From MAILER-DAEMON Sat Mar 03 15:12:39 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1esDWJ-00028d-HV for mharc-igraph-help@gnu.org; Sat, 03 Mar 2018 15:12:39 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:47538) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1esDWH-00028E-2G for igraph-help@nongnu.org; Sat, 03 Mar 2018 15:12:38 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1esDWF-0007kq-Vg for igraph-help@nongnu.org; Sat, 03 Mar 2018 15:12:36 -0500 Received: from mail-vk0-x231.google.com ([2607:f8b0:400c:c05::231]:38809) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1esDWF-0007iG-Qr for igraph-help@nongnu.org; Sat, 03 Mar 2018 15:12:35 -0500 Received: by mail-vk0-x231.google.com with SMTP id s1so7672019vke.5 for ; Sat, 03 Mar 2018 12:12:34 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=up.edu.ph; s=up.edu.ph; h=mime-version:from:date:message-id:subject:to; bh=siBkd0GnX2ijU1H021UXBzvUBmk2DoIMOVeItb93mRM=; b=fTzN9E7b1YckCG8j2W3Wu8QjlTXnM4aXD8QbRN5HcO+6FQl1laM64nJdamatuecsKI v5/5Ndq8E63J5LjhfZAI+OlOeHsob2Cs9OGicrpHu/ILsmMtjnW3R3VWtkQNkOjlEupI BdWyeKAUvGQsvFwWpmgs+rrefTBLtmtrear+kcgmZDhgDIAFy7wUJh6sCrHzAx0WKNFu XsYLx7tBAsisnjMgXkagTVRbqbN5ubooZaXAXyUNdqldObqMJZaIm3X9NtuXzA1fPZxa GeMzMdoZel4KhB7mDCuSskNX4ck8QTzaumylVK+jBI2p2fYFGNgW1JLAyaRfOW33/aGj /x8g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=siBkd0GnX2ijU1H021UXBzvUBmk2DoIMOVeItb93mRM=; b=Hz+ICimsr62on1YEVO0LdsjZ6mdIngbVzJ1VXdmasoDwHGYud5V05HtKI4WXVHiJbi QqqeH7I0Nr+/Zx7rjz9G56EVp15nldGshEIRaVd/it17maSrLLjs8hjXGYbv8sQQBYso XX4K1yEMjr0z/Faz8rie2iiIhBKvZpTvRkMxCAiE5g1AxN6aBLRDt3xsW9pj1r37L5R9 fQ5ix4J6fwbKeHzjcu0AQ4UkLYFgycxV4NYrgTLxsBiGilLdTM6mwUQ49fK60G9i65ef 09XorKTmeXJyrdNwVeDtkY8NCAJhY/S6ODHwzhw42e+f7OH1Ea0I2xmtA6hBz8XaTN/v hhCQ== X-Gm-Message-State: APf1xPAAUrrpsLmOrfFOMlxn7Az7VYjgH9JEVEMCIsskj1vgE0GhmGoB TGwW3is/X75tRYNePPkcdrQo3oYdG0ZsT24k6NQXxwE= X-Google-Smtp-Source: AG47ELtjodNYCyqR+tgn+n4c9R/Vxji1EnIeee7pV2ArO9tsnrTKhsRN8b7X6p7+w+8eEWE908/ELRNwuFt41QYKYvk= X-Received: by 10.31.255.14 with SMTP id p14mr7079673vki.161.1520107953878; Sat, 03 Mar 2018 12:12:33 -0800 (PST) MIME-Version: 1.0 Received: by 10.103.208.143 with HTTP; Sat, 3 Mar 2018 12:12:33 -0800 (PST) From: John Erwin Banez Date: Sun, 4 Mar 2018 04:12:33 +0800 Message-ID: To: igraph-help@nongnu.org Content-Type: multipart/alternative; boundary="f4030436f98e9c9332056687b625" X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2607:f8b0:400c:c05::231 Subject: [igraph] bootstrap a graph X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 03 Mar 2018 20:12:38 -0000 --f4030436f98e9c9332056687b625 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Is there a way to bootstrap an igraph? similar question with https://stats.stackexchange.com/questions/330616/monte-carlo-or-bootstrappi= ng-for-network-in-r --=20 John Erwin Ba=C3=B1ez Assistant Professor College of Social Work and Community Development University of the Philippines, Diliman --f4030436f98e9c9332056687b625 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Is there a way to bootstrap an igraph?

