () values to be used in
cQE
Campione, N. E., Evans, D. C., Brown, C. M. and Carrano, M. T. (2014) Body mass estimation in non-avian bipeds using a theoretical conversion to quadruped stylopodial proportions. Methods in Ecology and Evolution, 5(9), 913-923.
This function estimates the body mass of an immature specimen based on the mass of a presumed adult and a standard measurement (e.g., femur length or circumference), as described by Erickson and Tumanova (2000).
DME(juv_proxy, adu_proxy, adu_mass, scale_fac = 3)
DME(juv_proxy, adu_proxy, adu_mass, scale_fac = 3)
juv_proxy |
numeric value or vector corresponding to the measurement taken on the immature specimen(s) of interest |
adu_proxy |
numeric value corresponding to the measurement taken on the presumed adult representative |
adu_mass |
numeric value corresponding to the body mass of the adult representative |
scale_fac |
numeric value corresponding to the growth allometric scaling factor applied to the immature and adult specimens, defaults to 3 (i.e., isometry) |
It cannot be assumed that growth-related allometric scaling coefficients will be consistent with those derived from interspecific relationships of adults (e.g.,QE). DME
was developed by Erickson and Tumanova (2000) in order to extrapolate the body mass of an adult to that of an immature specimen through the use of a growth-related scaling factor. Although the assumed scaling factor is that of isometry between a linear and volumetric measurement (scale_fac = 3
), if an alternate scaling factor is known, then it can be incorporated by adjusting the scale_fac
value.
A numeric value or vector representing the mass estimate(s) in grams of the immature specimen(s).
Nicolas E. Campione
Brassey C. A., Maidment, S. C. R. & Barrett, P. M. (2015). Body mass estimates of an exceptionally complete Stegosaurus (Ornithischia: Thyreophora): comparing volumetric and linear bivariate mass estimation methods. Biology Letters, 11, 20140984.
Erickson G. M. and Tumanova, T. A. (2000). Growth curve of Psittacosaurus mongoliensis Orborn (Ceratopsia; Psittacosauridae) inferred from long bone histology. Zoological Journal of the Linnean Society, 130, 551-566.
##Based on the immature Stegosaurus from Brassey et al. (2015) ## Immature (NHMUK R36730: HC = 282, FC = 339, FL = 863 ## Adult (YPM1853): HC = 352, FC = 425, FL = 1348 ##DME estimate, adult extracted from dinos dataset DME(juv_proxy = 863, adu_proxy = 1348, adu_mass = QE(352+425)[2])
##Based on the immature Stegosaurus from Brassey et al. (2015) ## Immature (NHMUK R36730: HC = 282, FC = 339, FL = 863 ## Adult (YPM1853): HC = 352, FC = 425, FL = 1348 ##DME estimate, adult extracted from dinos dataset DME(juv_proxy = 863, adu_proxy = 1348, adu_mass = QE(352+425)[2])
Humeral and Femoral data for 245 living tetrapods, including mammals and reptiles
data(extants)
data(extants)
A data frame with 245 observations and the following 13 variables.
Mon.Groups
a character vector representing the inclusive clade
Family
a character vector representing the family level taxonomy
Species
a character vector identifying the mammal or reptile species
Common.Name
a character vector identifying the common species name
SP.
a character vector specifying the specimen number (see Campione and Evans 2012 for more details)
BM
a numeric vector of body masses (in g)
Humerus.Length
a numeric vector of humeral lengths (in mm)
HC
a numeric vector of humeral circumferences (in mm)
Femur.Length
a numeric vector of femoral lengths (in mm)
FC
a numeric vector of femoral circumferences (in mm)
HCFC
a numeric vector of combined humeral and femoral circumferences (in mm)
log.BM
a numeric vector of the base-10 logarithms of body masses
log.HCFC
a numeric vector of the base-10 logarithms of combined humeral and femoral circumferences
Campione, N. E. and Evans, D. C. (2012) A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biology, 10, 60.
The main function for projecting a body mass estimate from a reconstruction onto the limb circumference standard of accuracy, as presented by Campione & Evans (2020).
MASSunite(HFC = NULL, HC, FC, BM, ES.type = "QE", gait, VD.par = NULL, line = FALSE, ...)
