Description Usage Arguments Details Value Note Author(s) References Examples
Calculates the Fst from a conditional kinship matrix.
1 |
rval |
is a conditional kinship matrix, normally obtained by the functions 'R' and 'rel.cond' in the Biodem library. |
N |
the vector of effective populations size, nominally obtained by dividing the total population size by three. Starting form surname data, effective population size coincides with the number of marriages |
The use of the Fst function follows Harpending and Jenkins 1974, and Jorde 1982. It gives an estimate of Wright's Fst, which is a measure of between-subdivision genetic heterogeneity.
Fst returns one numeric value.
...
Federico C. F. Calboli f.calboli@gmail.com
Harpending, H. C. and T. jenkins. 1974. !Kung population structure. In: J. F. Crow and C. F. Denniston (eds.), Genetic distance, pp 137-161. Plenum Press, NY.
Jorde, L. B. 1982. The genetic structure of the Utah mormons: migration analysis. Human Biology 54(3): 583-597.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | # Swedlund data again...
data(P); data(S); data(N)
# starting with how many cycles to equilibrium
x<-mal.eq(S,P,N)
# calculation of phi
phi<-mal.phi(S,P,N,x)
# calculation of the conditional kinship matrix
cond<-mal.cond(phi,N)
# finally! we get the Fst value
fst<-Fst(cond,N)
fst
# starting from a raw marriage records dataset:
data(valley)
tot <- sur.freq(valley,valley$PAR,valley$SURM,valley$SURF)
tot # a frequency table calculated above all the surnames
iso.matrix <- uri(tot)
iso.matrix # an unbiased random isonymy matrix
reg <- rri(tot)
reg # a coefficient of unbiased Regional Random Isonymy
kin.cond <- rel.cond(iso.matrix,reg)
kin.cond # a conditional kinship matrix
N <- colSums(tot) # effective population size
fst<-Fst(kin.cond,N)
fst
|
[,1]
[1,] 0.0002614661
1 2 3 4
AGOSTI 0 1 0 0
ALBASINI 0 4 0 0
ALBERTI 0 1 0 0
AMBROSI 1 0 0 0
ANGELI 0 5 0 1
ARMANI 0 0 0 1
BARBETTI 1 0 15 0
BEGNUDELLI 0 1 0 0
BELFANTI 0 12 0 0
BERGAGNINI 0 1 0 0
BERNARDELLI 0 32 0 0
BERTOLAS 0 1 0 0
BEVILACQUA 3 1 1 3
BEZZI 1 1 0 0
BISOFFI 0 1 0 0
BONAN 1 0 0 0
BONAPOZZA 0 1 0 0
BONETTI 0 4 0 1
BONI 0 1 1 1
BONTEMPELLI 0 2 1 0
BORGA 0 1 0 0
BORONI 0 11 0 0
BORTOLAMEOLLI 35 0 1 0
BORTOLOTTO 0 1 0 0
BORZATTI 0 12 0 0
BOSINELLI 0 0 0 1
BOSINI 0 0 2 0
BOTTEA 0 2 0 0
BOZZETTA 0 1 0 0
BRAJONI 0 0 0 1
BRESADOLA 3 1 1 69
BRIANI 0 1 0 0
BRUSACORAM 0 21 0 0
CABONETTI 0 5 0 0
CARNESALINI 0 6 0 0
CASANOVA 0 0 0 1
CASEROTTI 0 0 0 3
CASNA 0 0 0 1
CAVALLAR 0 12 5 0
CAZZUFFI 0 1 0 0
CHIESA 0 0 0 1
CHINI 0 0 0 1
CIPRIANI 0 1 0 0
CLASER 0 18 0 0
COGOLI 2 0 0 1
COMENOLI 0 0 1 0
CONTA 0 6 0 1
COSI 0 1 0 0
COSTANZI 0 2 0 0
COVA 0 0 0 1
DALDOSS 1 0 0 0
DALLAGO 1 0 0 0
DALLASERRA 0 0 11 1
DALLATORRE 1 7 49 1
DALLAVALLE 0 0 1 0
DALLECASE 0 1 0 0
DALPEZ 0 0 1 0
DALPIAZ 0 0 1 0
DAPRA' 1 4 3 6
DELL'EVA 0 2 0 0
DELPERO 0 0 0 1
DI PIETRO 0 0 0 1
DOLFI 0 0 1 0
DOLZANI 0 2 0 0
