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Anyone have a clue why hclust() and agnes() produce different results in the
example below when both use method="average"?? I'm not able to reproduce
the problem with other datasets.
ereck<-read.table("Ereck.txt",header=TRUE,sep="\t")
emol<-subset(ereck,select=c(11:18,20:32))
library(cluster)
library(mva)
daisemol<-daisy(emol,type=list(asymm=c(1:21)))
layout(matrix(c(1,1,2,2),2,2,byrow=TRUE))
hclustmol<-hclust(daisemol,method="average")
plot(hclustmol,cex=0.6)
agnesmol<-agnes(daisemol,method="average")
pltree(agnesmol,cex=0.6)
coagnes<-cophenetic(agnesmol)
cor(coagnes,daisemol)
cohclust<-cophenetic(hclustmol)
cor(cohclust,daisemol)
I'm using R 1.7.1 (2003-06-16) on Windows XP. Library "cluster" version
1.7.4 and library "mva" version 1.7.1.
Best wishes,
Mikkel
Mikkel Grum
International Plant Genetic Resources Institute (IPGRI)
Sub-Saharan Africa Group
***
PO Box 30677
00100 Nairobi, Kenya
Tel: +254 20 524505(direct)/524500(IPGRI)
Fax: +254 20 524501(IPGRI)/524001(ICRAF)
[EMAIL PROTECTED]
www.ipgri.org
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Content-Type: text/plain;
name="Ereck.txt"
Content-Transfer-Encoding: quoted-printable
Content-Disposition: attachment;
filename="Ereck.txt"
COLLNUM NPGRC No LOCALNAME DISTRICT VILLAGE PROVINCE
DISEASERESISTANCE =
PLANTUSES PARTUSED FARMER V1 V2 V3 V4 V5 V6
V7 V8 V9 V10 V11 V12 V13 =
V14 V15 V16 V17 V18 V19 V20 V21 V22
MMB05 1343 Nhongoro Nyanga Samakande Manicaland food
"stalk, seed" Mr =
Bulawayo 0 1 0 0 0 0 0 1 1
0 0 0 1 0 1 0 0 0 0 1
0 1
MMB07 1345 Ipwa Nyanga Samakande Manicaland food
"stalk, seed" Mr =
Bulawayo 0 1 0 0 0 0 0 1 1
0 0 0 1 0 1 0 0 0 0 1
0 1
MMBO8 1346 Ipwa Nyanga Samakande Manicaland food
"stalk, seed" Mr =
Bulawayo 0 0 0 0 1 0 0 1 1
0 0 1 0 0 1 0 0 0 0 1
1 0
MMB17 1355 Musoswe Nyanga Chibvembe Manicaland "food,
beverage" =
"stalk, seed" Mr Mupunwa 0 0 1 0 0 0 0
1 1 0 0 0 1 0 1 0 0 0
1 0 1 0
MMB40 1378 Nzende Nyanga Mangezi Manicaland grasshoppers "food, =
beverage" seed Mr Kambara 0 1 0 0 0 0
0 1 1 0 0 0 1 0 0 1 0
0 0 1 0 1
MMB46 1384 Nzende Nyanga Mangezi Manicaland low resistance to rotting
=
food seed Mrs Chitimas 0 1 0 0 0 0 0
1 1 0 0 0 1 0 1 0 0 0
1 0 0 1
MMB47 1385 Musoswe Nyanga Mangezi Manicaland food seed Mrs
Chitimas 0 =
0 0 1 0 0 1 0 1 0 0 0
1 0 1 0 0 0 1 0 0 1
MMB54 1392 Nhongoro Nyanga Mangezi Manicaland black sports on head
food =
" seed, stalk" Mrs P Mangezi 0 0 1 0 0 0 0
1 1 0 0 0 1 0 0 0 0 1
0 1 0 =
1
MMB57 1395 Mudhabhure Nyanga Mangezi Manicaland food seed
Mrs P =
Mangezi 0 1 0 0 0 0 0 1 1 0
0 0 1 0 0 1 0 0 1 0 1
0
MMB61 1399 Nzende Nyanga Mangezi Manicaland "food, beverage"
seed Mrs =
I Mangezi 0 0 0 1 0 0 1 0 1
0 0 0 1 0 1 0 0 0 0 1
0 1
MMB62 1400 Nhongoro Nyanga Mangezi Manicaland "food,
beverage" seed =
Mrs I Mangezi 0 0 0 1 0 0 0 1 1
0 0 0 1 0 0 1 0 0 1 0