MASSunite(HFC = NULL, HC, FC, BM, ES.type = "QE", gait, VD.par = NULL, line = FALSE, ...)
HFC |
a numeric value or vector representing the combined humeral and femoral circumferences (in mm) |
HC |
a numeric value or vector representing humeral circumference (in mm) |
FC |
a numeric value or vector representing femoral circumference (in mm) |
BM |
a numeric value or vector associated with the limb circumferences, ideally generates by a reconstruction approach (in g) |
ES.type |
a character specifying whether a linear or quadratic equation should be used as the extant limb scaling standard, (default is linear |
gait |
a character specifying whether the reconstruction is |
VD.par |
a list of parameters to be used when plotting. Options include: |
line |
a logical value specifying whether a linear model should be run for the reconstruction (if |
... |
parameter arguments passed to scaling standard plot (e.g., |
This function will take a set of body masses estimated via volumetric-density (VD) approaches, their accociated limb circumference data (such as that of the humerus and femur for a quadruped), and project them onto the extant standard of accuracy (Campione & Evans, 2010, Campione et al. 2014, Campione & Evans 2020). In addition, there is an option to fit a linear model to the VD reconstructions, allowing visual comparison to the extant relationship (see line = TRUE
).
Both the linear and quadratic extant models can be used (see Campione, 2017) and residual deviations are calculated in accordance with the specified model. Residual plot, however, will depict both the upper and lower extremes of the prediction intervals as these can vary along the regression lines, especially is ES.type = "qQE"
.
A list of variable length depending on the parameters specified. Permanent values include:
Residual |
a numeric value or vector with the residual deviation between VD reconstructions and the ES standard |
mean.Residual |
a numeric value of the average residual value |
PPE |
a list with output of the |
Optional values include:
Inferred.Line |
object of class |
Outliers |
an optional vector specifying VD resconstruction data points that occur outside the prediction intervals of the extant standard |
Caution |
if |
Nicolas E. Campione
Campione, N. E. and Evans, D. C. (2012) A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biology, 10, 60.
Campione, N. E., Evans, D. C., Brown, C. M. and Carrano, M. T. (2014) Body mass estimation in non-avian bipeds using a theoretical conversion to quadruped stylopodial proportions. Methods in Ecology and Evolution, 5(9), 913-923.
Campione, N. E. (2017) Extrapolation of a universal scaling relationship for estimating body masses in extinct terrestrial vertebrates. Paleobiology, 43 (4), 693-699.
Campione, N. E. and Evans, D. C. (2020) The accuracy and precisions of body mass estimation in non-avian dinosaurs. Biological Reviews.
# metadata from Campione & Evans (2020) data(dino_comparisons) # using linear standard and quadupedal dinosaurs w/ VD reconstruction line MASSunite(dino_comparisons$HCFC, BM = dino_comparisons$Recon.BM, gait = "quadruped", VD.par = list(pch = 19, col = "pink", names = NULL), line = TRUE) # using quadratic standard and bipedal dinsoaurs w/ no line MASSunite(FC = dino_comparisons$FC, BM = dino_comparisons$Recon.BM, ES.type = "qQE", gait = "biped", VD.par = list(pch = 19, col = "pink", names = NULL))
# metadata from Campione & Evans (2020) data(dino_comparisons) # using linear standard and quadupedal dinosaurs w/ VD reconstruction line MASSunite(dino_comparisons$HCFC, BM = dino_comparisons$Recon.BM, gait = "quadruped", VD.par = list(pch = 19, col = "pink", names = NULL), line = TRUE) # using quadratic standard and bipedal dinsoaurs w/ no line MASSunite(FC = dino_comparisons$FC, BM = dino_comparisons$Recon.BM, ES.type = "qQE", gait = "biped", VD.par = list(pch = 19, col = "pink", names = NULL))
This function is meant for quadrupedal mass estimates (in particularly sauropod dinosaurs) and offers some of the body mass prediction equations published by Mazzetta et al. (2004) derived from volumetric reconstructions of sauropod dinosaurs
MCF2004(X, eqn, data = NULL)
MCF2004(X, eqn, data = NULL)
X |
a value or vector representing the variable in the equation (in mm) |
eqn |
a character specifying the desired prediction equation (see Details) |
data |
an optional object of |
Possible equations (eqn =
) include: femur length ("FL"
), modified femur length ("FL*"
), femur circumference ("FC"
), tibia length ("TL"
), and tibia circumference ("TC"
). See Mazzetta et al. (2004) for specific details and Campione & Evans (2020) for evaluations of the models.
