VOSviewer Manual. Nees Jan van Eck and Ludo Waltman. 11 January Manual for VOSviewer version 1.6.0

Transcription

1 VOSviewer Manual Nees Jan van Eck and Lud Waltman 11 January 2015 Manual fr VOSviewer versin

2 Table f cntents 1 Intrductin User interface Main panel Optins panel Infrmatin panel Overview panel Actin panel Actin tab Items tab Map tab File types Map file Netwrk file Thesaurus file Cluster clrs file, scre clrs file, and density clrs file Advanced tpics Using cmmand line parameters Making a map available n the internet Increasing the availability f memry References

3 1 Intrductin VOSviewer is a cmputer prgram fr creating maps based n netwrk data and fr visualizing and explring these maps. The main features f VOSviewer can be summarized as fllws: Creating maps based n netwrk data. Maps can be created based directly n the adjacency matrix f a netwrk, but it is als pssible t create maps f publicatins, authrs, r jurnals based n bibligraphic cupling, c-citatin, r c-authrship netwrks extracted frm Web f Science r Scpus data. Term maps can be created directly based n a text crpus. Maps are created using the VOS mapping technique and the VOS clustering technique. 1 Visualizing and explring maps. Tw visualizatins are prvided, the netwrk visualizatin and the density visualizatin. Zming and scrlling functinality allws maps t be explred in full detail, which is essential when wrking with large maps cntaining hundreds r even thusands f items. Althugh VOSviewer is intended primarily fr analyzing biblimetric netwrks, the prgram can in fact be used t create, visualize, and explre maps based n any type f netwrk data. VOSviewer is written in the Java prgramming language, which means that it runs n mst hardware and perating system platfrms. VOSviewer can be btained frm The prgram can be used freely fr any purpse. This manual is cncerned with versin f VOSviewer. The manual is rganized as fllws. We first intrduce the user interface f VOSviewer in Chapter 2, we then explain the file types used by VOSviewer in Chapter 3, and finally we discuss sme advanced tpics in Chapter 4. Fr additinal infrmatin abut VOSviewer, we refer t a paper that we have written (Van Eck & Waltman, 2010). In this paper, a general intrductin t VOSviewer is prvided. Als, the technical implementatin f specific parts f the prgram is discussed in cnsiderable detail. Similar infrmatin, including a step-by-step tutrial, can als be fund in a recent bk chapter (Van Eck & Waltman, 2014). 1 Tgether, these tw techniques prvide a unified framewrk fr mapping and clustering. Fr mre infrmatin abut the techniques, we refer t Van Eck, Waltman, Dekker, and Van den Berg (2010) and Waltman, Van Eck, and Nyns (2010). 3

4 2 User interface The main windw f VOSviewer is shwn in Figure 1. As can be seen in the figure, the main windw cnsists f the fllwing five panels: Main panel. In this panel, a selected area in the currently active map is shwn. The zm and scrll functinality f VOSviewer can be used t select the area in the currently active map that is shwn in the main panel. Optins panel. This panel can be used t change the way in which the currently active map is shwn in the main panel. Infrmatin panel. In this panel, infrmatin abut an item in the currently active map can be shwn. Overview panel. In this panel, an verview f the currently active map is shwn. A rectangular frame is displayed in the verview panel t indicate the area in the currently active map that is shwn in the main panel. Actin panel. This panel can be used t undertake all kinds f actins, such as creating a new map, pening r saving an existing map, making a screensht, finding an item, and cnstructing r transfrming a map. VOSviewer prvides tw visualizatins, which are referred t as the netwrk visualizatin and the density visualizatin. As shwn in Figure 1, the Netwrk Visualizatin and Density Visualizatin tabs can be used t switch between the tw visualizatins. In the next sectins, we discuss the five panels f VOSviewer in mre detail. T get sme hands-n experience with VOSviewer, we encurage the reader t use the map file jurnal_map.txt, which is distributed tgether with VOSviewer. This file can be used t reprduce the figures in this chapter. The file cntains a map f 232 jurnals in the fields f ecnmics, management, and peratins research (fr mre details, see Van Eck & Waltman, 2010). T pen the map, press the Open buttn n the Actin tab in the actin panel, select the map file jurnal_map.txt, and press the OK buttn. 4

5 Figure 1. The main windw f VOSviewer. The numbers indicate (1) the main panel, (2) the ptins panel, (3) the infrmatin panel, (4) the verview panel, and (5) the actin panel. 2.1 Main panel As can be seen in Figure 1, the main panel f VOSviewer is used t shw a selected area in the currently active map. The zm and scrll functinality f VOSviewer can be used t determine which area in the currently active map is shwn. The way in which the currently active map is shwn depends n whether the netwrk visualizatin r the density visualizatin is selected. We first cnsider the netwrk visualizatin. When the netwrk visualizatin is selected, items are indicated by their label and, by default, als by a circle. Fr each item, the fnt size f the item s label and the size f the item s circle depend n the weight f the item. 2 The clr f the circle f an item can be determined in a 2 The weight f an item is determined by the weight r nrmalized weight clumn in a map file (see Sectin 3.1). When a new map is created withut prviding a map file with a weight r nrmalized weight clumn, the weight f an item is set equal t the ttal strength f all links f the item. When an existing map is pened withut prviding a map file with a weight r nrmalized weight clumn, all items in the map are given the same weight. 5