0 1
MMB63 1401 Musoswe Nyanga Mangezi Manicaland food seed Mrs I
Mangezi =
1 0 0 0 0 0 0 1 1 0 0
0 1 0 0 1 0 0 0 1 0 1
MMB64 1402 Sorghum Nyanga Mangezi Manicaland food seed Mrs I
Mangezi =
0 0 0 1 0 0 0 1 1 0 0
0 1 0 1 0 0 0 0 1 0 1
MMB71 1409 Nhongoro Nyanga Mangezi Manicaland "food,
beverage" seed =
Mr & Mrs S Charachimwe 0 0 1 0 0 0 0 1
1 0 0 0 1 0 0 1 0 0 0
1 1 0
MMB74 1412 Sorghum (white) Nyanga Mangezi Manicaland food seed
Mr & =
Mrs S Charachimwe 1 0 0 0 0 0 0 1
1 0 0 0 1 0 0 1 0 0 0
1 0 1
MMB 1425 0
0 1 0 0 1 0 1 1 0 0 1
0 0 0 1 0 0 0 1 1 0
MMB90 1428 Musoswe Nyanga Kamunhukamwe Manicaland black smuts "food,
=
beverage" " seed, stalk" Mrs Katanganda 0 0 0 1 0
0 1 0 1 0 0 1 0 0 1 0
=
0 0 1 0 0 1
MMB92 1430 Sorghum Nyanga Kamunhukamwe Manicaland food seed
Mrs =
Katanganda 0 0 0 0 1 0 0 1 1
0 0 0 1 0 1 0 0 0 0 1
1 0
MMB103 1441 Musoswe Nyanga Kamunhukamwe Manicaland smuts diseases food
=
" seed, stalk" Mrs M Makombe 0 1 0 0 0 0 0
1 1 0 0 0 1 0 0 1 0 0
1 0 1 =
0
MMB110 1448 Musoswe Nyanga Kamunhukamwe Manicaland "food,
beverage" =
seed Mr & Mrs Musambidzi 0 1 0 0 0 0 0
1 1 0 0 1 0 0 1 0 0 0
1 0 0 1
MMB112 1450 Sorghum (shodhani) Nyanga Kamunhukamwe Manicaland
"food, =
beverage" seed Mr & Mrs Musambidzi 0 0 1 0 1
0 0 1 1 0 0 0 1 0 1 0
0 0 =
0 1 1 0
MMB117 1455 Ipwa Nyanga Kamunhukamwe Manicaland food stalk
Mr & Mrs =
Musambidzi 0 0 1 0 0 0 0 1 1
0 0 0 1 0 0 1 0 0 1 0
1 0
MMB121 1459 Sorghum Nyanga Renzva Manicaland smuts "food, beverage"
=
seed Mrs Chikwati 0 0 1 0 0 0 1 0
1 0 0 0 1 0 1 0 0 0 1
0 0 1
MMB122 1460 Musoswe Nyanga Renzva Manicaland "food, beverage"
seed =
Mrs Chikwati 0 0 1 0 0 0 0 1 1
0 0 0 1 0 1 0 0 0 1 0
1 0
MMB123 1461 Sorghum Nyanga Renzva Manicaland "food, beverage"
seed =
Mrs Chikwati 0 0 0 1 0 0 0 1 1
0 0 0 1 0 1 0 0 0 1 0
0 1
MMB134 1472 Sorghum (mutanda) Nyanga Renzva Manicaland food
seed Mr & =
Mrs J Tungadza 0 0 0 1 0 0 0 1 1
0 0 0 1 0 0 1 0 0 1 0
0 1
MMB135 1473 Sorghum (malawi) Nyanga Renzva Manicaland food
seed Mr & =
Mrs Tungadza 0 0 0 0 0 1 0 1 1
0 0 0 0 1 0 1 0 0 0 1
0 1
MMB136 1474 Sorghum (malawi) Nyanga Renzva Manicaland food
seed Mr & =
Mrs Tungadza 0 1 0 0 0 0 0 1 1
0 0 0 0 1 1 0 0 0 0 1
0 1
MMB137 1475 Sorghum (shodhani) Nyanga Renzva Manicaland "food,
=
beverage" seed Mr & Mrs Tungadza 0 1 0 0 0
0 0 1 1 0 0 0 1 0 0 0
0 1 1 =
0 1 0
MMB139 1477 Sorghum (chipemu) Nyanga Renzva Manicaland food
seed Mr & =
Mrs Tungadza 0 0 1 0 0 0 0 1 1
0 0 0 1 0 1 0 0 0 1 0
0 1
MMB140 1478 Sorghum Nyanga Renzva Manicaland food seed Mr &
Mrs =
Tungadza 0 0 0 1 0 0 1 0 1
0 0 0 1 0 1 0 0 0 0 1
0 1
MMB142 1480 Sorghum Nyanga Renzva Manicaland food seed Mr &
Mrs =
Tungadza 0 0 1 0 0 0 0 1 1
0 0 0 1 0 0 1 0 0 1 0
0 1
MMB143 1482 Sorghum Nyanga Renzva Manicaland food seed Mr &
Mrs =
Tungadza 0 0 1 0 0 0 0 1 1
0 0 1 0 0 0 0 1 0 0 1
0 1
MMB145 1483 Nyamuwayawaya Nyanga Renzva Manicaland food seed
