Several osteometrical references are provided in zoolog to enable researchers to use the one of their choice. The user can also use their own osteometrical reference if preferred.
referencereferenceSets
referencesDatabase
Each reference is a data.frame including 4 columns:
The taxon to which each reference bone belongs.
The skeletal element.
The type of measurement taken on the bone.
The value of the measurement taken on the bone. All the measurements are expressed in millimetres.
Currently, the references include reference values for the main domesticates and their agriotypes (Bos, Ovis, Capra, Sus), and other less frequent species, such as red deer and donkey, drawn from the following publications and resources:
Bos taurus. Female cow dated to the Early Bronze Age (Minferri, Catalonia), in nieto2018element;textualzoolog.
Bos taurus. Inv.nr. 2426 (Hinterw<U+00E4>lder; female; 17 years old; live weight: 340 kg; withers height: 113 cm), from stopp2018Basel;textualzoolog.
Bos taurus. Standard values from means of cattle measures from Period II (Late Iron Age to Romano-British transition) of Elms Farm, Heybridge johnstone2002latezoolog.
Bos primigenius. Female aurochs from degerbol1970urus;textualzoolog.
Ovis aries. Mean values of measurements from a group of adult female Shetland sheep skeletons from a single flock davis1996measurementszoolog.
Ovis aries. Mean measurements from a group of male Soay sheep of known age clutton1990osteologyzoolog.
Ovis musimon. Inv.nr. 2266 (male; adult), from stopp2018Basel;textualzoolog.
Ovis orientalis. Field Museum of Chicago catalogue number: FMC 57951 (female; western Iran) from uerpmann1994animal;textualzoolog.
Capra hircus. Inv.nr. 1597 (male; adult), from stopp2018Basel;textualzoolog.
Capra hircus. Mean measurements from a group of goats of unknown age and sex clutton1990osteologyzoolog.
Capra aegagrus. Measurements based on female and male Capra aegagrus, Natural History Museum in London number: BMNH 651 M and L2 (Taurus Mountains in southern Turkey) from uerpmann1994animal;textualzoolog.
Sus domesticus. Mean measurements from a group of Late Neolithic pigs from Durrington Walls, England albarella2005neolithiczoolog.
Sus scrofa. Inv.nr. 1446 (male; 2-3 years old; life weight: 120 kg) from stopp2018Basel;textualzoolog.
Sus scrofa. Averaged left and right measurements of a female wild board from near Elazi<U+011F>, Turkey. Museum of Comparative Zoology, Harvard University, specimen #51621 hongo2000faunalzoolog.
Sus scrofa. Measurements based on a sample of modern wild boar, Sus scrofa libycus, (male and female; Kizilcahamam, Turkey) from payne1988components;textualzoolog, Appendix 2.
Cervus elaphus. Inv.nr. 2271 (male; adult) from stopp2018Basel;textualzoolog.
Dama mesopotamica. Adult female modern specimen from Israel (id #1047), curated in Archaeozoology Laboratory at the University of Haifa Harding2021zoolog.
Gazella gazella. Adult female modern specimen from Israel (id #1037), curated in Archaeozoology Laboratory at the University of Haifa Harding2021zoolog.
Equus asinus. Adult male modern specimen from Israel (id #1076), curated in Archaeozoology Laboratory at the University of Haifa Harding2021zoolog.
Equus caballus. 3 years old Icelandic mare (all bones fused, female) died in 1961, johnstone2004biometriczoolog. Skeleton held at the Zoologische Staatssammlung Munich in Germany. Specimen ID 1961/29.
Oryctolagus cuniculus. Adult male European rabbit from Audley End, Essex, UK, curated in the reference collection at University of Nottingham Arch department (ID RS139) Ameen2021zoolog.