6 number f different ways. If items have been assigned t clusters, the clr f the circle f an item can be determined by the cluster t which the item belngs. If scres have been given t items, the clr f the circle f an item can be determined by the item s scre, where by default clrs range frm blue (lw scre) t green (average scre) t red (high scre). 3 A third pssibility is t determine the clr f the circle f an item by the clr f the item as specified in a map file (using the red, green, and blue clumns; see Sectin 3.1). The ptins panel can be used t switch between the different ways f clring items. We nte that fr sme items the label may nt be visible. This is dne in rder t avid verlapping labels. Als, by default, n links between items are displayed. Hwever, this can be changed in the ptins panel. An example f the netwrk visualizatin is shwn in Figure 2. Figure 2. The netwrk visualizatin. 3 If clrs are determined by the scres f items, a clr bar is shwn in the lwer right crner f the main panel. This clr bar indicates which clrs crrespnd with which scres. 6

7 We nw cnsider the density visualizatin. There are in fact tw variants f the density visualizatin. We first discuss the item density visualizatin, fllwed by the cluster density visualizatin. The ptins panel can be used t switch between the tw variants f the density visualizatin. We refer t Van Eck and Waltman (2010) fr a detailed discussin f the technical implementatin f the density visualizatin. In the item density visualizatin, items are indicated by their label in a similar way as in the netwrk visualizatin. Each pint in a map has a clr that depends n the density f items at that pint. By default, this clr is smewhere in between red and blue. The larger the number f items in the neighbrhd f a pint and the higher the weights f the neighbring items, the clser the clr f the pint is t red. Cnversely, the smaller the number f items in the neighbrhd f a pint and the lwer the weights f the neighbring items, the clser the clr f the pint is t blue. An example f the item density visualizatin is shwn in Figure 3. The cluster density visualizatin is available nly if items have been assigned t clusters. The cluster density visualizatin is similar t the item density visualizatin except that the density f items is displayed separately fr each cluster f items. In the cluster density visualizatin, the clr f a pint in a map is clse t the clr f a certain cluster if there are a large number f items belnging t that cluster in the neighbrhd f the pint. Like in the item density visualizatin, items with high weights cunt mre heavily than items with lw weights. An example f the cluster density visualizatin is shwn in Figure 4. T facilitate the detailed examinatin f a map, VOSviewer ffers zm and scrll functinality. In the main panel, zming and scrlling can be dne in the fllwing three ways: Using the muse. T zm in, mve the muse upwards while keeping the right muse buttn pressed. Cnversely, t zm ut, mve the muse dwnwards while keeping the right muse buttn pressed. As an alternative, the muse wheel can be used t zm in and ut. T scrll thrugh a map, mve the muse while keeping the left muse buttn pressed. Using the navigatin buttns in the upper right crner f the main panel (see Figure 1). Use the plus and minus buttns t zm in and ut. Use the arrw buttns t scrll thrugh a map. Using the keybard. Use the plus and minus keys t zm in and ut. Use the arrw keys t scrll thrugh a map. 7

8 Figure 3. The item density visualizatin. Figure 4. The cluster density visualizatin. 8

9 2.2 Optins panel The ptins panel can be used t change the way in which the currently active map is shwn in the main panel. Different ptins are prvided fr the netwrk visualizatin and the density visualizatin. Sme f the ptins are nt always available. The ptins panel shws nly the ptins that are relevant given the currently available map data. When the netwrk visualizatin is selected, the fllwing ptins may be prvided: Labels. Size. This slider determines the size f the fnt used t display the labels f items in the main panel. Size variatin. The higher the weight f an item, the larger the fnt that is used t display the item s label in the main panel. The Size variatin slider determines the strength f this effect. Max. length. This text bx determines the maximum length f a label displayed in the main panel. If the length f a label exceeds the maximum length, the last part f the label is nt displayed. Fnt. This drp dwn list determines the fnt used t display the labels f items in the main panel. Links. N. f links. If the adjacency matrix f a netwrk is available, links between items can be displayed in the main panel. The N. f links text bx determines the maximum number f links t be displayed. If the number f links between items exceeds the maximum number f links t be displayed, nly the strngest links are displayed. Withut nrmalizatin and With nrmalizatin. These radi buttns determine the way in which the strngest links t be displayed in the main panel are selected. If the Withut nrmalizatin radi buttn is selected, the links with the highest unnrmalized link strength are displayed. If the With nrmalizatin radi buttn is selected, the links with the highest nrmalized link strength are displayed. Visualizatin. Circles and Frames. These radi buttns determine the way in which items are indicated in the main panel. If the Circles radi buttn is selected, items are indicated bth by their label and by a circle. If the Frames radi 9

10 buttn is selected, items are indicated by their label displayed within a rectangular frame. Clrs. User defined clrs, Scre clrs, Cluster clrs, and N clrs. These radi buttns determine the way in which items are clred in the main panel and the verview panel. If the User defined clrs radi buttn is selected, each item has its wn clr as specified in a map file (using the red, green, and blue clumns; see Sectin 3.1). If the Scre clrs radi buttn is selected, items are clred based n their scre. If the Cluster clrs radi buttn is selected, items are clred based n the cluster t which they belng. If the N clrs radi buttn is selected, all items are clred in gray. Black backgrund. This check bx determines whether the main panel has a black r a white backgrund clr. Min./Max. Scres. This buttn is available nly if the Scre clrs radi buttn is selected. The buttn brings up the Min./Max. Scres dialg bx. This dialg bx can be used t change the minimum and the maximum scre that determine hw scres are mapped t clrs. By default, scres less than r equal t the minimum scre are mapped t blue, scres equal t the average f the minimum and the maximum scre are mapped t green, and scres greater than r equal t the maximum scre are mapped t red. Scre Clrs. This buttn is available nly if the Scre clrs radi buttn is selected. The buttn ffers three ptins: Imprt. This ptin is the default chice. Chse this ptin t imprt scre clrs frm a scre clrs file (see Sectin 3.4). Exprt. Chse this ptin t exprt the current scre clrs t a scre clrs file (see Sectin 3.4). Restre riginal. Chse this ptin t restre the riginal scre clrs. Cluster Clrs. This buttn is available nly if the Cluster clrs radi buttn is selected. The buttn ffers fur ptins: Edit. This ptin is the default chice. Chse this ptin t edit the current cluster clrs in the Edit Cluster Clrs dialg bx. 10

