referencesDatabase: References
In josempozo/zoolog: Zooarchaeological Analysis with Log-Ratios
referencesDatabase R Documentation
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
reference
referenceSets
referencesDatabase
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.
An object of class data.frame with 4 rows and 15 columns.
An object of class list of length 15.
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.
Non-standard measures converted to more standard ones
\insertCitevon1976guidezoolog
- Steppan
-
Bos primigenius.
Female aurochs from \insertCitesteppan2001ur;textualzoolog.
Same specimen as in \insertCitedegerbol1970urus;textualzoolog,
but with new and more standandard measures \insertCitevon1976guidezoolog.
Mean measurements from left and right bones when available.
- 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.
- Canid - Canis
-
- Russell
-
Canis lupus.
Hungarian Agricultural Museum:
Specimen 73.4 (small mature female; probably local origin)
from \insertCiterussell1993hunting;textualzoolog.
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 15
#> $ 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 2
#> ..$ Degerbol:'data.frame': 50 obs. of 4 variables:
#> ..$ Steppan :'data.frame': 84 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': 75 obs. of 4 variables:
#> $ Oryctolagus cuniculus:List of 1
#> ..$ Nottingham:'data.frame': 58 obs. of 4 variables:
#> $ Canis lupus :List of 1
#> ..$ Russell:'data.frame': 77 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 Canis lupus
NietoDavisAlbarella Nieto Davis Albarella
Basel Basel Basel Basel Basel Basel
Combi Nieto Clutton Clutton Basel Basel Haifa Haifa Haifa Johnstone Nottingham Russell
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/ 26 levels "BFd","BFp","BT",..: 8 9 5 7 13 4 3 12 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': 635 obs. of 4 variables:
#> ..$ TAX : Factor w/ 11 levels "bota","OVAR",..: 1 1 1 1 1 1 1 1 1 1 ...
#> ..$ EL : Factor w/ 69 levels "AS","CAL","FE",..: 4 4 4 4 4 4 4 4 4 11 ...
#> ..$ Measure : Factor w/ 83 levels "BFd","BFp","BT",..: 8 9 5 7 13 4 3 12 6 8 ...
#> ..$ Standard: num [1:635] 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.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 Cattle - *Bos* Bos primigenius Steppan
#> 6 Sheep - *Ovis* Ovis aries Davis
#> 7 Sheep - *Ovis* Ovis aries Clutton
#> 8 Sheep - *Ovis* Ovis orientalis Basel
#> 9 Sheep - *Ovis* Ovis orientalis Uerpmann
#> 10 Goat - *Capra* Capra hircus Basel
#> 11 Goat - *Capra* Capra hircus Clutton
#> 12 Goat - *Capra* Capra aegagrus Uerpmann
#> 13 Pig - *Sus* Sus domesticus Albarella
#> 14 Pig - *Sus* Sus scrofa Basel
#> 15 Pig - *Sus* Sus scrofa Hongo
#> 16 Pig - *Sus* Sus scrofa Payne
#> 17 Red deer - *Cervus* Cervus elaphus Basel
#> 18 Fallow deer - *Dama* Dama mesopotamica Haifa
#> 19 Gazelle - *Gazella* Gazella gazella Haifa
#> 20 Equid - *Equus* Equus asinus Haifa
#> 21 Equid - *Equus* Equus caballus Johnstone
#> 22 European rabbit - *Oryctolagus* Oryctolagus cuniculus Nottingham
#> 23 Canid - *Canis* Canis lupus Russell
#> Filename
#> 1 referenceCattle_Nieto.csv
#> 2 referenceCattle_Basel.csv
#> 3 referenceCattle_Johnstone.csv
#> 4 referenceCattle_Degerbol.csv
#> 5 referenceCattle_Steppan.csv
#> 6 referenceSheep_Davis.csv
#> 7 referenceSheep_Clutton.csv
#> 8 referenceSheep_Basel.csv
#> 9 referenceSheep_Uerpmann.csv
#> 10 referenceGoat_Basel.csv
#> 11 referenceGoat_Clutton.csv
#> 12 referenceGoat_Uerpmann.csv
#> 13 referencePig_Albarella.csv
#> 14 referencePig_Basel.csv
#> 15 referencePig_Hongo.csv
#> 16 referencePig_Payne.csv
#> 17 referenceRedDeer_Basel.csv
#> 18 referenceDama_Haifa.csv
#> 19 referenceGazelle_Haifa.csv
#> 20 referenceEquid_Haifa.csv
#> 21 referenceEquid_Johnstone.csv
#> 22 referenceRabbit_Nottingham.csv
#> 23 referenceCanid_Russell.csv
Acknowledgement
We are grateful to Barbara Stopp and Sabine Deschler-Erb
(University of Basel, Switzerland)
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 (University of Groningen)
for providing the references for aurochs, mouflon, wild goat, and wild boar
\insertCitedegerbol1970urus,uerpmann1994animal,hongo2000faunalzoolog
in the Groningen set.
We thank Claudia Minniti (University of Salento) for providing Johnstone's
reference for cattle \insertCitejohnstone2002latezoolog.
We are also grateful to Sierra Harding and Nimrod Marom (University of Haifa)
for providing the Haifa standard measurements for donkey, mountain gazelle,
and Persian fallow deer \insertCiteHarding2021zoolog.
We thank Carly Ameen and Helene Benkert (University of Exeter) for providing
references for horse \insertCitejohnstone2004biometriczoolog and
European rabbit \insertCiteAmeen2021zoolog.
We thank Mikolaj Lisowski (University of York) for pointing to the existence
of the improved reference for Bos primigenius
\insertCitesteppan2001urzoolog and providing its source.