= similar question with




--
John Erwin Ba=C3=B1ez
Assistant Professor
Colleg= e of Social Work and Community Development
University of the Phil= ippines, Diliman
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Ip=[152.78.119.52]; Helo=[smtp.soton.ac.uk] X-MS-Exchange-CrossTenant-FromEntityHeader: HybridOnPrem X-MS-Exchange-Transport-CrossTenantHeadersStamped: DB7PR04MB4363 X-MS-Exchange-CrossPremises-AuthAs: Internal X-MS-Exchange-CrossPremises-AuthMechanism: 04 X-MS-Exchange-CrossPremises-AuthSource: SRV00045.soton.ac.uk X-MS-Exchange-CrossPremises-SCL: 1 X-MS-Exchange-CrossPremises-messagesource: StoreDriver X-MS-Exchange-CrossPremises-BCC: X-MS-Exchange-CrossPremises-originalclientipaddress: 90.254.85.122 X-MS-Exchange-CrossPremises-processed-by-journaling: Journal Agent X-MS-Exchange-CrossPremises-TransportTrafficType: Email X-MS-Exchange-CrossPremises-TransportTrafficSubType: X-MS-Exchange-CrossPremises-Antispam-ScanContext: DIR:Originating; SFV:NSPM; SKIP:0; X-OrganizationHeadersPreserved: DB7PR04MB4363.eurprd04.prod.outlook.com X-detected-operating-system: by eggs.gnu.org: Windows 7 or 8 [fuzzy] X-Received-From: 104.47.1.71 Subject: [igraph] R multilevel.community only shows 2 levels X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 04 Mar 2018 13:07:45 -0000 --_000_B877ADDF9C1ECC4AA31BDF02AA5AF68D9C46D5FDSRV00047sotonac_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I am new to Community Detection and to make things harder I am also a begin= ner in R - please keep this in mind when you kindly answer. I have a undirected graph with 2198 nodes and 1380771 edges with weights, I= use the walktrap algorithm to detect communities which will give me 10 com= munities, which is the partitioning with the best modularity value. However= , I want to extract the community membership and the modularity for each le= vel/partition. I believe I need to use the multilevel.communities function,= but it does not seem to give me the expected result. The data I use is here: https://www.dropbox.com/s/833784qseu7ybyc/IntLarger= ZeroFlows.csv?dl=3D0 Current code ### load data and create undirected graph with 2198 nodes and 1380771 edges= with weights > df <- read.csv("C:\\Users\\dh2r15\\Desktop\\Malaria\\CommunityDetection\\= input\\IntLargerZeroFlows.csv", header=3D TRUE, stringsAsFactors =3D FALSE= ) > mylinks <- df[,-1] > colnames(mylinks)[3] <- "weight" #rename pred_seed1 to weight > install.packages("igraph") > library(igraph) # create directed graph from dataframe > directed_graph <- graph.data.frame(mylinks, directed =3D TRUE) # collapse to undirected graph, summing weights > net <- as.undirected(directed_graph, mode =3D "collapse", edge.attr.comb = =3D "sum") ### community detection ### com <- walktrap.community(net, weights =3D E(net)$weight, steps =3D 4, merg= es =3DmTRUE, modularity =3D TRUE) # analyse communities length(com) # number of communities modularity(com) # how modular the graph partitioning is # communities for every level > mlc <- multilevel.community(net, weights=3DE(net)$weight) > write.csv(mlc$memberships, "MultilevelMembership.csv") The resulting MultilevelMembership.csv has 2198 columns, I guess each colum= n represents one node. First question is how can I link these back to my or= iginal node names (e.g. MMR_1)? Second problem is that this table has only 2 rows, each representing one le= vel/partition (I assume). Why are there only 2? I was expecting a table wit= h one row for each level, and as there are 2198 nodes surely there must be = 2198 levels (ranging from just one superlarge community including all nodes= , down to 2198 'communities' where each node is by itself in a community)? Maybe I need to use a totally different function, something along the lines= of createing a dendrogramm and cutting that? Any help on this matter is greatly appreciated, I am trying to solve this f= or weeks now and do not get anywhere. Many thanks for reading, Thea length(com) # number of communities: 10 modularity(com) # how modular the graph partitioning is library(igraph) net <- graph_from_data_frame(d=3Dmylinks, vertices=3Dmynodes, directed=3DT) I then use the walktrap algorithm to create communities: com <- walktrap.community(net, weights =3D E(net)$weight, steps =3D 4, merg= es =3D TRUE, modularity =3D TRUE) Walktrap splits the graph into 10 communities and gives me a modularity sco= re of 0.4819893 (which I think is quite good): length(com) # number of communities: 10 modularity(com) # how modular the graph partitioning is I can plot a dendrogram with the 10 communities on top: dendrogram <- dendPlot(com, mode=3D"hclust") Now my question: I need access to the modularity scores and memberships for= all levels, not just the best cut level with 10 communities. So basically = I want to be able to cut my dendrogram at each level and calculate the modu= larity as well as get the membership. How do I do this best please? I am af= ter something like this: * Level Modularity * 1 ? * 2 ? * 3 ? * ... ... * 10 0.4819893 * ... ... This list should include as many levels as the graph has nodes. Then in add= ition there should be something which shows me the membership for each leve= l. Second Problem The second problem I have is to visualize this graph, as it contains so man= y nodes and edges that one can't really see anything: com_plot <- plot(com, net) plotted graph with communities I would be glad for any ideas and solutions on this front. Thank you for reading all this! -- GeoData University of Southampton Southampton SO17 1BJ Tel: 023 8059 2719 Email: dh@geodata.soton.ac.uk www.geodata.soton.ac.uk Please note office hours Monday to Thursday --_000_B877ADDF9C1ECC4AA31BDF02AA5AF68D9C46D5FDSRV00047sotonac_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi,