11 Imprt. Chse this ptin t imprt cluster clrs frm a cluster clrs file (see Sectin 3.4). Exprt. Chse this ptin t exprt the current cluster clrs t a cluster clrs file (see Sectin 3.4). Restre riginal. Chse this ptin t restre the riginal cluster clrs. When the density visualizatin is selected, the fllwing ptins may be prvided: Labels. These ptins are identical t the nes prvided when the netwrk visualizatin is selected. Visualizatin. Item density r Cluster density. These radi buttns determine whether the item density visualizatin r the cluster density visualizatin is selected. Kernel width. This slider determines the value f the kernel width parameter. We refer t Van Eck and Waltman (2010) fr mre infrmatin abut this parameter. Clrs. White backgrund. This check bx is available nly if the cluster density visualizatin is selected. The check bx determines whether the main panel has a black r a white backgrund clr. Density Clrs. This buttn is available nly if the item density visualizatin is selected. The buttn ffers three ptins: Imprt. This ptin is the default chice. Chse this ptin t imprt density clrs frm a density clrs file (see Sectin 3.4). Exprt. Chse this ptin t exprt the current density clrs t a density clrs file (see Sectin 3.4). Restre riginal. Chse this ptin t restre the riginal density clrs. Cluster Clrs. This buttn is available nly if the cluster density visualizatin is selected. The buttn ffers fur ptins: Edit. This ptin is the default chice. Chse this ptin t edit the current cluster clrs in the Edit Cluster Clrs dialg bx. Imprt. Chse this ptin t imprt cluster clrs frm a cluster clrs file (see Sectin 3.4). 11

12 Exprt. Chse this ptin t exprt the current cluster clrs t a cluster clrs file (see Sectin 3.4). Restre riginal. Chse this ptin t restre the riginal cluster clrs. 2.3 Infrmatin panel In the infrmatin panel f VOSviewer, infrmatin abut an item in the currently active map can be shwn. Fr example, when the muse cursr is mved ver the label f an item in the main panel, infrmatin abut the item will be shwn in the infrmatin panel. If item descriptins have been prvided (using the descriptin clumn in a map file; see Sectin 3.1), the descriptin f the item will be shwn. If n item descriptins have been prvided, the label f the item will be shwn alng with the number f the cluster t which the item belngs and the scre f the item (assuming that items have been assigned t clusters and that scres have been given t items). Infrmatin abut a link between tw items can als be shwn in the infrmatin panel. When the muse cursr is mved ver a link between tw items, infrmatin abut the link will be shwn in the infrmatin panel. The labels f the items and the strength f the link will be shwn. 2.4 Overview panel In the verview panel f VOSviewer, an verview f the currently active map is shwn. Each item in the map is indicated by a small clred dt. A rectangular frame is displayed in the verview panel t indicate the area in the currently active map that is shwn in the main panel. By left-clicking in the verview panel, the area in the currently active map that is shwn in the main panel can be changed. 2.5 Actin panel The actin panel f VOSviewer can be used t undertake all kinds f actins. The panel cnsists f three tabs: The Actin tab, the Items tab, and the Map tab. These tabs are discussed in Subsectins 2.5.1, 2.5.2, and Actin tab The Actin tab can be used t perfrm a number f basic actins. The fllwing buttns are available n the Actin tab: Map. 12

13 Create. Use this buttn t create a new map. The buttn brings up the Create Map wizard. There are tw ways in which a new map can be created using this wizard: Create a map based n a netwrk. This ptin requires the adjacency matrix f a netwrk. The adjacency matrix indicates which pairs f items in the netwrk are linked t each ther, and fr each pair f linked items it indicates the strength f their link. The matrix can be read frm a netwrk file. In additin t a netwrk file, a map file may als be prvided. The map file may fr example cntain labels and descriptins f items. We refer t Sectins 3.1 and 3.2 fr a detailed discussin f map files and netwrk files. Instead f a map file and a netwrk file, it is als pssible t use Pajek files. 4 A third pssibility is t use Web f Science r Scpus files. The use f Web f Science r Scpus files ffers an easy way t create maps f scientific publicatins, scientific jurnals, researchers, r research rganizatins based n bibligraphic cupling relatins (i.e., multiple items citing the same publicatin), c-citatin relatins (i.e., multiple items being cited by the same publicatin), r c-authrship relatins (i.e., multiple items cauthring the same publicatin). Create a map based n a text crpus. 5 This ptin requires a text crpus. The crpus is stred in a crpus file. A crpus file is a text file that cntains n each line the text f a dcument. This text is assumed t be in English. Using natural language prcessing techniques, VOSviewer extracts terms frm the crpus file, where a term is defined as a sequence f nuns and adjectives (ending with a nun). Based n the extracted terms, VOSviewer creates a term map. This is a map in which terms are lcated in such a way that the distance between tw terms prvides an indicatin f the number f c-ccurrences f the terms. In general, the smaller the distance between tw terms, the larger the number f c-ccurrences f the terms. Tw terms are said t c-ccur if they bth ccur n the same line in the crpus file. In additin t a crpus file, a scres file may als be prvided. A scres file 4 Pajek is a well-knwn cmputer prgram fr scial netwrk analysis (De Ny, Mrvar, & Batagelj, 2011). It is available at VOSviewer supprts Pajek matrix, netwrk, partitin, and vectr files. 5 We refer t Van Eck and Waltman (2011) fr mre infrmatin abut this ptin. 13

