thr3ads.net - R devel - [Rd] hclust() and agnes() method="average" divergence (PR#3648) [Aug 2003]

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m.grum@cgiar.org

2003-Aug-04 08:51 UTC

[Rd] hclust() and agnes() method="average" divergence (PR#3648)

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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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maechler@stat.math.ethz.ch

2003-Aug-14 09:25 UTC

head link

[Rd] hclust() and agnes() method="average" divergence (PR#3648)

>>>>> "MikG" == m grum <m.grum@cgiar.org>
>>>>>     on Mon, 4 Aug 2003 08:51:30 +0200 (MET DST) writes:

    MikG> Anyone have a clue why hclust() and agnes() produce
    MikG> different results in the example below when both use
    MikG> method="average"??  I'm not able to reproduce the
    MikG> problem with other datasets.

    MikG> ereck <-
read.table("Ereck.txt",header=TRUE,sep="\t")
    MikG> emol <- subset(ereck,select=c(11:18,20:32))
    MikG> library(cluster)
    MikG> library(mva)
    MikG> daisemol <- daisy(emol,type=list(asymm=c(1:21)))

The reason is that most of the distances/dissimilarities are the
same: there are only 20 different values in the 1326 distances.
> sort(table(daisemol), decreasing=TRUE)
starts as>> 0.666666666666667               0.5               0.8 0.285714285714286
>>               387               284               251                94
i.e. the distance 2/3 appears 387 times,  1/2 does 284 times, etc.
With so many ties in the distances, choosing the next
observation / cluster for "merging" is often chosing among many
possibilities and hence the arbitrariness and the difference
between too algorithms.

For your situation, you might be able to use some continuous
variable along with the factors and the many binary ones such
that the distances won't have ties.

NO bug! {i.e. you should have posted to R-help (you did have a
good question!)} not R-bugs.

Regards,
Martin Maechler <maechler@stat.math.ethz.ch>
http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum  LEO C16	Leonhardstr. 27
ETH (Federal Inst. Technology)	8092 Zurich	SWITZERLAND
phone: x-41-1-632-3408		fax: ...-1228			<><

R devel - Aug 2003 - hclust() and agnes() method="average" divergence (PR#3648)

[Rd] hclust() and agnes() method="average" divergence (PR#3648)

[Rd] hclust() and agnes() method="average" divergence (PR#3648)

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