If a data object is specified, the mass estiamtes will be added as a column to the data.frame or matrix within that object.
MCF2004 |
A numeric value or vector representing the mass estimate(s) in grams |
Nicolas E. Campione
Mazzetta, G. V., Christiansen, P. and Farina, R. A. (2004) Giants and bizzares: body size of some southern South American Cretaceous dinosaurs. Historical Biology, 16, 71-83.
Campione, N. E. and Evans, D. C. (2020) The accuracy and precisions of body mass estimation in non-avian dinosaurs. Biological Reviews.
##Quadrupedal dinosaurs data(dinos) MCF2004(dinos$FC, eqn = "FC", data = dinos)
##Quadrupedal dinosaurs data(dinos) MCF2004(dinos$FC, eqn = "FC", data = dinos)
An internal function used by MASSunite
to project a VD recontruction onto a standard of accuracy.
mod_OLS(xvar = extants$log.HCFC, yvar = extants$log.BM, xlab = "Log Stylopodial Circumference",ylab = "Log Body Mass", xlim = c(1, 3.5), ylim = c(1.5, 8), cex = 0.5, pch = 4, col = "gray", fit.col = "black", pred.seq = seq(from = 1, to = 4, by = 0.01), PI.col = "blue", PI.lty = 2, CI.col = "red", CI.lty = 1, verbose = FALSE, plot = TRUE, ...)
mod_OLS(xvar = extants$log.HCFC, yvar = extants$log.BM, xlab = "Log Stylopodial Circumference",ylab = "Log Body Mass", xlim = c(1, 3.5), ylim = c(1.5, 8), cex = 0.5, pch = 4, col = "gray", fit.col = "black", pred.seq = seq(from = 1, to = 4, by = 0.01), PI.col = "blue", PI.lty = 2, CI.col = "red", CI.lty = 1, verbose = FALSE, plot = TRUE, ...)
xvar , yvar
|
the x and y coordinates of the model, defaults to the log combined humeral and femoral circumferences and their associated log body mass, respectively. |
xlab , ylab
|
single character objects specifying the axes labels, as in |
xlim , ylim
|
numeric vector specifying the axes ranges, as in |
cex , pch , col
|
main plotting parameters, as in |
fit.col |
character object specifying the colour of the fitted line. |
pred.seq |
integer or numeric sequence use as |
PI.col , PI.lty
|
colour and line-type parameters for the prediction interval lines. |
CI.col , CI.lty
|
colour and line-type parameters for the confidence interval lines. |
verbose |
a logical value indicating whether the results of the model fitting are returned. |
plot |
a logical value indicating whether the plot should be produced, defaults to |
... |
parameter arguments passed to |
This function is mostly used internally by MASSunite
to project volumetric reconstruction models onto the linear limb circumferences standard of accuracy, as presented in Campione & Evans (2020). However, the function can technically be used to generate a plot of any x-y coordinates with their fitted ordinary least squares line and associated confidence/prediction intervals. N.B. If modified, the defaults may not suite.
The default function will generate a plot. If verbose = TRUE
a 3 item list will be returned with:
model |
the output from |
prediction |
a 3-column matrix with the fitted, lower, and upper prediction intervals for the vector given in |
confidence |
a 3-column matrix with the fitted, lower, and upper confidence intervals for the vector given in |
Nicolas E. Campione
Campione, N. E. and Evans, D. C. (2012) A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biology, 10, 60.