14 is a text file that cntains n each line the scre f a dcument. Based n the scres in a scres file, VOSviewer calculates a scre fr each term in the term map. The scre f a term equals the average scre f the dcuments in which the term ccurs. In the netwrk visualizatin, clrs can be used t indicate the scres f terms. It is als pssible t create a term map based n Web f Science, Scpus, r PubMed files instead f a crpus file. In that case, terms are extracted frm the titles and abstracts f scientific publicatins. Open. Use this buttn t pen an existing map. The buttn brings up the Open Map dialg bx. Map data can be read frm a map file. The map file must cntain crdinates f items. The file may als cntain, fr example, labels, descriptins, weights, scres, and cluster numbers f items. In additin t a map file, a netwrk file may als be prvided. The netwrk file cntains the adjacency matrix f a netwrk. Based n this matrix, links between the items in a map can be displayed. Instead f a map file and a netwrk file, it is als pssible t use Pajek files. Fr a detailed discussin f map files and netwrk files, we refer t Sectins 3.1 and 3.2. Save. This buttn ffers three ptins: Save map. This ptin is the default chice. Chse this ptin t save the currently active map in a map file. Map files are discussed in Sectin 3.1. Instead f a map file, it is als pssible t use a Pajek file. Save netwrk. This ptin can be chsen nly if the adjacency matrix f a netwrk is available. Chse this ptin t save the adjacency matrix in a netwrk file. Netwrk files are discussed in Sectin 3.2. Instead f a netwrk file, it is als pssible t use a Pajek file. Save nrmalized netwrk. This ptin can be chsen nly if the adjacency matrix f a netwrk is available. Chse this ptin t save the nrmalized adjacency matrix in a netwrk file. Nrmalizatin f an adjacency matrix is discussed in Subsectin Netwrk files are discussed in Sectin 3.2. Instead f a netwrk file, it is als pssible t use a Pajek file. Print. Use this buttn t print a screensht f the main panel. Screensht. This buttn ffers three ptins: Save t file. This ptin is the default chice. Chse this ptin t save a screensht f the main panel. The screensht resembles the 14

15 main panel as clsely as pssible. Hwever, the navigatin buttns in the upper right crner f the main panel are nt shwn in the screensht. If the Optimize labeling check bx in the Screensht Optins dialg bx (see belw) is checked, the number f labels visible in the screensht is ptimized. This means that sme labels nt visible in the main panel may be visible in the screensht. Screenshts can be saved in a number f graphic file frmats. Fr mst applicatins, we recmmend the PNG frmat. Sme frmats, such as EPS, PDF, and SVG, use vectr graphics when saving a screensht. This has the advantage that the screensht can be resized withut lss f quality. We nte that Figures 2 t 4 were btained using the screensht functinality f VOSviewer. Cpy t clipbard. Chse this ptin t cpy a screensht f the main panel t the clipbard. The screensht can fr example be pasted int a Wrd dcument r a PwerPint presentatin. Screensht ptins. Chse this ptin t bring up the Screensht Optins dialg bx. This dialg bx can be used t change sme screensht-related settings f VOSviewer. The Scaling drp dwn list determines the reslutin (i.e., the number f pixels) f a screensht. The reslutin is calculated relative t the reslutin f the main panel. Using a scaling f 100%, screenshts have the same reslutin as the main panel. Using the default scaling f 200%, screenshts have a reslutin that is twice as high (i.e., twice as many pixels hrizntally and vertically) as the reslutin f the main panel. The Scaling drp dwn list has n effect n screenshts that are saved in a file frmat that uses vectr graphics. The Optimize labeling check bx determines whether the number f labels visible in a screensht is ptimized. Optimizing the number f labels visible in a screensht means that sme labels nt visible in the main panel itself may be visible in a screensht f the main panel. The Include brder check bx determines whether a brder is included arund a screensht. Inf. Manual. Use this buttn t pen the VOSviewer manual. This requires an internet cnnectin. Abut VOSviewer. This buttn brings up the Abut VOSviewer dialg bx. This dialg bx prvides sme general infrmatin abut VOSviewer, 15

16 such as the versin number, a cpyright ntice, a license text, the address f the VOSviewer web site, and a list f sftware libraries used by VOSviewer. Update VOSviewer. This buttn is available nly if a new versin f VOSviewer is available. Use this buttn t pen the VOSviewer website. The new versin f VOSviewer can then be dwnladed frm the website Items tab The Items tab prvides a list f items in the currently active map. By default, a list f all items in the map is prvided. Hwever, a filter can be used t restrict the list t a subset f the items in the map. T d s, enter a filter string in the Filter text bx. This yields a list f all items whse label cntains the filter string. The Grup items by cluster check bx determines the way in which items are listed. If the check bx is unchecked, items are simply listed alphabetically. If the check bx is checked, items are first gruped by cluster and then listed alphabetically within each cluster. By duble-clicking n an item n the Items tab, the item is shwn in the main panel Map tab The Map tab can be used t cnstruct r transfrm a map. Maps are cnstructed using the VOS mapping technique and the VOS clustering technique. 6 The Map tab can als be used t change the parameters f these techniques. The fllwing parameters and cntrls are available n the Map tab: Parameters. Mapping attractin and Mapping repulsin. These parameters influence the way in which items are lcated in a map by the VOS mapping technique. The Mapping attractin parameter must have an integer value between -9 and +10. The Mapping repulsin parameter must have an integer value between -10 and +9. The value f the Mapping repulsin parameter must be lwer than the value f the Mapping attractin parameter. Fr mst purpses, ur recmmendatin is t wrk with the default parameter values. 6 We refer t Van Eck et al. (2010), Waltman and Van Eck (2013), and Waltman et al. (2010) fr mre infrmatin abut these techniques. 16