DONATI 0 11 0 1
ECCHER 0 0 0 1
ENDRIZZI 0 2 0 0
FANTELLI 0 11 0 0
FAVA 0 1 0 0
FEDRICI 0 0 1 0
FEDRIGONI 0 0 1 0
FEDRIZZI 1 0 0 0
FEZZI 5 0 0 0
FLESSATI 0 31 1 0
FONTANARI 0 0 1 0
FORTUNATI 0 0 0 1
GABRIELLI 1 0 0 0
GASPERETTI 0 0 0 1
GENTILINI 0 0 0 1
GHIRARDI 0 0 3 0
GIACONI 0 2 2 0
GIAROLLI 0 2 0 0
GIONTA 0 0 1 0
GIRARDI 0 1 7 1
GOSETTI 1 3 38 1
GOSSER 0 0 0 1
GRAMOLA 0 15 0 1
GRAZIOLLI 1 0 0 0
GREIFEMBERG 0 1 0 1
GUARDI 0 5 0 0
IACHELINI 0 5 1 0
IANES 0 1 0 0
KERSCHBAMER 0 1 0 0
LANA 10 0 0 1
LARGAIOLLI 1 2 0 0
LONGHI 1 2 0 0
LORENZONI 0 0 0 1
LUCIETTI 2 0 0 0
MAGAGNA 0 1 0 0
MANINI 0 1 0 0
MANZONI 0 1 0 0
MAPROVE 0 0 1 0
MARACANI 5 7 0 0
MARCHESI 1 1 0 0
MARINI 4 0 0 0
MARINOLLI 0 4 0 1
MARK 0 1 0 0
MARTINELLI 0 0 1 1
MARTINI 0 0 0 2
MARTINOLLI 0 2 0 0
MATTEOTTI 0 1 0 0
MATURI 0 0 1 0
MELCHIORI 0 13 0 0
MENGHINI 1 0 0 0
MENGON 1 0 0 1
MENON 0 1 0 0
MICHELI 0 0 0 1
MISSERONI 0 1 0 0
MOCHEN 0 3 0 0
MOLIGNONI 49 0 0 1
MORATELLI 0 1 0 0
MORATTI 8 0 1 1
MORESCHINI 0 0 1 0
MOSER 0 22 0 0
NOLDIN 0 0 0 2
PANGRAZZI 0 0 1 1
PANIZZA 2 0 0 0
PARIS 0 0 0 2
PAROLARI 0 0 0 33
PATERNOSTER 0 1 0 0
PEDERGNANA 0 7 3 3
PEDRAZZOLI 6 1 0 3
PEDRI 0 3 0 0
PEDROTTI 0 0 1 0
PEGOLOTTI 0 1 0 0
PENASA 0 13 0 1
PIAZZA 0 0 0 2
PIAZZOLA 0 0 2 0
PICCININI 0 0 1 0
PICHLER 1 0 0 0
PIETRO 0 0 1 0
PLACHI 1 0 1 0
PODETTI 0 58 1 0
POLLI 0 2 0 0
PONTIROLLI 0 5 0 0
PORT 0 3 0 0
POVINELLI 0 1 0 0
PREGHENELLA 0 1 0 0
PULLER 2 1 0 0
RAHLER 1 0 0 0
RAMPONI 0 1 0 0
RAVELLI 2 5 75 4
REDOLFI 2 1 74 0
RESSIAMEV 0 1 0 0
RIZZI 0 0 2 0
ROMAGNA 0 2 0 0
ROMEDIO 1 0 0 0
ROSSI 1 64 3 0
RUATTI 0 1 0 0
RUFFINI 0 0 1 0
SALVADORI 0 0 27 1
SALVATERRA 1 0 0 0
SANTINI 1 0 0 0
SARTORI 0 8 0 0
SAVINELLI 0 9 0 0
SCHMITH 0 1 0 0
SCHWEITZER 1 0 0 1
SERRA 0 1 0 0
SILVESTRI 0 1 0 0
SLANZI 1 0 0 0
SMALZI 0 1 0 0
STABLUM 0 3 0 0
STANCHINA 0 0 0 1
STAUDER 2 0 0 0
STOCCHETTI 1 0 0 0
TABACCHINI 0 10 0 0
TADDEI 0 1 0 0
TAPPARELLI 0 2 0 1
TEVINI 0 6 0 0
TOFFENETTI 2 0 0 37
TOGNALI 0 1 12 0
TOLARDO 0 1 0 0
TOMASI 16 1 0 0
TONNER 0 0 1 0
TRETTEL 0 3 0 0
VALENTINELLI 0 3 0 0
VALENTINOTTI 0 2 0 0
VALLORZ 0 5 1 0
VANZETTA 0 0 1 0
VANZOLAS 0 1 0 0
VARESCHI 0 1 0 0
VEGHER 0 3 0 0
VENERI 1 0 0 0
VERONESI 1 0 0 0
VIVIANI 0 1 0 0
VOLCAN 0 0 1 0
VOLTOLINI 0 0 0 2
ZALLA 0 0 0 21
ZAMBELLI 10 0 0 3
ZANELLA 1 0 0 0
ZANETTI 2 0 0 0
ZANINI 0 1 0 0
ZANON 0 15 1 0
ZENI 0 1 0 0
ZORZI 0 2 0 0
[,1] [,2] [,3] [,4]
[1,] 0.101719127 0.001328383 0.006167830 0.008915086
[2,] 0.001328383 0.035080690 0.006070128 0.001504237
[3,] 0.006167830 0.006070128 0.119455049 0.006193850
[4,] 0.008915086 0.001504237 0.006193850 0.136711143
[1] 0.0236185
[,1] [,2] [,3] [,4]
[1,] 0.019641131 -0.005605628 -0.004388580 -0.003697686
[2,] -0.005605628 0.002882569 -0.004413151 -0.005561403
[3,] -0.004388580 -0.004413151 0.024101448 -0.004382036
[4,] -0.003697686 -0.005561403 -0.004382036 0.028441095
[,1]
[1,] 0.01512128
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