The zoolog variable referencesDatabase collects all these
references. It is structured as a named list of named lists, following the
hierarchy described above:
str(referencesDatabase, max.level = 2)
## List of 14 ## $ Bos taurus :List of 3 ## ..$ Nieto :'data.frame': 68 obs. of 4 variables: ## ..$ Basel :'data.frame': 50 obs. of 4 variables: ## ..$ Johnstone:'data.frame': 24 obs. of 4 variables: ## $ Bos primigenius :List of 1 ## ..$ Degerbol:'data.frame': 50 obs. of 4 variables: ## $ Ovis aries :List of 2 ## ..$ Davis :'data.frame': 23 obs. of 4 variables: ## ..$ Clutton:'data.frame': 71 obs. of 4 variables: ## $ Ovis orientalis :List of 2 ## ..$ Basel :'data.frame': 36 obs. of 4 variables: ## ..$ Uerpmann:'data.frame': 50 obs. of 4 variables: ## $ Capra hircus :List of 2 ## ..$ Basel :'data.frame': 35 obs. of 4 variables: ## ..$ Clutton:'data.frame': 60 obs. of 4 variables: ## $ Capra aegagrus :List of 1 ## ..$ Uerpmann:'data.frame': 50 obs. of 4 variables: ## $ Sus domesticus :List of 1 ## ..$ Albarella:'data.frame': 42 obs. of 4 variables: ## $ Sus scrofa :List of 3 ## ..$ Basel:'data.frame': 41 obs. of 4 variables: ## ..$ Hongo:'data.frame': 96 obs. of 4 variables: ## ..$ Payne:'data.frame': 33 obs. of 4 variables: ## $ Cervus elaphus :List of 1 ## ..$ Basel:'data.frame': 14 obs. of 4 variables: ## $ Dama mesopotamica :List of 1 ## ..$ Haifa:'data.frame': 60 obs. of 4 variables: ## $ Gazella gazella :List of 1 ## ..$ Haifa:'data.frame': 63 obs. of 4 variables: ## $ Equus asinus :List of 1 ## ..$ Haifa:'data.frame': 48 obs. of 4 variables: ## $ Equus caballus :List of 1 ## ..$ Johnstone:'data.frame': 73 obs. of 4 variables: ## $ Oryctolagus cuniculus:List of 1 ## ..$ Nottingham:'data.frame': 58 obs. of 4 variables:
The references' database is organized per taxon. However, in general the
zooarchaeological data to be analysed includes several taxa. Thus, the
reference dataframe should include one reference standard for each relevant
taxon.
The zoolog variable referenceSets defines four possible
references:
referenceSets
| Bos taurus | Bos primigenius | Ovis aries | Ovis orientalis | Capra hircus | Capra aegagrus | Sus domesticus | Sus scrofa | Cervus elaphus | Dama mesopotamica | Gazella gazella | Equus asinus | Equus caballus | Oryctolagus cuniculus | |
| NietoDavisAlbarella | Nieto | Davis | Albarella | |||||||||||
| Basel | Basel | Basel | Basel | Basel | Basel | |||||||||
| Combi | Nieto | Clutton | Clutton | Basel | Basel | Haifa | Haifa | Haifa | Johnstone | Nottingham | ||||
| Groningen | Degerbol | Uerpmann | Uerpmann | Hongo |
Each row defines a reference set consisting of a reference source for
each taxon (column). The function
AssembleReference allows us to build the reference set
taking the selected taxon-specific references from the
referencesDatabase.
The zoolog variable reference is a named list including the
references defined by referenceSets:
str(reference)
## List of 4 ## $ NietoDavisAlbarella:'data.frame': 133 obs. of 4 variables: ## ..$ TAX : Factor w/ 3 levels "bota","ovar",..: 1 1 1 1 1 1 1 1 1 1 ... ## ..$ EL : Factor w/ 27 levels "AS","CAL","FE",..: 4 4 4 4 4 4 4 4 4 11 ... ## ..$ Measure : Factor w/ 24 levels "BFd","BFp","BT",..: 8 9 5 7 12 4 3 11 6 8 ... ## ..$ Standard: num [1:133] 259 234 78.3 90.2 29 ... ## $ Basel :'data.frame': 176 obs. of 4 variables: ## ..$ TAX : Factor w/ 5 levels "BOTA","Ovis orientalis",..: 1 1 1 1 1 1 1 1 1 1 ... ## ..$ EL : Factor w/ 28 levels "Astragalus","Calcaneus",..: 14 14 14 14 5 5 5 13 13 13 ... ## ..$ Measure : Factor w/ 26 levels "BFd","BFp","BG",..: 21 13 18 3 5 4 19 6 19 5 ... ## ..$ Standard: num [1:176] 65.9 83 66.9 58.1 95.3 ... ## $ Combi :'data.frame': 556 obs. of 4 variables: ## ..$ TAX : Factor w/ 10 levels "bota","OVAR",..: 1 1 1 1 1 1 1 1 1 1 ... ## ..$ EL : Factor w/ 56 levels "AS","CAL","FE",..: 4 4 4 4 4 4 4 4 4 11 ... ## ..$ Measure : Factor w/ 63 levels "BFd","BFp","BT",..: 8 9 5 7 12 4 3 11 6 8 ... ## ..$ Standard: num [1:556] 259 234 78.3 90.2 29 ... ## $ Groningen :'data.frame': 246 obs. of 4 variables: ## ..$ TAX : Factor w/ 4 levels "Bos primigenius",..: 1 1 1 1 1 1 1 1 1 1 ... ## ..$ EL : Factor w/ 23 levels "Astragalus","Calcaneus",..: 13 13 13 5 5 5 5 5 12 12 ... ## ..$ Measure : Factor w/ 45 levels "BFp","BG","BT",..: 14 12 2 8 9 4 3 13 8 5 ... ## ..$ Standard: num [1:246] 69 70 60 359 309 97 89 46 320 100 ...