Campione, N. E. and Evans, D. C. (2020) The accuracy and precisions of body mass estimation in non-avian dinosaurs. Biological Reviews.
mod_OLS()
mod_OLS()
An internal function used by MASSunite
to project a VD recontruction onto a standard of accuracy.
mod_QUAD(xvar = extants$log.HCFC, yvar = extants$log.BM, xlab = "Log Stylopodial Circumference",ylab = "Log Body Mass", xlim = c(1, 3.5), ylim = c(1.5, 8), cex = 0.5, pch = 4, col = "gray", fit.col = "black", pred.seq = seq(from = 1, to = 4, by = 0.01), PI.col = "blue", PI.lty = 2, CI.col = "red", CI.lty = 1, verbose = FALSE, plot = TRUE, ...)
mod_QUAD(xvar = extants$log.HCFC, yvar = extants$log.BM, xlab = "Log Stylopodial Circumference",ylab = "Log Body Mass", xlim = c(1, 3.5), ylim = c(1.5, 8), cex = 0.5, pch = 4, col = "gray", fit.col = "black", pred.seq = seq(from = 1, to = 4, by = 0.01), PI.col = "blue", PI.lty = 2, CI.col = "red", CI.lty = 1, verbose = FALSE, plot = TRUE, ...)
xvar , yvar
|
the x and y coordinates of the model, defaults to the log combined humeral and femoral circumferences and their associated log body mass, respectively. |
xlab , ylab
|
single character objects specifying the axes labels, as in |
xlim , ylim
|
numeric vector specifying the axes ranges, as in |
cex , pch , col
|
main plotting parameters, as in |
fit.col |
character object specifying the colour of the fitted line. |
pred.seq |
integer or numeric sequence use as |
PI.col , PI.lty
|
colour and line-type parameters for the prediction interval lines. |
CI.col , CI.lty
|
colour and line-type parameters for the confidence interval lines. |
verbose |
a logical value indicating whether the results of the model fitting are returned. |
plot |
a logical value indicating whether the plot should be produced, defaults to |
... |
parameter arguments passed to |
This function is mostly used internally by MASSunite
to project volumetric reconstruction models onto the non-linear limb circumferences standard of accuracy, as presented in Campione & Evans (2020). However, the function can technically be used to generate a plot of any x-y coordinates with their fitted quadratic line and associated confidence/prediction intervals. N.B. If modified, the defaults may not suite.
The default function will generate a plot. If verbose = TRUE
a 3 item list will be returned with:
model |
the output from |
prediction |
a 3-column matrix with the fitted, lower, and upper prediction intervals for the vector given in |
confidence |
a 3-column matrix with the fitted, lower, and upper confidence intervals for the vector given in |
Nicolas E. Campione
Campione, N. E. and Evans, D. C. (2012) A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biology, 10, 60.
Campione, N. E. (2017) Extrapolation of a universal scaling relationship for estimating body masses in extinct terrestrial vertebrates. Paleobiology, 43 (4), 693-699.
Campione, N. E. and Evans, D. C. (2020) The accuracy and precisions of body mass estimation in non-avian dinosaurs. Biological Reviews.
mod_QUAD()
mod_QUAD()
This function presents the multiple regressions equations from Campione and Evans (2012) for esimating body mass in terretrial vertebartes using humeral and femoral circumferences
MR(HC, FC, equation = c("raw","phylocor"), data = NULL)
MR(HC, FC, equation = c("raw","phylocor"), data = NULL)
HC |
a value or vector representing humeral circumference (in mm) |
FC |
a value or vector representing femoral circumference (in mm) |
equation |
desired estimation equation. Two possible choices (See Details) |
data |
an optional object of |
The function includes two different equations. equation = "raw"
applies the multiple regression based on the raw (non-phylogenetically corrected) relationship - equation 5 of Campione and Evans (2012). equation = "phylocor"
applies the multiple regressions taking phylogenetic relationships into account - equation 6 of Campione and Evans (2012).
If a data object is specified, the mass estiamtes and additional results will be added as columns to the data.frame or matrix within that object.
Four numeric values or columns are returned:
log.masstimate |
A numeric value or vector representing the mass estimate(s) in log10 grams |
MR |
A numeric value or vector representing the mass estimate(s) in grams |
upper.MR |
A numeric value or vector representing the upper prediction error based on that derived for the specific equation by Campione and Evans (2012) |
lower.MR |
A numeric value or vector representing the lower prediction error |
Nicolas E. Campione
Campione, N. E. and Evans, D. C. (2012) A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biology, 10, 60.
