The Hierarchical Agglomerative Clustering with Gower index: a methodology for automatic design of OLAP cube in ecological data processing context Lucile Sautot, Bruno Faivre, Ludovic Journaux, Paul Molin PII: DOI: Reference:
S1574-9541(14)00107-1 doi: 10.1016/j.ecoinf.2014.07.011 ECOINF 505
To appear in:
Ecological Informatics
Received date: Revised date: Accepted date:
29 November 2013 25 July 2014 29 July 2014
Please cite this article as: Sautot, Lucile, Faivre, Bruno, Journaux, Ludovic, Molin, Paul, The Hierarchical Agglomerative Clustering with Gower index: a methodology for automatic design of OLAP cube in ecological data processing context, Ecological Informatics (2014), doi: 10.1016/j.ecoinf.2014.07.011
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ACCEPTED MANUSCRIPT !"#$%&'() *+# ,%%( "#%- '( ./01 #2#$%3# $4 '35&46% 5%&74&3+( %# 47 8"%&'%# 9:+&;! %$ +!<= >???@ 4& $4 -%#')( ./01 # *%3+ 9A#3+( %$ +!<= BC>C@< D*% *'%&+& *' +! +))!43%&+$'6% !"#$%&'() '# + !"#$%&'() 3%$*4-< D*'# 3%$*4- '# +( "(#"5%&6'#%- 3%$*4- 9 !"! (4 !%+&('() '# (%%-7"!@< D*% +'3 47 $*'# 3%$*4- '# $*% ,"'!-'() 47 + *'%&+& *2 74& E(- )&4"5# '($4 $*% -+$+< F( + *'%&+& *' +! +))!43%&+$'6% !"#$%&'()= %+ * ,&+( * 47 $*% ,"'!$ *'%&+& *2 '# + !"#$%&< D*'# 3%$*4- *+# #%6%&+! #$%5# 9D"G%&2= BC>>@H
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AC CE P
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
PT
ACCEPTED MANUSCRIPT
ACCEPTED MANUSCRIPT ! "#$%&' (&)*+)',-.&$ ! "#$ %&!"$'" &( "#)* *"+,- .$ .&/0 .)"# 1 ,)2$!*)&! "#1" %&!"1)!* 133/&')21"$4- 566 &78$%"* 9"#$ %$!*+* 3&)!"* 14&!: "#$ ;&)/$ <)=$/> ?$$ *$%")&! @A> B+" C;DE *-*"$2* 1/$ ,$*):!$, "& 21!1:$ 41/:$ F+1!")")$* &( ,1"1> G#+* .$ *+::$*" 2$1*+/)!: 3$/(&/21!%$* &( &+/ *-*"$2 )! &/,$/ "& 3/$,)%" %14%+41")&! ")2$ 1!, !$$,(+4 2$2&/.)"# 1 41/:$/ ,1"1 *$">
G#$ !$$,(+4 ")2$ (&/ %14%+41")&! &( "#$ #)$/1/%#- .)"# I&.$/ )!,$'>
PT
G#$ *-*"$2 3$/(&/21!%$* %1! 7$ 2$1*+/$, 7- ".& .1-*H
G#$ !+27$/ &( 4$=$4* &( "#$ &7"1)!$, #)$/1/%#-> G#)* !+27$/ &( 4$=$4* "144)$* .)"# "#$ !+27$/ &( %&4+2!*
RI
&( "#$ "174$ .#)%# /$3/$*$!" "#$ !$. %14%+41"$, #)$/1/%#- )! "#$ ,1"171*$> G#+* "#$ !+27$/ &( 4$=$4* )* 1! $*")21")&! &( "#$ !$$,(+4 2$2&/- "& *1=$ "#$ #)$/1/%#->
SC
G#$ %14%+41")&! ")2$ 1!, "#$ !+27$/ &( 4$=$4* .$/$ 2$1*+/$, 1%%&/,)!: "& "#$ !+27$/ &( )!,)=),+14* 1!, "#$ !+27$/ &( =1/)174$* +*$, "& 7+)4, "#$ #)$/1/%#-> G#$ !+27$/ &( )!3+" ,1"1 )* /$J$%"$, )! "#$*$ ".& 31/12$"$/* 1!, .$ %1! $'3$%" "#1" "#$ )231%" &( "#$*$ 31/12$"$/* )* )!,$3$!,$!" "& "#$ %&23+"$/ %&!K:+/1")&!>
NU
C! "#$ L):+/$ @@ .$ *#&. "#$ !+27$/ &( 4$=$4* 1%%&/,)!: "& "#$ !+27$/ &( )!,)=),+14* 1!, "#$ !+27$/ &( 4$=$4* 1%%&/,)!: "& "#$ !+27$/ &( =1/)174$*> D7&+" "#$*$ :/13#*M .$ !&"$ "#1"H G#$ "#$&/$")%14 2)!)2+2 &( 4$=$4* 1%%&/,)!: "& "#$ !+27$/ &( )!,)=),+14* &7$-* "& 1 4&:1/)"#2)% (+!%")&!