reference$Combi includes the most comprehensive reference for each
species so that more measurements can be considered. It is the default
reference for computing the log ratios.
If desired, the user can define their own combinations or can also use their own references, which must be a dataframe with the format described above.
referencesDatabase, refereceSets, and reference are exported variables
automatically loaded in memory. In addition, zoolog provides in the
extdata folder a set of semicolon separated files (csv), generating
them:
referenceSets.csvDefines referenceSets.
referencesDatabase.csvDefines the structure of
referencesDatabase.
A csv file for each taxon-specific reference, as named in
referencesDatabase.csv.
utils::read.csv2(system.file("extdata", "referencesDatabase.csv",
package = "zoolog"))
## Genus Taxon Source ## 1 Cattle - *Bos* Bos taurus Nieto ## 2 Cattle - *Bos* Bos taurus Basel ## 3 Cattle - *Bos* Bos taurus Johnstone ## 4 Cattle - *Bos* Bos primigenius Degerbol ## 5 Sheep - *Ovis* Ovis aries Davis ## 6 Sheep - *Ovis* Ovis aries Clutton ## 7 Sheep - *Ovis* Ovis orientalis Basel ## 8 Sheep - *Ovis* Ovis orientalis Uerpmann ## 9 Goat - *Capra* Capra hircus Basel ## 10 Goat - *Capra* Capra hircus Clutton ## 11 Goat - *Capra* Capra aegagrus Uerpmann ## 12 Pig - *Sus* Sus domesticus Albarella ## 13 Pig - *Sus* Sus scrofa Basel ## 14 Pig - *Sus* Sus scrofa Hongo ## 15 Pig - *Sus* Sus scrofa Payne ## 16 Red deer - *Cervus* Cervus elaphus Basel ## 17 Fallow deer - *Dama* Dama mesopotamica Haifa ## 18 Gazelle - *Gazella* Gazella gazella Haifa ## 19 Equid - *Equus* Equus asinus Haifa ## 20 Equid - *Equus* Equus caballus Johnstone ## 21 European rabbit - *Oryctolagus* Oryctolagus cuniculus Nottingham ## Filename ## 1 referenceCattle_Nieto.csv ## 2 referenceCattle_Basel.csv ## 3 referenceCattle_Johnstone.csv ## 4 referenceCattle_Degerbol.csv ## 5 referenceSheep_Davis.csv ## 6 referenceSheep_Clutton.csv ## 7 referenceSheep_Basel.csv ## 8 referenceSheep_Uerpmann.csv ## 9 referenceGoat_Basel.csv ## 10 referenceGoat_Clutton.csv ## 11 referenceGoat_Uerpmann.csv ## 12 referencePig_Albarella.csv ## 13 referencePig_Basel.csv ## 14 referencePig_Hongo.csv ## 15 referencePig_Payne.csv ## 16 referenceRedDeer_Basel.csv ## 17 referenceDama_Haifa.csv ## 18 referenceGazelle_Haifa.csv ## 19 referenceEquid_Haifa.csv ## 20 referenceEquid_Johnstone.csv ## 21 referenceRabbit_Nottingham.csv
We are grateful to Barbara Stopp and Sabine Deschler-Erb for providing the Basel references for cattle, sheep, goat, wild boar, and red deer stopp2018Baselzoolog, together with the permission to publish them as part of zoolog.
We thank also Francesca Slim and Dimitris Filioglou for providing the references for aurochs, mouflon, wild goat, and wild boar degerbol1970urus,uerpmann1994animal,hongo2000faunalzoolog in the Groningen set.
We thank Claudia Minniti for providing Johnstone's reference for cattle. johnstone2002latezoolog.
We are also grateful to Sierra Harding and Nimrod Marom for providing the Haifa standard measurements for donkey, gazelle, and fallow deer Harding2021zoolog.
We thank Carly Ameen for providing references for horse johnstone2004biometriczoolog and rabbit Ameen2021zoolog.