##Dinosaur data from Campione and Evans (2012) for quadrupedal dinosaurs data(dinos) ##Combined equation based on the raw regression MR(dinos$HC, dinos$FC, equation = "raw", data = dinos) ##Combined equation based on the phylogenetically corrected regression, data not specified MR(dinos$HC, dinos$FC, equation = "phylocor")
##Dinosaur data from Campione and Evans (2012) for quadrupedal dinosaurs data(dinos) ##Combined equation based on the raw regression MR(dinos$HC, dinos$FC, equation = "raw", data = dinos) ##Combined equation based on the phylogenetically corrected regression, data not specified MR(dinos$HC, dinos$FC, equation = "phylocor")
This function is meant for dinosaur mass estimation from femoral length as presented by O'Gorman & Hone (2012)
OH2012(FL, eqn, data=NULL)
OH2012(FL, eqn, data=NULL)
FL |
a value or vector representing femoral length (in mm) |
eqn |
a character specifying the desired prediction equation (see Details) |
data |
an optional object of |
Possible estimation equations (eqn =
) include: "theropods"
, "sauropods"
, and "ornithischians"
. See O'Gorman & Hone (2012) for specific details and Campione & Evans (2020) for evaluations of the models.
If a data object is specified, the mass estiamtes will be added as a column to the data.frame or matrix within that object.
OH2012 |
A vector representing the mass estimate(s) in log grams and grams |
Nicolas E. Campione
O'Gorman, E. J. and Hone, D. W. E. (2012) Body Size Distribution of the Dinosaurs. PLoS ONE 7(12): e51925.
Campione, N. E. and Evans, D. C. (2020) The accuracy and precisions of body mass estimation in non-avian dinosaurs. Biological Reviews.
This function calculates the percent prediction error of a sample based on the predicted and true values
ppe(true, pred, abs = TRUE)
ppe(true, pred, abs = TRUE)
true |
a numeric vector representing the true value on which a prediction ( |
pred |
a numeric vector with the predicted values, must be equal length to |
abs |
a logical value indicating whether to return the absolute values for ppe, default is |
This function calculates the percent prediction error (ppe) as a scaled residual (Smith 1980), generally based on the absolute residual, so:
Function returns a list of results, including the a list of all the precent prediction errors, along with the mean, 95 percent confidence intervals, range, and standard deviation.
Nicolas E. Campione
Smith, R. J. (1980) Rethinking allometry. Journal of Theoretical Biology, 87, 97-111.
This function is based on the bivariate regression equations from Campione and Evans (2012) for esimating body mass in terretrial vertebartes using the combined humeral and femoral circumferences
QE(HFC = NULL, HC, FC, equation = "raw", quadratic = FALSE, data = NULL, return_PI = FALSE)
QE(HFC = NULL, HC, FC, equation = "raw", quadratic = FALSE, data = NULL, return_PI = FALSE)
HFC |
a value or vector representing the combined humeral and femoral circumferences |
HC |
a value or vector representing humeral circumference (in mm) |
FC |
a value or vector representing femoral circumference (in mm) |
equation |
desired estimation equation. Two possible choices (See Details) |
quadratic |
a logical indicating whether estimates based on the quadratic equation should be used (See Details) |
data |
an optional object of |
return_PI |
an optional logical value to also provide the wider prediction intervals on the estimate, currenly only works if |
The function includes two different equations. equation = "raw"
(default) applies the non-phylogenetically corrected regression equation - equation 1 of Campione and Evans (2012). equation = "phylocor"
applies the phylogenetically corrected regression equation - equation 2 of Campione and Evans (2012).
If HFC is specified, then HC and FC are ignored.
If quadratic = TRUE
, then a second set of estimates will be returned based on a quadratic view of the Campione and Evans (2012) data set (Campione, 2017).
If a data object is specified, the mass estiamtes and additional results will be added as columns to the data.frame or matrix within that object.
Eight numeric values or columns are returned if quadratic = TRUE
(identified by q
):
log.QE |
A numeric value or vector representing the mass estimate(s) in log10 grams |
QE |
A numeric value or vector representing the mass estimate(s) in grams |
lower.QE |
A numeric value or vector representing the lower prediction error derived for the specific equation by Campione and Evans (2012) |
upper.QE |
A numeric value or vector representing the upper prediction error |
log.qQE |
A numeric value or vector representing the mass estimate(s) in log10 grams using a quadratic equation |
qQE |
A numeric value or vector representing the mass estimate(s) in grams |
lower.qQE |
A numeric value or vector representing the lower prediction error derived for the specific equation by Campione (2017) |
upper.qQE |
A numeric value or vector representing the upper prediction error |
Nicolas E. Campione
Campione, N. E. and Evans, D. C. (2012) A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biology, 10, 60.