Mr & Mrs =
Tungadza 0 1 0 0 0 0 0 1 1
0 0 0 1 0 1 0 0 0 0 1
1 0
MMB147 1485 Nzende Nyanga Renzva Manicaland food seed Mr &
Mrs =
Tungadza 0 0 0 1 0 0 1 0 1
0 0 0 1 0 1 0 0 0 1 0
0 1
MMB149 1487 Sorghum Nyanga Renzva Manicaland food seed Mr &
Mrs =
Tungadza 0 0 0 1 0 0 0 1 1
0 0 0 1 0 0 1 0 0 0 1
1 0
MMB158 1496 Sweet sorghum Nyanga Renzva Manicaland food stalk
Mr & Mrs =
J Tungadza 0 1 0 0 0 0 0 1 1
0 0 1 0 0 1 0 0 0 0 1
1 0
TSH03 1499 Sorghum Tsholotsho Siyabalandela Matebeleland North high
=
"food, beverage" Mrs Rose Nxumalo 1 0 0 0
0 0 0 1 1 1 0 0 0 0 0
1 0 0 =
0 1 0 1
TSH25 1521 Sorghum Tsholotsho Siyabalandela Matebeleland North high
=
"food, beverage" seed Mrs Maggie Ndlovu 0 0 0 1
0 0 1 0 1 0 0 1 0 0 1
0 =
0 0 1 0 0 1
TSH27 1523 Sorghum (Isigobane) Tsholotsho Siyabalandela Matebeleland =
North high "food, beverage" "seed, stalk" Mrs M Nxumale 0 1
0 0 0 0 0 1 =
1 0 0 0 1 0 1 0 0 0 0
1 1 0
TSH31 1527 Sorghum Tsholotsho Siyabalandela Matebeleland North high
=
"food, beverage" "stalk, seed" Mrs M Nxumale 0 1 0 0
0 0 0 1 1 0 0 0 1 =
0 0 0 0 1 0 1 1 1
TSH40 1535 Sorghum Tsholotsho Sizanani Matebeleland North low
"food, =
beverage" "seed, stalk, leaf" Mr George Ndebele 0 0 1
0 0 0 1 0 1 0 0 0 =
1 0 0 1 0 0 0 1 0 1
TSH42 1537 Sorghum Tsholotsho Sizanani Matebeleland North low
"food, =
beverage" "seed, stalk, leaf" Mr George Ndebele 0 0 0
1 0 0 0 1 1 0 0 0 =
1 0 0 1 0 0 0 1 1 0
TSH45 1540 Sorghum Tsholotsho Sizanani Matebeleland North low
"food, =
beverage" "seed, leaf" Mr George Ndebele 0 0 1 0
0 0 0 1 1 0 0 0 1 0 1
=
0 0 0 0 0 1 0
TSH55 1550 Sorghum Tsholotsho SizananiMabhanda Matebeleland North
high =
"food, beverage" "seed, stalk" Mrs Malethi Sibanda 0 1 0
0 0 0 0 1 1 0 =
0 0 1 0 0 1 0 0 0 1 0
1
TSH60 1555 Sorghum Tsholotsho SizananiMabhanda Matebeleland North
high =
"food, beverage" "seed, stalk, leaf" Mrs Malethi Sibanda 0 1
0 0 0 0 0 =
1 1 0 0 0 1 0 1 0 0 0
0 1 0 1
TSH61 1556 Sorghum Tsholotsho SizananiMabhanda Matebeleland North
high =
"food, beverage" "seed, stalk, leaf" Mrs Malethi Sibanda 0 0
0 0 0 1 0 =
1 1 0 0 0 1 0 1 0 0 0
0 1 0 1
TSH62 1557 Sorghum Tsholotsho SizananiMabhanda Matebeleland North
low =
"food, beverage" "seed, stalk, leaf" Mrs Malethi Sibanda 0 1
0 0 0 0 0 =
1 1 0 0 0 1 0 1 0 0 0
0 1 0 1
MZA10 1572 Sorghum Tsholotsho Siyazama Matebeleland North yes
food seed =
Mrs Mantombi Ndlovu 0 0 0 0 0 1 0 1
1 0 0 1 0 0 1 0 0 0 0
1 0 1
MZA30 1592 Sorghum Tsholotsho Siyazama Matebeleland North yes
"food, =
beverage" seed Mrs Selina Gumbo 0 0 0 0 0
1 0 1 1 1 0 0 0 0 1 0
0 0 0 1 =
0 1
MZA31 1593 Sorghum Tsholotsho Siyazama Matebeleland North yes
"food, =
beverage" seed Mrs Selina Gumbo 0 1 0 0 0
0 0 1 1 0 0 0 1 0 1 0
0 0 0 1 =
0 1
MZA73 1627 Sorghum Tsholotsho Phakamani Matebeleland North
0 0 0 0 =
1 0 0 1 1 0 1 0 0 0 1
0 0 0 0 1 0 1
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