References
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josempozo/zoolog documentation built on Sept. 12, 2022, 12:10 p.m.
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| referencesDatabase | R Documentation |
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
reference referenceSets referencesDatabase
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.
An object of class data.frame with 4 rows and 15 columns.
An object of class list of length 15.
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. Non-standard measures converted to more standard ones \insertCitevon1976guidezoolog
- Steppan
-
Bos primigenius. Female aurochs from \insertCitesteppan2001ur;textualzoolog. Same specimen as in \insertCitedegerbol1970urus;textualzoolog, but with new and more standandard measures \insertCitevon1976guidezoolog. Mean measurements from left and right bones when available.
- 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.
- Canid - Canis
-
- Russell
-
Canis lupus. Hungarian Agricultural Museum: Specimen 73.4 (small mature female; probably local origin) from \insertCiterussell1993hunting;textualzoolog.
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 15 #> $ 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 2 #> ..$ Degerbol:'data.frame': 50 obs. of 4 variables: #> ..$ Steppan :'data.frame': 84 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': 75 obs. of 4 variables: #> $ Oryctolagus cuniculus:List of 1 #> ..$ Nottingham:'data.frame': 58 obs. of 4 variables: #> $ Canis lupus :List of 1 #> ..$ Russell:'data.frame': 77 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 | Canis lupus | |
| NietoDavisAlbarella | Nieto | Davis | Albarella | ||||||||||||
| Basel | Basel | Basel | Basel | Basel | Basel | ||||||||||
| Combi | Nieto | Clutton | Clutton | Basel | Basel | Haifa | Haifa | Haifa | Johnstone | Nottingham | Russell | ||||
| 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/ 26 levels "BFd","BFp","BT",..: 8 9 5 7 13 4 3 12 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': 635 obs. of 4 variables: #> ..$ TAX : Factor w/ 11 levels "bota","OVAR",..: 1 1 1 1 1 1 1 1 1 1 ... #> ..$ EL : Factor w/ 69 levels "AS","CAL","FE",..: 4 4 4 4 4 4 4 4 4 11 ... #> ..$ Measure : Factor w/ 83 levels "BFd","BFp","BT",..: 8 9 5 7 13 4 3 12 6 8 ... #> ..$ Standard: num [1:635] 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.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 Cattle - *Bos* Bos primigenius Steppan
#> 6 Sheep - *Ovis* Ovis aries Davis
#> 7 Sheep - *Ovis* Ovis aries Clutton
#> 8 Sheep - *Ovis* Ovis orientalis Basel
#> 9 Sheep - *Ovis* Ovis orientalis Uerpmann
#> 10 Goat - *Capra* Capra hircus Basel
#> 11 Goat - *Capra* Capra hircus Clutton
#> 12 Goat - *Capra* Capra aegagrus Uerpmann
#> 13 Pig - *Sus* Sus domesticus Albarella
#> 14 Pig - *Sus* Sus scrofa Basel
#> 15 Pig - *Sus* Sus scrofa Hongo
#> 16 Pig - *Sus* Sus scrofa Payne
#> 17 Red deer - *Cervus* Cervus elaphus Basel
#> 18 Fallow deer - *Dama* Dama mesopotamica Haifa
#> 19 Gazelle - *Gazella* Gazella gazella Haifa
#> 20 Equid - *Equus* Equus asinus Haifa
#> 21 Equid - *Equus* Equus caballus Johnstone
#> 22 European rabbit - *Oryctolagus* Oryctolagus cuniculus Nottingham
#> 23 Canid - *Canis* Canis lupus Russell
#> Filename
#> 1 referenceCattle_Nieto.csv
#> 2 referenceCattle_Basel.csv
#> 3 referenceCattle_Johnstone.csv
#> 4 referenceCattle_Degerbol.csv
#> 5 referenceCattle_Steppan.csv
#> 6 referenceSheep_Davis.csv
#> 7 referenceSheep_Clutton.csv
#> 8 referenceSheep_Basel.csv
#> 9 referenceSheep_Uerpmann.csv
#> 10 referenceGoat_Basel.csv
#> 11 referenceGoat_Clutton.csv
#> 12 referenceGoat_Uerpmann.csv
#> 13 referencePig_Albarella.csv
#> 14 referencePig_Basel.csv
#> 15 referencePig_Hongo.csv
#> 16 referencePig_Payne.csv
#> 17 referenceRedDeer_Basel.csv
#> 18 referenceDama_Haifa.csv
#> 19 referenceGazelle_Haifa.csv
#> 20 referenceEquid_Haifa.csv
#> 21 referenceEquid_Johnstone.csv
#> 22 referenceRabbit_Nottingham.csv
#> 23 referenceCanid_Russell.csv
Acknowledgement
We are grateful to Barbara Stopp and Sabine Deschler-Erb (University of Basel, Switzerland) 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 (University of Groningen) for providing the references for aurochs, mouflon, wild goat, and wild boar \insertCitedegerbol1970urus,uerpmann1994animal,hongo2000faunalzoolog in the Groningen set.
We thank Claudia Minniti (University of Salento) for providing Johnstone's reference for cattle \insertCitejohnstone2002latezoolog.
We are also grateful to Sierra Harding and Nimrod Marom (University of Haifa) for providing the Haifa standard measurements for donkey, mountain gazelle, and Persian fallow deer \insertCiteHarding2021zoolog.
We thank Carly Ameen and Helene Benkert (University of Exeter) for providing references for horse \insertCitejohnstone2004biometriczoolog and European rabbit \insertCiteAmeen2021zoolog.
We thank Mikolaj Lisowski (University of York) for pointing to the existence of the improved reference for Bos primigenius \insertCitesteppan2001urzoolog and providing its source.
References
\insertAllCitedR Package Documentation
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