From m.grum at cgiar.org  Mon Aug  4 09:51:30 2003
From: m.grum at cgiar.org (m.grum@cgiar.org)
Date: Mon Aug  4 08:51:27 2003
Subject: [Rd] hclust() and agnes() method="average" divergence (PR#3648)
Message-ID: <200308040651.h746pUJH028091@pubhealth.ku.dk>

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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)
m.grum@cgiar.org
www.ipgri.org


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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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[Rd] hclust() and agnes() method="average" divergence (PR#3648)
m.grum@cgiar.org