referencesDatabase: References

Description Usage Format Data Source Reference Sets File Structure Acknowledgement References

Description

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.

Usage

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Format

Each reference is a data.frame including 4 columns:

TAX

The taxon to which each reference bone belongs.

EL

The skeletal element.

Measure

The type of measurement taken on the bone.

Standard

The value of the measurement taken on the bone. All the measurements are expressed in millimetres.

Data Source

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:

Cattle - Bos
Nieto

Bos taurus. Female cow dated to the Early Bronze Age (Minferri, Catalonia), in \insertCitenieto2018element;textualzoolog.

Basel

Bos taurus. Inv.nr. 2426 (Hinterwälder; female; 17 years old; live weight: 340 kg; withers height: 113 cm), from \insertCitestopp2018Basel;textualzoolog.

Johnstone

Bos taurus. Standard values from means of cattle measures from Period II (Late Iron Age to Romano-British transition) of Elms Farm, Heybridge \insertCitejohnstone2002latezoolog.

Degerbøl

Bos primigenius. Female aurochs from \insertCitedegerbol1970urus;textualzoolog.

Sheep - Ovis
Davis

Ovis aries. Mean values of measurements from a group of adult female Shetland sheep skeletons from a single flock \insertCitedavis1996measurementszoolog.

Clutton

Ovis aries. Mean measurements from a group of male Soay sheep of known age \insertCiteclutton1990osteologyzoolog.

Basel

Ovis musimon. Inv.nr. 2266 (male; adult), from \insertCitestopp2018Basel;textualzoolog.

Uerpmann

Ovis orientalis. Field Museum of Chicago catalogue number: FMC 57951 (female; western Iran) from \insertCiteuerpmann1994animal;textualzoolog.

Goat - Capra
Basel

Capra hircus. Inv.nr. 1597 (male; adult), from \insertCitestopp2018Basel;textualzoolog.

Clutton

Capra hircus. Mean measurements from a group of goats of unknown age and sex \insertCiteclutton1990osteologyzoolog.

Uerpmann

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 \insertCiteuerpmann1994animal;textualzoolog.

Pig - Sus
Albarella

Sus domesticus. Mean measurements from a group of Late Neolithic pigs from Durrington Walls, England \insertCitealbarella2005neolithiczoolog.

Basel

Sus scrofa. Inv.nr. 1446 (male; 2-3 years old; life weight: 120 kg) from \insertCitestopp2018Basel;textualzoolog.

Hongo

Sus scrofa. Averaged left and right measurements of a female wild board from near Elaziğ, Turkey. Museum of Comparative Zoology, Harvard University, specimen #51621 \insertCitehongo2000faunalzoolog.

Payne

Sus scrofa. Measurements based on a sample of modern wild boar, Sus scrofa libycus, (male and female; Kizilcahamam, Turkey) from \insertCitepayne1988components;textualzoolog, Appendix 2.

Red deer - Cervus
Basel

Cervus elaphus. Inv.nr. 2271 (male; adult) from \insertCitestopp2018Basel;textualzoolog.

Fallow deer - Dama
Haifa

Dama mesopotamica. Adult female modern specimen from Israel (id #1047), curated in Archaeozoology Laboratory at the University of Haifa \insertCiteHarding2021zoolog.

Gazelle - Gazella
Haifa

Gazella gazella. Adult female modern specimen from Israel (id #1037), curated in Archaeozoology Laboratory at the University of Haifa \insertCiteHarding2021zoolog.

Equid - Equus
Haifa

Equus asinus. Adult male modern specimen from Israel (id #1076), curated in Archaeozoology Laboratory at the University of Haifa \insertCiteHarding2021zoolog.

Johnstone

Equus caballus. 3 years old Icelandic mare (all bones fused, female) died in 1961, \insertCitejohnstone2004biometriczoolog. Skeleton held at the Zoologische Staatssammlung Munich in Germany. Specimen ID 1961/29.

European rabbit - Oryctolagus
Nottingham

Oryctolagus cuniculus. Adult male European rabbit from Audley End, Essex, UK, curated in the reference collection at University of Nottingham Arch department (ID RS139) \insertCiteAmeen2021zoolog.

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)
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## 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:

Reference Sets

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)
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## 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.

File Structure

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.csv

Defines referenceSets.

referencesDatabase.csv

Defines 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"))
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##                              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

Acknowledgement

We are grateful to Barbara Stopp and Sabine Deschler-Erb for providing the Basel references for cattle, sheep, goat, wild boar, and red deer \insertCitestopp2018Baselzoolog, 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 \insertCitedegerbol1970urus,uerpmann1994animal,hongo2000faunalzoolog in the Groningen set.

We thank Claudia Minniti for providing Johnstone's reference for cattle. \insertCitejohnstone2002latezoolog.

We are also grateful to Sierra Harding and Nimrod Marom for providing the Haifa standard measurements for donkey, gazelle, and fallow deer \insertCiteHarding2021zoolog.

We thank Carly Ameen for providing references for horse \insertCitejohnstone2004biometriczoolog and rabbit \insertCiteAmeen2021zoolog.

References

\insertAllCited
zoolog documentation built on Sept. 5, 2021, 5:37 p.m.