17 Clustering reslutin. This parameter determines the level f detail prvided by the VOS clustering technique. The parameter must have a nnnegative value. The larger the value f the parameter, the larger the number f clusters that will be btained. Our recmmendatin is t try ut different values fr the parameter and t use the value that yields the level f detail cnsidered mst satisfactry fr the particular applicatin at hand. Min. cluster size. This parameter determines the minimum cluster size used by the VOS clustering technique. Each cluster prduced by the VOS clustering technique must cnsist f the minimum number f items specified by this parameter. The Min. cluster size parameter can be useful t simplify the clustering slutins btained frm the VOS clustering technique by getting rid f small and uninteresting clusters. Advanced Parameters. This buttn brings up the Advanced Parameters dialg bx. This dialg bx can be used t change a number f mre advanced parameters f the VOS mapping and clustering techniques. These parameters are discussed belw. Run. The Run buttn is available nly after a new map has been created (using the Create buttn n the Actin tab in the actin panel). The buttn can be used t run the VOS mapping and clustering techniques. The radi buttns determine whether bth techniques are run r nly ne f them. Rtate/flip. Rtate. Use this buttn t rtate the currently active map. The Degrees t rtate parameter determines the number f degrees by which the map will be rtated. Flip Hrizntally. Use this buttn t flip the currently active map in hrizntal directin. Flip Vertically. Use this buttn t flip the currently active map in vertical directin. As mentined abve, the Advanced Parameters dialg bx can be used t change a number f mre advanced parameters f the VOS mapping and clustering techniques. The fllwing parameters are available: Nrmalizatin. N nrmalizatin. If this radi buttn is selected, n nrmalizatin f the adjacency matrix f a netwrk is perfrmed. In general, we d nt recmmend this ptin. 17

18 Nrmalizatin methd 1. If this radi buttn is selected, nrmalizatin methd 1 is used fr nrmalizing the adjacency matrix f a netwrk. This is the default nrmalizatin methd. This methd uses the s-called assciatin strength measure (Van Eck & Waltman, 2009). Nrmalizatin methd 2. If this radi buttn is selected, nrmalizatin methd 2 is used fr nrmalizing the adjacency matrix f a netwrk. This is an alternative nrmalizatin methd. The difference between nrmalizatin methd 1 and nrmalizatin methd 2 is smewhat technical, and we will therefre nt discuss it here. Use LinLg/mdularity nrmalizatin. If this check bx is checked, nrmalizatin is perfrmed in the same way as in the LinLg mapping technique and the mdularity clustering technique. Fr mre infrmatin abut these techniques, we refer t Newman (2004) and Nack (2007, 2009). Randm number generatr. Fixed seed. This text bx determines the seed f the randm number generatr used by the ptimizatin algrithms f the VOS mapping and clustering techniques. The seed must be a nn-negative integer. D nt use fixed seed. If this check bx is checked, the randm number generatr used by the ptimizatin algrithms f the VOS mapping and clustering techniques des nt have a fixed seed. Instead, each time the VOS mapping and clustering techniques are run, a different seed will be used, pssibly leading t different results. Mapping. Randm starts. This parameter determines the number f times the ptimizatin algrithm f the VOS mapping technique is run. Each time the ptimizatin algrithm is run, a different mapping slutin may be btained. The best mapping slutin btained in all runs f the ptimizatin algrithm will be used as the final mapping slutin. The larger the value f the Randm starts parameter, the mre accurate the final mapping slutin that will be btained. Max. iteratins. This parameter determines the maximum number f iteratins perfrmed by the ptimizatin algrithm f the VOS mapping technique. The larger the value f the parameter, the mre accurate the 18

19 mapping slutin that will be btained. In general, the default value f the parameter wrks well and des nt need t be changed. Initial step size, Step size reductin, and Step size cnvergence. These are technical parameters f the ptimizatin algrithm f the VOS mapping technique. The parameters must have values between and 1. The smaller the value f the Step size cnvergence parameter, the mre accurate the mapping slutin that will be btained. In general, the default values f the parameters wrk well and d nt need t be changed. Clustering. Randm starts. This parameter determines the number f times the ptimizatin algrithm f the VOS clustering technique is run. Each time the ptimizatin algrithm is run, a different clustering slutin may be btained. The best clustering slutin btained in all runs f the ptimizatin algrithm will be used as the final clustering slutin. The larger the value f the Randm starts parameter, the mre accurate the final clustering slutin that will be btained. Iteratins. This parameter determines the number f iteratins perfrmed by the ptimizatin algrithm f the VOS clustering technique. The larger the value f the parameter, the mre accurate the clustering slutin that will be btained. In general, the default value f the parameter wrks well and des nt need t be changed. 19