Campione, N. E. (2017) Extrapolation of a universal scaling relationship for estimating body masses in extinct terrestrial vertebrates. Paleobiology, 43 (4), 693-699.
cQE
quadrupeds
MR
AHR1985
MCF2004
##Dinosaur data from Campione and Evans (2012) for quadrupedal dinosaurs data(dinos) ##Combined equation based on the raw regression QE(HC = dinos$HC, FC = dinos$FC, quadratic = TRUE, data = dinos, return_PI = TRUE) ##Combined equation based on the phylogenetically corrected regression, data not specified QE(HC = dinos$HC, FC = dinos$FC, equation = "phylocor")
##Dinosaur data from Campione and Evans (2012) for quadrupedal dinosaurs data(dinos) ##Combined equation based on the raw regression QE(HC = dinos$HC, FC = dinos$FC, quadratic = TRUE, data = dinos, return_PI = TRUE) ##Combined equation based on the phylogenetically corrected regression, data not specified QE(HC = dinos$HC, FC = dinos$FC, equation = "phylocor")
This function returns body mass estimates for quadrupeds using humeral and/or femoral circumferences (intended for non-avian dinosaurs)
quadrupeds(HC, FC, QE_MR.eq = "raw", data = NULL)
quadrupeds(HC, FC, QE_MR.eq = "raw", data = NULL)
HC |
a value or vector representing humeral circumference (in mm) |
FC |
a value or vector representing femoral circumference (in mm) |
QE_MR.eq |
desired estimation equations to used by QE and MR. Two possible choices. |
data |
an optional object of |
This function returns estimates from five equations intented for terrestrial quadrupeds (in particular non-avian dinosaurs): two from Campione and Evans (2012) based on bivariate and multiple regression approaches; a quadratic view of the bivariate regression (Campione in review); Anderson et al. (1985); Mazzetta et al. (2004). For more details please see the specific functions.
If a data object is specified, the mass estiamtes and additional results will be added as columns to the data.frame or matrix within that object.
11 numeric values or columns are returned (all masses are in grams):
QE |
A numeric value or vector of mass estimates using QE (bivariate regression) |
upper.QE |
A numeric value or vector representing the upper prediction error of the QE based on that derived for the specific equation by Campione and Evans (2012) |
lower.QE |
A numeric value or vector representing the lower prediction error of the QE |
qQE |
A numeric value or vector of mass estimates using qQE (quadratic equation) |
upper.qQE |
A numeric value or vector representing the upper prediction error of qQE derived for the specific equation in Campione (in review) |
lower.qQE |
A numeric value or vector representing the lower prediction error of qQE |
MR |
A numeric value or vector of mass estimates using MR (multiple regression) |
upper.MR |
A numeric value or vector representing the upper prediction error of the MR based on that derived for the specific equation by Campione and Evans (2012) |
lower.MR |
A numeric value or vector representing the lower prediction error of the MR |
AHR1985 |
A numeric value or vector of mass estimates using Anderson et al. (1985) |
MCF2004 |
A numeric value or vector of mass estimates using Mazzetta et al. (2004) |
Nicolas E. Campione
Anderson, J. F., Hall-Martin, A. and Russell, D. A. (1985) Long-bone circumference and weight in mammals, birds and dinosaurs. Journal of the Zoological Society of London A, 207, 53-61.
Campione, N. E. and Evans, D. C. (2012) A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biology, 10, 60.
Campione, N. E. (2017) Extrapolation of a universal scaling relationship for estimating body masses in extinct terrestrial vertebrates. Paleobiology, 43, 693-699.
Mazzetta, G. V., Christiansen, P. and Farina, R. A. (2004) Giants and bizzares: body size of some southern South American Cretaceous dinosaurs. Historical Biology, 16, 71-83.
This function computes the standard error of the estimate based on the actual and predicted values
see(true, pred)
see(true, pred)
true |
a numeric vector representing the true values |
pred |
a numeric vector representing the predicted values, must be equal length to |
This function calculates the standard error of the estimate (see) as a scaled residual, so:
Function returns a length one value of the standard error of the estimate
Nicolas E. Campione