MA
9N$=/&-$M @OPQA>
G#$ !+27$/ &( 4$=$4* 1%%&/,)!: "& "#$ !+27$/ &( )!,)=),+14* )* !$1/ "& "#)* 2)!)2+2H 1! 1*-23"&")% 7$#1=)&/> B- %&!"/1*"M "#$ !+27$/ &( =1/)174$* #1* !& $R$%" &! "#$ !+27$/ &( 4$=$4*>
D
G& 2&,$4 "#$ !+27$/ &( 4$=$4 1%%&/,)!: "& "#$ !+27$/ &( )!,)=),+14*M "#$ ".& 7$*" 2&,$4* 1/$ 1 3&.$/ (+!%")&! &/ 1 4&:1/)"#2)% (+!%")&!> N$*3)"$ "#$ (1%" "#1" "#$ 3&.$/ (+!%")&! #1* 1 %&//$41")&! %&$S%)$!" #):#$/ 9 R!
TE
"#1! "#$ %&//$41")&! %&$S%)$!" &( "#$ 4&:1/)"#2)% (+!%")&! 9 R!
= 0.47AM
= 0.54A
.$ 7$4)$=$ "#1" "#$ 4&:1/)"#2)% (+!%")&! )*
2&/$ /$4$=1!"M 7$%1+*$ .$ 0!&. "#1" "#$ 2)!)2+2 (&44&.* 1 4&:1/)"#2)% (+!%")&!> T&/$&=$/ "#$ 7$*" 2&,$4 (&/ "#$ !+27$/ &( 4$=$4* 1%%&/,)!: "& "#$ !+27$/ &( =1/)174$* )* 1 F+1,/1")% (+!%")&!> B+" "#$
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x
%&$S%)$!" 1/$ =$/- !$1/ "& 6> U$ %1! $'%$3" "#1" "#$ !+27$/ &( =1/)174$* #1* 1
AC CE P
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 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
=$/- 4)""4$ )231%" &! "#$ !+27$/ &( 4$=$4*> G#$ %&//$41")&! %&$S%)$!" (&/ "#)* 2&,$4 )* =$/- 4&. 9 R!
= 0.02A>
U$ !&"$ "#1" "#$ %&//$41")&! %&$S%)$!"* 1/$ 4&. (&/ $1%# $*")21")&! &( !+27$/ &( 4$=$4*> G#+* "#$ #)$/1/%#)%14 1::4&2$/1")=$ %4+*"$/)!: 3$/(&/2$, .)"# 1 I&.$/ )!,$' 1* ,)*"1!%$ 2$1*+/$2$!" 3/&,+%$* 7)!1/- "/$$* .#&*$ #$):#" ,$3$!,* &( "#$ !+27$/ &( )!,)=),+14*> G#$ 1=$/1:$ #$):#" &( "#$*$ 7)!1/- "/$$* )* =$/!$1/ "#$ 2)!)2+2 #$):#"> G#$ !$$,(+4 2$2&/- +*$, "& /$%&/, "#$ #)$/1/%#- )* *& !$1/ "#$ 2)!)2+2>
@Q
ACCEPTED MANUSCRIPT y = 2,3994x0,2943 R² = 0,5414
y = 2,1701ln(x) - 0,4112 R² = 0,4741
18 16
Height
12 Minimum of height Log. (Height)
10 8
PT
Number of levels
14
6 2 0
20 18 16 14 12 10 8 6 4 2 0
20
40
60
80 100 120 Number of individuals
160
180
200
NU
y = -0,0004x2 + 0,0516x + 9,8333 R² = 0,0247
140
Puissance (Height)
SC
0
RI
4
MA
Height
20
40
60 Number of variables
Poly. (Height)
80
100
120
TE
0
D
Number of levels
!"#$% &&' (%!")* +, *)% )!%$-$.)/ -..+$0!1" *+ 1#23%$ +, !10!4!0#-56 -10 -..+$0!1" *+ 1#23%$ +, 4-$!-35%6
! "#$ %&'()$ *+ ,$ -#., "#$ /01/(10"&.! "&2$ 0//.)3&!' ". "#$ !(24$) .5 &!3&6&3(01- 0!3 "#$ !(24$) .5 60)&041$-7 8$ !."$ "#0"9 :#$ /01/(10"&.! "&2$ 0//.)3&!' ". "#$ !(24$) .5 60)&041$- .4$;- ". 0 1&!$0) 5(!/"&.!7 :#$ /01/(10"&.! "&2$ 0//.)3&!' ". "#$ !(24$) .5 &!3&6&3(01- .4$;- ". 0 <(03)0"&/ 5(!/"&.!7 :#$ /.2=1$"$ 2.3$1> ,#&/# /0! $?=)$-- "#$ /01/(10"&.! "&2$ 0//.)3&!' ". 0 1&!$0) 5(!/"&.! .5 "#$ !(24$) .5 60)&041$0!3 0 <(03)0"&/ 5(!/"&.! .5 "#$ !(24$) .5 &!3&6&3(01-> &-9
AC CE P
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
t(v, M ) = b1 M 2 + b2 M + b3 M 2 v + b4 M v + b5 v + b6