I am new to Community Detection and to make things harder I am also a begin= ner in R - please keep this in mind when you kindly answer. 

I have a undirected graph with 2198 nodes and 1380771 edges with weights, I= use the walktrap algorithm to detect communities which will give me 10 com= munities, which is the partitioning with the best modularity value. However= , I want to extract the community membership and the modularity for each level/partition. I believe I need t= o use the multilevel.communities function,but it does not seem to give me t= he expected result.

The data I use is here: https://www.dropbox.com/s/833784qseu7ybyc/IntL= argerZeroFlows.csv?dl=3D0 


Current code

### load data and create undirected graph with 2198 nodes and 1380771 edges= with weights

> df <- read.csv("C:\\Users\= \dh2r15\\Desktop\\Malaria\\CommunityDetection\\input\\IntLargerZeroFlows.cs= v", header=3D TRUE,  stringsAsFactors =3D FALSE)

> mylinks <- df[,-1]

> colnames(mylinks)[3] <- "w= eight" #rename pred_seed1 to weight<= /font>


> install.packages("igraph"= ;)

> library(igraph)


# create directed graph from dataframe<= /span>

> directed_graph <- graph.data.fr= ame(mylinks, directed =3D TRUE)

# collapse to undirected graph, summing= weights

> net <- as.undirected(directed_g= raph,&nb= sp;mode =3D "collapse", edge.attr.comb =3D "sum")


### community detection ###

com <- walktrap.com= munity(net, weights =3D E(net)$weight, steps =3D 4, merges =3DmTRUE, modularity =3D TRUE)

# analyse communities

length(com) #  number of communities=

modularity(com) # how modular the graph partitioning= is

# communities for every level

> mlc <- multilevel.community(net= , weights=3DE(net)$weight)

> write.csv(mlc$memberships, "M= ultilevelMembership.csv")


The resulting MultilevelMembership.csv has 2198 columns, I guess each column represents one node. First question is h= ow can I link these back to my original node names (e.g. MMR_1)? 

Second problem is that this table has o= nly 2 rows, each representing one level/partition (I assume). Why are there= only 2? I was expecting a table with one row for each level, and as there are 2198 n= odes surely there must be 2198 levels (ranging from just one superlarge com= munity including all nodes, down to 2198 'communities' where each node is b= y itself in a community)?


Maybe I need to use a totally different= function, something along the lines of createing a dendrogramm and cutting= that?


