wj - Daria-Maltseva/mixedmethods GitHub Wiki
Journals analysis
WJ distributions
WJ
==============================================================================
Info on 2-Mode Network 1. C:\Mail.Ru Cloud\ANR HSE\ANR Projects\Mixed methods\Data\2019_FINAL DATASET_copy\WJ.net [2-Mode] (581529)
==============================================================================
Number of vertices (n): 581529
----------------------------------------------------------
Arcs Edges
----------------------------------------------------------
Total number of lines 552218 0
----------------------------------------------------------
Number of loops 0 0
Number of multiple lines 4617 0
----------------------------------------------------------
2-Mode Network: Rows=547407, Cols=34122
Density [2-Mode] = 0.00002956
Average Degree = 1.89919333
Simplification (multiple line - single line)
==============================================================================
Info on 2-Mode Network 2. Simplification (Single Line) of N1 (581529)
==============================================================================
Number of vertices (n): 581529
----------------------------------------------------------
Arcs Edges
----------------------------------------------------------
Total number of lines 547601 0
----------------------------------------------------------
Number of loops 0 0
Number of multiple lines 0 0
----------------------------------------------------------
2-Mode Network: Rows=547407, Cols=34122
Density [2-Mode] = 0.00002932
Average Degree = 1.88331450
Indegree
==============================================================================
1. Input Degree of N2 (581529)
==============================================================================
Dimension: 581529
The lowest value: 0.0000
The highest value: 184167.0000
Highest values:
Rank Vertex Value Id
--------------------------------------------------------
1 547408 184167.0000 *****
2 547415 2589.0000 SOC SCI MED
3 547426 1959.0000 J ADV NURS
4 547447 1836.0000 LANCET
5 547480 1640.0000 JAMA-J AM MED ASSOC
6 547591 1614.0000 AM J PUBLIC HEALTH
7 547575 1581.0000 BRIT MED J
8 547490 1387.0000 PEDIATRICS
9 547712 1215.0000 ACAD MED
10 547596 1100.0000 NEW ENGL J MED
11 548149 1085.0000 J CLIN NURS
12 548075 1056.0000 J GEN INTERN MED
13 547444 1022.0000 PATIENT EDUC COUNS
14 548233 961.0000 MED EDUC
15 547597 911.0000 AM J PREV MED
16 547606 909.0000 J PERS SOC PSYCHOL
17 547818 805.0000 J AM GERIATR SOC
18 547413 775.0000 QUAL HEALTH RES
19 548231 772.0000 MED TEACH
20 547908 768.0000 NURS EDUC TODAY
21 547633 724.0000 INT J NURS STUD
22 548452 710.0000 J ADOLESCENT HEALTH
23 547965 709.0000 TEACH TEACH EDUC
24 547431 709.0000 J CONSULT CLIN PSYCH
25 547411 679.0000 AIDS CARE
26 548245 672.0000 COMPUT EDUC
27 547593 662.0000 ANN INTERN MED
28 547848 660.0000 MED CARE
29 548066 638.0000 BRIT J PSYCHIAT
30 547823 637.0000 GERONTOLOGIST
31 548660 629.0000 PREV MED
32 547418 629.0000 AIDS BEHAV
33 548830 628.0000 ARCH PHYS MED REHAB
34 548805 620.0000 DISABIL REHABIL
35 548659 619.0000 HEALTH AFFAIR
36 548403 611.0000 J CLIN ONCOL
37 548210 603.0000 MED J AUSTRALIA
38 547769 602.0000 ACAD MANAGE J
39 547708 591.0000 J RES SCI TEACH
40 547787 585.0000 J APPL PSYCHOL
41 547414 580.0000 COMPUT HUM BEHAV
42 547677 579.0000 J BUS ETHICS
43 548734 572.0000 ARCH INTERN MED
44 548423 571.0000 J PAIN SYMPTOM MANAG
45 547978 568.0000 CHILD DEV
46 548179 564.0000 J EDUC PSYCHOL
47 548115 564.0000 CHILD YOUTH SERV REV
48 548187 558.0000 DIABETES CARE
49 547560 558.0000 AM PSYCHOL
50 548293 554.0000 ADDICTION
51 548285 537.0000 PSYCHIAT SERV
52 548514 528.0000 AM J PSYCHIAT
53 547636 521.0000 PALLIATIVE MED
54 547981 507.0000 WORLD DEV
55 547935 500.0000 B WORLD HEALTH ORGAN
56 547759 486.0000 ACAD MANAGE REV
57 548962 481.0000 QUAL LIFE RES
58 547992 476.0000 SCIENCE
59 548762 470.0000 J INTERPROF CARE
60 547561 466.0000 PSYCHOL BULL
--------------------------------------------------------
Sum (all values): 547601.0000
Place of J MIX METHOD RES - 547433 = 403 (75th place)