20 3 File types The tw primary file types used by VOSviewer are the map file and the netwrk file. Map files and netwrk files are simple text files that can easily be viewed and edited using a text editr (e.g., Ntepad) r a spreadsheet prgram (e.g., Excel). Map files and netwrk files cnsist f multiple clumns. Hence, each line in a map file r a netwrk file cntains multiple pieces f infrmatin. Different pieces f infrmatin n the same line are separated frm each ther by a cmma, a semicln, r a tab. If a piece f infrmatin (e.g., the label f an item) itself cntains a cmma r a semicln, the whle piece f infrmatin needs t be enclsed within duble qutes. We discuss map files and netwrk files in mre detail in Sectins 3.1 and 3.2. Fur additinal file types, the thesaurus file, the cluster clrs file, the scre clrs file, and the density clrs file, are discussed in Sectins 3.3 and 3.4. We nte that all example files mentined in this chapter are distributed tgether with VOSviewer. 3.1 Map file A map file is a text file that cntains infrmatin abut the items in a map. Each line in a map file crrespnds with an item. The nly exceptin is the first line. This is a header line that indicates what is cntained in each f the clumns f a map file. Belw, we list the clumns that can be used in a map file. Fr each clumn, we prvide the clumn header and we specify what the clumn cntains. id label sublabel descriptin url x y weight The ID f an item. Items need t have an ID nly if a map file is used in cmbinatin with a netwrk file. The label f an item. The sublabel f an item. In the main panel, the sublabel f an item is displayed belw the item s rdinary label. Sublabels are displayed in a smaller fnt. The descriptin f an item. The descriptin f an item is used t prvide infrmatin abut the item in the infrmatin panel. HTML frmatting can be used in this clumn. The URL f an item. This clumn can be used t assciate a web page with an item. Clicking n the label f an item in the main panel will cause the web page assciated with the item t be pened in a web brwser. The hrizntal crdinate f an item. The vertical crdinate f an item. The weight f an item. Only nn-negative numbers are allwed in this clumn. The higher the weight f an item, the mre prminent the item is presented in the 20

21 main panel. nrmalized weight scre cluster red The nrmalized weight f an item. Only nn-negative numbers are allwed in this clumn. The higher the nrmalized weight f an item, the mre prminent the item is presented in the main panel. The default presentatin f an item is btained by setting the item s nrmalized weight t 1. The scre f an item. In the main panel and the verview panel, items can be clred based n their scres, with by default clrs ranging frm blue t green t red. The number f the cluster t which an item belngs. Only integers between 1 and 1000 are allwed in this clumn. The red cmpnent f the clr f an item. Only integers between 0 and 255 are allwed in this clumn. green The green cmpnent f the clr f an item. Only integers between 0 and 255 are allwed in this clumn. blue The blue cmpnent f the clr f an item. Only integers between 0 and 255 are allwed in this clumn. In a map file, ne always uses nly a subset f the abve clumns. The rder in which the clumns are used is nt imprtant. There are a number f restrictins n the clumns that are used in a map file: There must be an id clumn r a label clumn. (If there is n label clumn, the ID f an item is used as the item s label.) If there is a sublabel clumn, there must be a label clumn as well. The x and y clumns must be used tgether. The red, green, and blue clumns must be used tgether. The weight clumn and the nrmalized weight clumn cannt be used tgether. Fr an example f a map file, see the file jurnal_map.txt. 3.2 Netwrk file A netwrk file is a text file that cntains the adjacency matrix f a netwrk. The adjacency matrix f a netwrk is a square matrix that indicates fr each pair f items in the netwrk the strength f the link between the items. The strength f a link is given by a nn-negative number. If there is n link between tw items, the strength f the link between the items equals zer. VOSviewer wrks with symmetric adjacency matrices. If a netwrk file cntains an asymmetric adjacency matrix, VOSviewer will make the matrix symmetric by averaging crrespnding elements n bth sides f the main diagnal. 21

22 A netwrk file has either a full frmat r a sparse frmat: Full frmat. The entire adjacency matrix, including elements that are equal t zer, is stred in the netwrk file. The file cnsists f n lines and n + 1 clumns, where n dentes the number f items in the netwrk. The element in the ith rw and the jth clumn f the adjacency matrix is stred n the ith line and in the (j + 1)th clumn f the netwrk file. The first clumn f the netwrk file cntains IDs f items. This clumn indicates fr each rw and clumn f the adjacency matrix the ID f the crrespnding item. Fr an example f a netwrk file in full frmat, see the file jurnal_netwrk_full.txt. Sparse frmat. Only the nn-zer elements f the adjacency matrix are stred in the netwrk file. The file cnsists f tw r three clumns. The first tw clumns cntain IDs f items. The third clumn cntains the nn-zer elements f the adjacency matrix. This clumn indicates the strength f the link between the items referred t in the first tw clumns. If there is n third clumn, the strength f the link between the items referred t in the first tw clumns always equals ne. In the case f a symmetric adjacency matrix, it is sufficient t stre nly half f the matrix (either the upper triangular part r the lwer triangular part) in the netwrk file. Fr an example f a netwrk file in sparse frmat, see the file jurnal_netwrk_sparse.txt. A netwrk file is usually used in cmbinatin with a map file. Fr each item ID in the netwrk file, there must then be a crrespnding item ID in the map file. 3.3 Thesaurus file A thesaurus file is a text file that can be used in the fllwing situatins: When creating a map based n Web f Science r Scpus files (see Subsectin 2.5.1), a thesaurus file can be used t merge different variants f a surce title, an authr name, an rganizatin name, r a cited reference. This may fr example be useful when the name f a researcher is written in different ways in different publicatins (e.g., with first initial nly and with all initials). A thesaurus file can then be used t indicate that different names in fact refer t the same researcher. When creating a map based n a crpus file (see Subsectin 2.5.1), a thesaurus file can be used t merge synnyms int a single term. This may be useful nt nly fr merging different terms referring t the same cncept, but als fr merging different spellings f the same term (e.g., behavir and 22