@! "#&- 5.)2(10> t &- "#$ $-"&20"$3 /01/(10"&.! "&2$> M &- "#$ !(24$) .5 &!3&6&3(01-> v &- "#$ !(24$) .5 60)&041$0!3 bi ,&"# i &! {1, 2, 3, 4, 5, 6} 0)$ /.$A/&$!"- "#0" 3$=$!3 .! "#$ /.!B'()0"&.! .5 "#$ /.2=("$) ,#&/# =$)5.)2 "#$ #&$)0)/#; /01/(10"&.!7 8$ =$)5.)2 0 -"$=,&-$ 1&!$0) )$')$--&.! ". B? "#$ /.$A/&$!"-7 :#$ /.$A/&$!"-> ,#&/# /0! 4$ -"0"&-/011; /.!-&3$)$3 $<(01 ". C$).> 0)$ )$2.6$37 8$ .4"0&! 0 5.)2(10 1&D$9 t(v, M ) = (b1 + b3 v)M 2 + b2 M + b6
8&"# "#$ /.2=("$)> "#0" ,$ (-$ 5.) "#$ =$)5.)20!/$- "$-"-> ,$ .4"0&! b1 = 1.83?10−3 > b2 = −1.06?10−6 > b3 = 1.51?10−5 0!3 b6 = 1.15 7 :#$ /.))$10"&.! /.$A/&$!" 4$",$$! "#&- 2.3$1 0!3 "#$ 2$0-()$3 /01/(10"&.! "&2$ &- $<(01 ". 99.7%7 ! "#$ %&'()$ *E ,$ -#., "#$ 2$0-()$3 /01/(10"&.! "&2$ 0!3 "#$ 2.3$1 "#0" ,$ -(''$-" 04.6$7 :#$ $-"&20"&.! -#.,- ,$11 "#$ /#0!'$- .5 /01/(10"&.! "&2$ 0//.)3&!' ". "#$ !(24$) .5 &!3&6&3(01- 0!3 "#$ !(24$) .5 60)&041$-7
*F
ACCEPTED MANUSCRIPT Number of individuals 30
50
5 4 3 2 1 0 0
20
40 60 80 Number of variables
10
20
30
50
100
NU
Time (s)
20
100
SC
Number of variables
30
PT
20
RI
Time (s)
10
10
MA
0 0
20
40 60 80 Number of individuals
100
23
18
13
AC CE P
TE
D
!"#$% &'( )*+,#+*-!./ -!0% *,,.$1!/" -. -2% /#03%$ .4 !/1!5!1#*+6 */1 -2% /#03%$ .4 5*$!*3+%6
Calculation time (s)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
measured data
model 8
3
-2
10 20 30 50 100 10 20 30 50 100 10 20 30 50 100 10 20 30 50 100 10 20 30 50 100
10
20
30
50
100
Number of variables (first row) & number of individuals (second row)
!"#$% &7( )*+,#+*-!./ -!0% *,,.$1!/" -. /#03%$ .4 5*$!*3+%6 89$6- $.: .4 ; *
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PT
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SC
RI
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TE
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
AC CE P
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
N^
ACCEPTED MANUSCRIPT
MA
NU
SC
RI
PT
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p
D
0,30
significance level of p
TE
0,25
AC CE P
0,20
0,15
0,10
0,05
qualitative
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quantitative
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IURB
HARI
HMAX
FORP
FORB
DVIL
DFOR
ALTI
CULT
SUBS
VEAQ
GRVL
STRAT
FRAG
CONF
0,00 COUR
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RI SC NU
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AC CE P
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PT
ACCEPTED MANUSCRIPT
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ACCEPTED MANUSCRIPT
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!!"#$%&' ()*+%,%-./ #0+1+%0#2
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NU
SC
RI
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TE
0 ' $#1*,3#$/ -# 4$+8*3# "%# ,+"'"*+,0 3#;,#3 2. :'(*,+-0>* ',3 H*1',.* *, I:'(*,+-0>* ',3 H*1',.*/ JKKLM "+ 3#0&$*2# ' 3'"' -'$#%+)0# '" "%# &+,")'( (#8#(< =%# !+((+-*,? ;?)$# 0)11'$*G#0 "%# ,+"'"*+,0 C
AC CE P
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