Plot
setwd("C:/Mail.Ru Cloud/ANR HSE/ANR Projects/Mixed methods/Analysis/Journals")
number<-read.table(file="WJn_Indegree.vec", sep=",", header=FALSE, skip=1)
t<-table(number)
head(t)
t
length (t)
names(t)
articles <- as.integer(names(t))
typeof(articles)
length(articles)
x <- articles[2:387]
y <- as.vector(t[2:387]
xt <- c(1,5,10,50,100,500, 1000, 2000, 2500)
plot (x,y,log="xy",pch=16, xlab="N of works", ylab="N of journals", main="N of works per journal")
axis(side=1,at=xt, labels=xt)
> head(t)
number
0 1 2 3 4 5
547407 18156 4353 2218 1346 875
Reduced network
WJ
Info: Rows=547407, Cols=34122
Make constant partition with the 2nd number (34122) (value = 1)
Open DC.clu - 1st partition
Constant partition - 2nd partition
Fuse partitions
==============================================================================
3. Fusion of C1 and C2 (581529)
==============================================================================
Dimension: 581529
The lowest value: 0
The highest value: 2
Frequency distribution of cluster values:
Cluster Freq Freq% CumFreq CumFreq% Representative
----------------------------------------------------------------
0 529238 91.0080 529238 91.0080 ABBOTT_L(2015)26:340
1 18169 3.1243 547407 94.1324 HILL_M(2018)34:71
2 34122 5.8676 581529 100.0000 *****
----------------------------------------------------------------
Sum 581529 100.0000
Extract subnetwork according to partition
==============================================================================
Extracting Subnetwork according to Partition
==============================================================================
Time spent: 0:00:00
==============================================================================
Info on 2-Mode Network 3. Extracting N2 according to C3 [1-*] (52291)
==============================================================================
Number of vertices (n): 52291
----------------------------------------------------------
Arcs Edges
----------------------------------------------------------
Total number of lines 18363 0
----------------------------------------------------------
Number of loops 0 0
Number of multiple lines 0 0
----------------------------------------------------------
2-Mode Network: Rows=18169, Cols=34122
Density [2-Mode] = 0.00002962
Average Degree = 0.70233883
Network - 2-mode networks - Partition into 2 modes.
(We see that we have reduced N of works and all the journals)
==============================================================================
5. 2-Mode partition of N3 (52291)
==============================================================================
Dimension: 52291
The lowest value: 1
The highest value: 2
Frequency distribution of cluster values:
Cluster Freq Freq% CumFreq CumFreq% Representative
----------------------------------------------------------------
1 18169 34.7459 18169 34.7459 HILL_M(2018)34:71
2 34122 65.2541 52291 100.0000 *****
----------------------------------------------------------------
Sum 52291 100.0000
Binarise partition (1)
==============================================================================
6. Binarized C5 [1] (52291)
==============================================================================
Dimension: 52291
The lowest value: 0
The highest value: 1
Frequency distribution of cluster values:
Cluster Freq Freq% CumFreq CumFreq% Representative
----------------------------------------------------------------
0 34122 65.2541 34122 65.2541 *****
1 18169 34.7459 52291 100.0000 HILL_M(2018)34:71
----------------------------------------------------------------
Sum 52291 100.0000
Input degree partition
==============================================================================
7. Input Degree Partition of N3 (52291)
==============================================================================
Dimension: 52291
The lowest value: 0
The highest value: 481
Frequency distribution of cluster values:
Cluster Freq Freq% CumFreq CumFreq% Representative
----------------------------------------------------------------