23 behaviur). It may als be useful fr merging an abbreviatin f a term with the term itself. Each line in a thesaurus file cntains a label and indicates an alternative label that replaces the riginal label. The nly exceptin is the first line. This is a header line that indicates what is cntained in each f the clumns f a thesaurus file. A thesaurus file must have tw clumns: A label clumn and a replace by clumn. The label clumn cntains a label. Depending n the situatin (see abve), a label may represent a surce title, an authr name, an rganizatin name, a cited reference, r a term. The replace by clumn cntains an alternative label that replaces the riginal label. The replace by clumn may als be empty. In that case, the riginal label is nt replaced by an alternative ne, but instead the riginal label is simply ignred. When creating a map based n a crpus file, this allws a thesaurus file t be used as a kind f stp wrd list. A thesaurus file may fr example indicate that certain uninteresting terms (e.g., cpyright and Elsevier in the case f a crpus f abstracts f scientific publicatins) shuld be ignred. Fr examples f thesaurus files, see the files thesaurus_authrs.txt and thesaurus_terms.txt. 3.4 Cluster clrs file, scre clrs file, and density clrs file A cluster clrs file is a text file that cntains the clrs f clusters. Each line in a cluster clrs file crrespnds with a cluster. The nly exceptin is the first line. This is a header line that indicates what is cntained in each f the clumns f a cluster clrs file. A cluster clrs file must have fur clumns: A cluster clumn, a red clumn, a green clumn, and a blue clumn. The cluster clumn cntains cluster numbers. Only integers between 1 and 1000 are allwed in this clumn. The red, green, and blue clumns cntain the red, green, and blue cmpnents f the clrs f clusters. Only integers between 0 and 255 are allwed in these clumns. Fr an example f a cluster clrs file, see the file cluster_clrs.txt. A scre clrs file is similar t a cluster clrs file except that instead f a cluster clumn it has a clr value clumn, with values between 0 and 1. If scres have been given t items, items can be clred by transfrming their scres int clr values and by matching these clr values with the clr values in the clr value clumn f the scre clrs file. Exact matching f clr values is usually nt pssible, and in that case the clrs in the scre clrs file are interplated. Fr an example f a scre clrs file, see the file scre_clrs.txt. A density clrs file is identical t a scre clrs file. In the item density visualizatin, the clr f a pint in a map is determined by transfrming the 23

24 density f items at that pint int a clr value and by matching this clr value with the clr values in the clr value clumn f the density clrs file. Exact matching f clr values is usually nt pssible, and in that case the clrs in the density clrs file are interplated. Fr an example f a density clrs file, see the file density_clrs.txt. 24

25 4 Advanced tpics In this chapter, sme advanced tpics are addressed. We first cnsider the use f cmmand line parameters (Sectin 4.1). We then discuss hw a map can be made available n the internet (Sectin 4.2) and hw the amunt f memry available t VOSviewer can be increased (Sectin 4.3). 4.1 Using cmmand line parameters VOSviewer supprts a number f cmmand line parameters. These parameters can fr example be used t autmatically pen a map when VOSviewer is started r t verride sme f the default settings f VOSviewer. The cmmand line parameters supprted by VOSviewer are listed belw. Cmmand line parameters fr pening r creating a map based n a map file and/r a netwrk file map netwrk Use this parameter t specify a map file (see Sectin 3.1). The map in this file will be pened when VOSviewer is started. Use this parameter t specify a netwrk file (see Sectin 3.2). An adjacency matrix will be read frm this file when VOSviewer is started. The adjacency matrix can be used t display links between the items in a map r t create a new map. Cmmand line parameters fr pening r creating a map based n ne r mre Pajek files pajek_netwrk pajek_partitin pajek_vectr Use this parameter t specify a Pajek netwrk (r matrix) file. Based n this file, a map will be pened r created when VOSviewer is started. Use this parameter t specify a Pajek partitin file. Cluster numbers f items will be read frm this file when VOSviewer is started. Use this parameter t specify a Pajek vectr file. Weights f items will be read frm this file when VOSviewer is started. Cmmand line parameters fr creating a term map based n a crpus file crpus cunting_methd min_n_ccurrences n_terms Use this parameter t specify a crpus file. Based n this file, a term map will be created when VOSviewer is started. Use this parameter t specify the cunting methd t be used in the creatin f the term map (1 fr binary cunting and 2 fr full cunting). Use this parameter t specify the minimum number f ccurrences a term must have t be included in the term map. Use this parameter t specify the number f terms t be included in the term map. VOSviewer will select the terms that seem mst relevant. 25

26 scres thesaurus Use this parameter t specify a scres file. In the creatin f the term map, this file will be used t calculate a scre fr each term. Use this parameter t specify a thesaurus file (see Sectin 3.3). In the creatin f the term map, this file can be used t merge synnyms int a single term. Visualizatin-related cmmand line parameters cluster_clrs density_clrs label_size label_size_variatin min_scre max_scre n_links scre_clrs visualizatin zm_level Use this parameter t specify a cluster clrs file (see Sectin 3.4). Cluster clrs will be imprted frm this file when VOSviewer is started. Use this parameter t specify a density clrs file (see Sectin 3.4). Density clrs will be imprted frm this file when VOSviewer is started. Use this parameter t specify the initial value f the Size slider in the ptins panel. Use this parameter t specify the initial value f the Size variatin slider in the ptins panel. Use this parameter t specify the initial value f the Min. scre text bx in the Min./Max. Scres dialg bx. Use this parameter t specify the initial value f the Max. scre text bx in the Min./Max. Scres dialg bx. Use this parameter t specify the initial value f the N. f links text bx in the ptins panel. Use this parameter t specify a scre clrs file (see Sectin 3.4). Scre clrs will be imprted frm this file when VOSviewer is started. Use this parameter t specify which visualizatin will be selected when VOSviewer is started (1 fr the netwrk visualizatin and 2 fr the density visualizatin). Use this parameter t specify the initial zm level in the main panel. The zm level must have a value f at least 1. The higher the zm level, the mre the main panel will be zmed in n the center f a map. Miscellaneus cmmand line parameters encding file_lcatin n_clustering Use this parameter t specify the character encding that is used by VOSviewer t read and write text files. Fr a list f the available encdings, see If this parameter is nt used, VOSviewer will attempt t autmatically determine the crrect encding when reading a text file (which in sme cases may result in the use f an incrrect encding), while it will use the default encding when writing a text file. Use this parameter t specify the flder that is used by VOSviewer as the default file lcatin. Use this parameter t indicate that n clustering must be perfrmed when VOSviewer is started. This parameter can fr example be used tgether with the pajek_netwrk parameter. A map will then be pened r created based n a Pajek netwrk file, but n clustering f the items in the map will be perfrmed. 26

