mort.func: Analysis of Mortality Profiles
In zooaRch: Analytical Tools for Zooarchaeological Data

Description Usage Arguments Details Value Author(s) References Examples

This is a function used to conduct mortality analyses of zooarchaeological data

1 2	mort.func(mortData, labels = NULL, models = NULL, ci = 95, plot = TRUE, iter = 1000, usermod = NULL, lsize = 0.1)

`mortData`	is the age-at-death dataset. This function inputs datasets composed of three columns. The first column denotes the genus; the second is the age class (this MUST be numeric) if data contains nominal age classes (e.g., 'A', 'B', 'C', etc.) these data must be converted to numbers (e.g., A = 1, B = 2, etc.).
`labels`	Character value indicating wether age class labels wishing to be displayed.
`models`	A numerical value (1-5) indiacting the models to compare the data to. Currently mort.func makes use of 5 mortality models: 1) Security (ref); 2) Milk (ref); 3) Wool (ref); 4) Catastrophic (Stiner 1990); and 5) Attritional (Stiner 1990). More models will be added soon. An option to include user's own model will also be available.
`ci`	Numerical value indicating desired CI level (e.g., 90, 95, 99). Defaults to 95.
`plot`	A logical value indicating wether user wishes an output plot. Default = TRUE.
`iter`	A numeric value indicating the number of bootstrap iterations. Defaults to 1000.
`usermod`	numeric list (see help(list)) user-specified mortality model. See example 3 below. Data must be entered as a list, else user will receive error.
`lsize`	A numeric value indicating the vertical spacing value in a legend.

This function plots mortality profiles, along with Confidence Intervals using dental eruption and wear data. Optionally, plotted mortality profiles can be compared to idealized models of mortality.

Function returns a matrix with the following components

`Lower and Upper CI`	typically the 97.5 and 2.5 percentile markers
`Point Value`	the y value on the mortality profile

Erik Otarola-Castillo.

Klein, R.G., Cruz-Uribe, K., 1983. The Analysis of Animal Bones from Archaeological Sites, University of Chicago Press, Chicago.

Stiner, M. C. 1990 The Use of Mortality Patterns in Archaeological Studies of Hominid Predatory Adaptations. Journal of Anthropological Archaeology 9:305 - 351.

Lyman, R.L., 1994. Vertebrate Taphonomy, Cambridge University Press, Cambridge.

Voorhies, M. R., 1969 Taphonomy and Population Dynamics of an Early Pliocene Vertebrate Fauna, Knox County, Nebraska. University of Wymonig Press. Contributions to Geology, Special Paper No. 1, Laramie (WY).

Reitz, E. and E. Wing 2008 Zooarchaeology. Second Edition. Cambridge University Press, Cambridge.

# Example 1: Payne 1973
 data(marjRab)

# Inspect data structure  
 head(marjRab)
 
# create age-class labels: Payne 1973 uses ageclasses A-I
 Labels <-c('A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I')
 mort.func(mortData=marjRab,labels=Labels, models=1:3, ci=95, plot=TRUE, iter=1000)
 
# Example 2: Garnsey Site Bison Data (from Speth 1983)
 data(speth83)

# Inspect data structure  
 head(speth83)

# create age-class labels using the 13 age classes of Speth's (1983) scheme.
 Labels <-c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)

# Use the catastrophic and attritional mortality curves (after Stiner 1990).
 mort.func(mortData=speth83,labels=Labels, models=4:5, ci=95, plot=TRUE, iter=1000)

Loading required package: ggplot2
       Genus Ageclass
1 Ovis/Capra        1
2 Ovis/Capra        2
3 Ovis/Capra        3
4 Ovis/Capra        3
5 Ovis/Capra        3
6 Ovis/Capra        3
       Taxon AgeClassLabs LowerCI PointValue UpperCI
1 Ovis/Capra            A  0.0000     0.0238  0.0714
2 Ovis/Capra            B  0.0000     0.0238  0.0714
3 Ovis/Capra            C  0.1190     0.2381  0.3810
4 Ovis/Capra            D  0.0476     0.1667  0.2857
5 Ovis/Capra            E  0.0476     0.1429  0.2381
6 Ovis/Capra            F  0.0476     0.1429  0.2619
7 Ovis/Capra            G  0.0476     0.1429  0.2619
8 Ovis/Capra            H  0.0000     0.0714  0.1667
9 Ovis/Capra            I  0.0000     0.0476  0.1190
  Genus Ageclass
1 Bison        1
2 Bison        1
3 Bison        2
4 Bison        3
5 Bison        3
6 Bison        3
   Taxon AgeClassLabs LowerCI PointValue UpperCI
1  Bison            1  0.0000     0.0667  0.1667
2  Bison            2  0.0000     0.0333  0.1000
3  Bison            3  0.0333     0.1333  0.2667
4  Bison            4  0.0333     0.1333  0.2667
5  Bison            5  0.0000     0.0333  0.1000
6  Bison            6  0.0000     0.0667  0.1667
7  Bison            7  0.0000     0.1000  0.2333
8  Bison            8  0.0333     0.1333  0.2667
9  Bison            9  0.0000     0.0667  0.1667
10 Bison           10  0.0000     0.0667  0.1667
11 Bison           11  0.0000     0.0667  0.1667
12 Bison           12  0.0000     0.0667  0.1667
13 Bison           13  0.0000     0.0333  0.1000