0 48154 92.0885 48154 92.0885 HILL_M(2018)34:71
1 1841 3.5207 49995 95.6092 SOC NETWORKS
2 695 1.3291 50690 96.9383 BEHAV MED
Max of 2 partitions
=============================================================================
8. Max of C6 and C7 (52291)
==============================================================================
Dimension: 52291
The lowest value: 0
The highest value: 481
Frequency distribution of cluster values:
Cluster Freq Freq% CumFreq CumFreq% Representative
----------------------------------------------------------------
0 29985 57.3426 29985 57.3426 ISSUES MENT HEALTH NURS
1 20010 38.2666 49995 95.6092 HILL_M(2018)34:71
Extract subnetwork
==============================================================================
Info on 2-Mode Network 4. Extracting N3 according to C8 [1-*] (22306)
==============================================================================
Number of vertices (n): 22306
----------------------------------------------------------
Arcs Edges
----------------------------------------------------------
Total number of lines 18363 0
----------------------------------------------------------
Number of loops 0 0
Number of multiple lines 0 0
----------------------------------------------------------
2-Mode Network: Rows=18169, Cols=4137
Density [2-Mode] = 0.00024430
Average Degree = 1.64646284
We have 18169 of works (hits) + 4137 journals
Saved as WJr
Indegree of WJr
==============================================================================
2. Input Degree of N4 (22306)
==============================================================================
Dimension: 22306
The lowest value: 0.0000
The highest value: 481.0000
Highest values:
Rank Vertex Value Id
--------------------------------------------------------
1 18170 481.0000 *****
2 20173 293.0000 BMJ OPEN
3 18193 291.0000 J MIX METHOD RES
4 18840 245.0000 BMC HEALTH SERV RES
5 18852 209.0000 BMC PUBLIC HEALTH
6 19251 208.0000 PLOS ONE
7 18793 166.0000 IMPLEMENT SCI
8 18187 121.0000 J ADV NURS
9 18576 97.0000 J CLIN NURS
10 18177 93.0000 SOC SCI MED
11 18458 87.0000 NURS EDUC TODAY
12 19610 84.0000 TRIALS
13 18904 83.0000 BMC MED EDUC
14 18400 76.0000 PROCD SOC BEHV
15 18555 72.0000 CHILD YOUTH SERV REV
16 18416 72.0000 GERONTOLOGIST
17 18178 71.0000 INT J QUAL METH
18 18325 60.0000 INT J NURS STUD
19 19526 59.0000 BMC PREGNANCY CHILDB
20 18913 57.0000 J INTERPROF CARE
21 18533 56.0000 J GEN INTERN MED
22 18175 56.0000 QUAL HEALTH RES
23 19069 55.0000 J MED INTERNET RES
24 19018 54.0000 QUAL LIFE RES
25 18584 53.0000 EVAL PROGRAM PLANN
26 18198 52.0000 MIDWIFERY
27 18986 49.0000 BMC FAM PRACT
28 18619 49.0000 MED TEACH
29 18934 48.0000 DISABIL REHABIL
30 18860 47.0000 QUAL QUANT
31 18201 47.0000 PATIENT EDUC COUNS
32 21751 46.0000 EDULEARN PROC
33 18245 46.0000 PSYCHO-ONCOLOGY
34 21376 45.0000 INTED PROC
35 18486 45.0000 TEACH TEACH EDUC
36 20091 43.0000 BMC MED INFORM DECIS
37 18465 43.0000 INT J ENV RES PUB HE
38 21754 42.0000 EUR CONF RES METH
39 20218 41.0000 JMIR RES PROTOC
40 18179 41.0000 AIDS BEHAV
41 19056 38.0000 TEACH COLL REC
42 18731 37.0000 J PAIN SYMPTOM MANAG
43 18207 37.0000 HEALTH EXPECT
44 19587 36.0000 HEALTH RES POLICY SY
45 18312 36.0000 J ADOLESCENT RES
46 18328 35.0000 PALLIATIVE MED
47 21860 34.0000 ICERI PROC
48 18456 34.0000 NURSE EDUC PRACT
49 18348 34.0000 QUAL REP
50 18826 33.0000 FRONT PSYCHOL
51 18719 33.0000 EUR J CANCER CARE
52 18660 33.0000 HEALTH SOC CARE COMM
53 18277 33.0000 BMC PSYCHIATRY
54 19513 32.0000 J PUBLIC HEALTH MAN
55 18745 32.0000 J ADOLESCENT HEALTH
56 18176 32.0000 COMPUT HUM BEHAV
57 19542 31.0000 INT J EQUITY HEALTH
58 18479 31.0000 EDUC RESEARCHER
59 18249 31.0000 SUPPORT CARE CANCER
60 18206 31.0000 BMJ QUAL SAF
--------------------------------------------------------
Sum (all values): 18363.0000
Plot in R
setwd("C:/Mail.Ru Cloud/ANR HSE/ANR Projects/Mixed methods/Analysis/Journals")
number<-read.table(file="WJr_Indegree.vec", sep=",", header=FALSE, skip=1)
t<-table(number)
head(t)
t
length (t)
names(t)
articles <- as.integer(names(t))
typeof(articles)