27 view_nly Use this parameter t start VOSviewer in the view nly mde. In this mde, the Run buttn n the Map tab in the actin panel is nt available. T use the abve cmmand line parameters, VOSviewer needs t be run frm the cmmand line. When using the Windws executable f VOSviewer, this can fr example be dne as fllws: VOSviewer map map.txt visualizatin 2 zm_level 2.5 In this way, VOSviewer will be started and the map in the map file map.txt will be pened. Als, the density visualizatin will be selected, and the main panel will be zmed in n the center f the map. When instead f the Windws executable f VOSviewer the VOSviewer JAR file is used, VOSviewer can fr example be run in the fllwing way: java jar VOSviewer.jar map map.txt visualizatin 2 zm_level 2.5 We nte that sme cmmand line parameters cannt be used tgether. Fr example, the map and pajek_netwrk parameters and the map and crpus parameters cannt be used tgether. On the ther hand, sme parameters can nly be used in cmbinatin with anther parameter. The pajek_partitin parameter fr example can nly be used in cmbinatin with the pajek_netwrk parameter. Similarly, the cunting_methd parameter can nly be used in cmbinatin with the crpus parameter. 4.2 Making a map available n the internet Suppse ne wants t make a map available n the internet. One way t d this is simply by making a map file and a netwrk file (r nly a map file) available n the internet. T pen the map, ne then needs t take tw steps. In the first step, the map file and the netwrk file are dwnladed frm the internet. In the secnd step, VOSviewer is started and the dwnladed map file and netwrk file are used t pen the map. The abve tw-step apprach is nt very cnvenient, and therefre an alternative apprach is available as well. In this alternative apprach, a map can be pened in VOSviewer directly frm a web page. The alternative apprach wrks as fllws. A map file and a netwrk file (r nly a map file) need t be made available n the internet. Suppse these files are lcated at and 27

28 The map can then be made available n a web page by creating a hyperlink that pints t txt&netwrk= Using this hyperlink, the map can be pened directly in VOSviewer. We nte that all cmmand line parameters discussed in Sectin 4.1 can als be used in a hyperlink. Fr example, t pen a map, t select the density visualizatin, and t zm in n the center f the map, the fllwing hyperlink can be used: txt&netwrk= vel= Increasing the availability f memry When using VOSviewer t wrk with large maps (e.g., maps cntaining several thusands f items), the memry requirements can be quite substantial. VOSviewer will prduce an ut f memry errr if there is nt enugh memry available. The availability f memry can be increased by running the VOSviewer JAR file frm the cmmand line and specifying the amunt f memry that needs t be available. Fr example, if 1000 MB f memry needs t be available, the VOSviewer JAR file can be run as fllws: java -Xmx1000m -jar VOSviewer.jar When wrking with large maps, VOSviewer may als prduce a stack verflw errr. T prevent this errr frm ccurring, the stack size needs t be increased. This can be dne by running the VOSviewer JAR file frm the cmmand line in the fllwing way: java -Xss1000k -jar VOSviewer.jar In this case, the stack size is set t 1000 KB, but ther values are pssible as well. 28

29 References De Ny, W., Mrvar, A., & Batagelj, V. (2011). Explratry scial netwrk analysis with Pajek (2nd ed.). Cambridge University Press. Newman, M.E.J. (2004). Fast algrithm fr detecting cmmunity structure in netwrks. Physical Review E, 69, Nack, A. (2007). Energy mdels fr graph clustering. Jurnal f Graph Algrithms and Applicatins, 11(2), Nack, A. (2009). Mdularity clustering is frce-directed layut. Physical Review E, 79, Van Eck, N.J., & Waltman, L. (2009). Hw t nrmalize cccurrence data? An analysis f sme well-knwn similarity measures. Jurnal f the American Sciety fr Infrmatin Science and Technlgy, 60(8), Van Eck, N.J., & Waltman, L. (2010). Sftware survey: VOSviewer, a cmputer prgram fr biblimetric mapping. Scientmetrics, 84(2), Van Eck, N.J., & Waltman, L. (2011). Text mining and visualizatin using VOSviewer. ISSI Newsletter, 7(3), Van Eck, N.J., & Waltman, L. (2014). Visualizing biblimetric netwrks. In Y. Ding, R. Russeau, & D. Wlfram (Eds.), Measuring schlarly impact: Methds and practice (pp ). Springer. Van Eck, N.J., Waltman, L., Dekker, R., & Van den Berg, J. (2010). A cmparisn f tw techniques fr biblimetric mapping: Multidimensinal scaling and VOS. Jurnal f the American Sciety fr Infrmatin Science and Technlgy, 61(12), Waltman, L., & Van Eck, N.J. (2013). A smart lcal mving algrithm fr largescale mdularity-based cmmunity detectin. Eurpean Physical Jurnal B, 86(11), 471. Waltman, L., Van Eck, N.J., & Nyns, E.C.M. (2010). A unified apprach t mapping and clustering f biblimetric netwrks. Jurnal f Infrmetrics, 4(4),