length(articles)
x <- articles[2:70]
y <- as.vector(t[2:70])
plot (x,y,log="xy",pch=16, xlab="N of works", ylab="N of journals", main="N of works per journal")
number
0 1 2 3 4 5
18169 1841 695 422 259 186
Citations between journals
Citation reduced
Simplified
==============================================================================
7. CiteR (547407)
==============================================================================
Number of vertices (n): 547407
----------------------------------------------------------
Arcs Edges
----------------------------------------------------------
Total number of lines 769508 0
----------------------------------------------------------
Number of loops 0 0
Number of multiple lines 0 0
----------------------------------------------------------
Density1 [loops allowed] = 0.00000257
Density2 [no loops allowed] = 0.00000257
Average Degree = 2.81146569
CiteSimpl + DCbin - Extract 1 = CiteR.net
==============================================================================
8. Extracting N7 according to C1 [1] (18169)
==============================================================================
Number of vertices (n): 18169
----------------------------------------------------------
Arcs Edges
----------------------------------------------------------
Total number of lines 25365 0
----------------------------------------------------------
Number of loops 0 0
Number of multiple lines 0 0
----------------------------------------------------------
Density1 [loops allowed] = 0.00007684
Density2 [no loops allowed] = 0.00007684
Average Degree = 2.79211844
Not normalized JCJ
Counting JCJ = t(WJr) * CiteR * WJr
WJr - Transpose 2-mode
CiteR - 1 mode to 2-mode
Select Transposed
Select CiteR 2-mode
Multiply
Select WJr - as 2nd
Multiply
JCJ.net
==============================================================================
12. JCJ (4137)
==============================================================================
Number of vertices (n): 4137
----------------------------------------------------------
Arcs Edges
----------------------------------------------------------
Number of lines with value=1 8775 0
Number of lines with value#1 3288 0
----------------------------------------------------------
Total number of lines 12063 0
----------------------------------------------------------
Number of loops 381 0
Number of multiple lines 0 0
----------------------------------------------------------
Density [loops allowed] = 0.00070483
Average Degree = 5.83176215
Loops
==============================================================================
3. Loops from N12 (4137)
==============================================================================
Dimension: 4137
The lowest value: 0.0000
The highest value: 900.0000
Highest values:
Rank Vertex Value Id
--------------------------------------------------------
1 24 900.0000 J MIX METHOD RES
2 1 501.0000 *****
3 691 40.0000 QUAL QUANT
4 435 26.0000 ANN FAM MED
5 18 23.0000 J ADV NURS
6 6 22.0000 QUAL HEALTH RES
7 156 18.0000 INT J NURS STUD
8 486 16.0000 ADM POLICY MENT HLTH
9 113 15.0000 HEALTH SERV RES
10 849 14.0000 QUAL LIFE RES
11 289 14.0000 NURS EDUC TODAY
12 170 13.0000 QUAL INQ
13 142 13.0000 J COUNS PSYCHOL
14 1933 12.0000 J DEV EFFECT
15 744 12.0000 J INTERPROF CARE
16 3528 11.0000 SPE J
17 129 11.0000 AM J PREV MED
18 29 10.0000 MIDWIFERY
19 415 10.0000 EVAL PROGRAM PLANN
20 1814 9.0000 J SUSTAIN TOUR
21 657 9.0000 FRONT PSYCHOL
22 1082 9.0000 PLOS ONE
23 407 8.0000 J CLIN NURS
24 386 8.0000 CHILD YOUTH SERV REV
25 1344 8.0000 J PUBLIC HEALTH MAN
26 483 7.0000 PSYCHIAT SERV
27 900 7.0000 J MED INTERNET RES
28 856 7.0000 J SPORT EXERCISE PSY
29 1569 7.0000 LIBR INFORM SCI RES
30 1535 7.0000 QUAL RES ACCOUNT MAN
--------------------------------------------------------
Sum (all values): 2367.0000
Count proportion of self-citation
Loops
Vector - Weighted outdegree
1st vec, 2nd vec - divide
Then we need to order them
Order by loops:
select the loops vector
Vector/Make Permutation
Permutation/Mirror Permutation
Operations/Network+Permutation/Reorder Network
Operations/Vector+Permutation/Reorder Vector
File/Vector/Change Label JCJ loops perm (save)
select the divided vector:
Operations/Vector+Permutation/Reorder Vector
File/Vector/Change Label JCJ_divide perm (save)
Saved both files, open in Excel - Table JCJ vectors self citation
JCJ Reduction
!!! Remove ***** 1. - network JCJ 4136 nodes
Remove loops
Line values
Threshold 15 - Remove lines
All degree - Extract partition
JCJ line cut (42 nodes)
Fractional approach
JJf = t(WJ) * n(Cite) * WJ
CiteR norm1.mcr (write N of nodes 18169) CiteR_norm
the same procedure:
WJr - Transpose 2-mode
CiteR norm - 1 mode to 2-mode
Select Transposed
Select CiteR normalized 2-mode
Multiply
Select WJr - as 2nd
Multiply
JCJnorm.net
==============================================================================
38. JCJnorm (4137)
==============================================================================
Number of vertices (n): 4137
----------------------------------------------------------
Arcs Edges
----------------------------------------------------------
Number of lines with value=1 2426 0
Number of lines with value#1 9637 0
----------------------------------------------------------
Total number of lines 12063 0
----------------------------------------------------------
Number of loops 381 0
Number of multiple lines 0 0
----------------------------------------------------------
Density [loops allowed] = 0.00070483
Average Degree = 5.83176215
Remove ***** [1] Loops
Rank Vertex Value Id
--------------------------------------------------------
1 23 97.0435 J MIX METHOD RES
2 17 10.7619 J ADV NURS
3 434 8.3571 ANN FAM MED
4 485 8.3444 ADM POLICY MENT HLTH
5 1081 7.5000 PLOS ONE
6 288 7.3000 NURS EDUC TODAY
7 743 7.1167 J INTERPROF CARE
8 141 6.9167 J COUNS PSYCHOL
9 848 6.7492 QUAL LIFE RES
10 690 5.9711 QUAL QUANT
11 385 5.5000 CHILD YOUTH SERV REV
12 155 5.2833 INT J NURS STUD
13 406 4.6500 J CLIN NURS
14 5 4.4966 QUAL HEALTH RES
15 316 4.1667 TEACH TEACH EDUC
16 128 4.1667 AM J PREV MED
17 1343 4.1167 J PUBLIC HEALTH MAN
18 1568 4.0667 LIBR INFORM SCI RES
19 899 4.0333 J MED INTERNET RES
20 7 4.0000 SOC SCI MED
21 1932 3.9167 J DEV EFFECT
22 414 3.7556 EVAL PROGRAM PLANN
23 855 3.7500 J SPORT EXERCISE PSY
24 158 3.5110 PALLIATIVE MED
25 28 3.4524 MIDWIFERY
26 1287 3.3571 EMERG MED J
27 656 3.3278 FRONT PSYCHOL
28 2079 3.1667 OSTOMY WOUND MANAG
29 169 3.0525 QUAL INQ
30 1823 3.0000 FAM SOC
--------------------------------------------------------
Sum (all values): 535.1057
Vector - Weighted outdegree
1st vec, 2nd vec - divide
Then we need to order them
Order by loops:
select the loops vector
Vector/Make Permutation
Permutation/Mirror Permutation
Operations/Network+Permutation/Reorder Network
Operations/Vector+Permutation/Reorder Vector
File/Vector/Change Label JCJ loops perm (save)
select the divided vector:
Operations/Vector+Permutation/Reorder Vector
File/Vector/Change Label JCJ_divide perm (save)
Saved both files, open in Excel - Table JCJ vectors self citation
JCJnorm Reduction
Line cut - treshold 4
==============================================================================
41. Deleted loops in N39 (4136)
==============================================================================
Lowest value of line: 0.01785714
Highest value of line: 14.08333333
Line Values Frequency Freq% CumFreq CumFreq%
---------------------------------------------------------------------------------------------------
( ... 0.0179] 18 0.1918 18 0.1918
( 0.0179 ... 1.5807] 9151 97.4963 9169 97.6880
( 1.5807 ... 3.1435] 168 1.7899 9337 99.4779
( 3.1435 ... 4.7063] 26 0.2770 9363 99.7550
( 4.7063 ... 6.2692] 10 0.1065 9373 99.8615
( 6.2692 ... 7.8320] 8 0.0852 9381 99.9467
( 7.8320 ... 9.3948] 4 0.0426 9385 99.9893
( 9.3948 ... 10.9577] 0 0.0000 9385 99.9893
( 10.9577 ... 12.5205] 0 0.0000 9385 99.9893
( 12.5205 ... 14.0833] 1 0.0107 9386 100.0000
---------------------------------------------------------------------------------------------------
Total 9386 100.0000
JCJnorm_line cut(27)