Any help on this matte= r is greatly appreciated, I am trying to solve this for weeks now and do no= t get anywhere.

Many thanks for reading,<= /p>

Thea






length(com) #  number of communities: =
10 =0A=
modularity(com) # how modular the graph partitioning is



library(igraph)=0A=
net <- graph_from_data_frame(d=3Dmylinks, vertices=3D<=
span class=3D"pln" style=3D"margin: 0px; padding: 0px; border: 0px; font-st=
yle: inherit; font-variant: inherit; font-weight: inherit; font-stretch: in=
herit; font-size: inherit; line-height: inherit; font-family: inherit; vert=
ical-align: baseline; box-sizing: inherit; color: rgb(48, 51, 54);">mynodes=
, directed=3DT) 

I then use the walktrap algorithm to create communities:

com <- walktrap.community(net, weights =
=3D E(net)$weight, steps =3D 4, merges =3D=0A=
                        TRUE, modularity =3D TRUE)

Walktrap splits the graph into 10 communities and gives me a modularity sco= re of 0.4819893 (which I think is quite good):

length(com) #  number of communities: =
10 =0A=
modularity(com) # how modular the graph partitioning is

I can plot a dendrogram with the 10 communities on top:

dendrogram <- dendPlot(com, mode=3D=
"hclust") 

Now my question: I need access to the modularity scores and memberships for= all levels, not just the best cut level with 10 communities. So basically = I want to be able to cut my dendrogram at each level and calculate the modu= larity as well as get the membership. How do I do this best please? I am after something like this:

  • Level Modularity
  • 1 ?
  • 2 ?
  • 3 ?
  • ... ...
  • 10 0.4819893
  • ... ...

This list should include as many levels as the graph has nodes. Then in add= ition there should be something which shows me the membership for each leve= l.

Second Problem

The second problem I have is to visualize this graph, as it contains so man= y nodes and edges that one can't really see anything:

com_plot <- plot(com, net) =

plotted graph with communities

I would be glad for any ideas and solutions on this front.

Thank you for reading all this!


--
= GeoData
University of Southampton
Southampton
SO17 1BJ
 
Tel: 023 8059 2719
Email: dh@geodata.soton.ac.uk
 

Please note office hours Monday to Thursday<= /div>
--_000_B877ADDF9C1ECC4AA31BDF02AA5AF68D9C46D5FDSRV00047sotonac_-- From MAILER-DAEMON Sun Mar 04 14:03:32 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1esYuy-0002rM-Kr for mharc-igraph-help@gnu.org; Sun, 04 Mar 2018 14:03:32 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:40549) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1esYuv-0002qv-NU for igraph-help@nongnu.org; Sun, 04 Mar 2018 14:03:30 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1esYuu-0001v6-TJ for igraph-help@nongnu.org; Sun, 04 Mar 2018 14:03:29 -0500 Received: from mail-io0-x236.google.com ([2607:f8b0:4001:c06::236]:36208) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1esYuu-0001ur-Ou for igraph-help@nongnu.org; Sun, 04 Mar 2018 14:03:28 -0500 Received: by mail-io0-x236.google.com with SMTP id e30so15642876ioc.3 for ; Sun, 04 Mar 2018 11:03:27 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=XRmSa3/2AG7Hoc2Rw5z8IAwa7osel2ic9JgNYMGS4Ho=; b=X462p2TiPNbdCbRpmYAhoSg9tAnCpQMeEMURhwS8375jVp7wywR/9+6TfF8JCG6lrA slypfBAouagphphlWyWr1fVsO4qSQX4utyweDz7LFV09xXsYgR76fBIg1iIqafERUkDy JzvYldR761LafENc7i6Z6yBjQB1zoYF2JJReE2UDgCeWm3aU0CX0UB0kwjEKcUFJHsrY PRG/jMhJ3LeQWdiC5R/oz04d1reNmT17yWGKDFITivgy+MRZrtn7MGffrCVrOeHVdNgA DGilNAZh7GwXqyDFdYGwAej7HsNefxITj6cJvGpIXUixjuJSB55Akip6/rm5d/C03/ne w9yg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=XRmSa3/2AG7Hoc2Rw5z8IAwa7osel2ic9JgNYMGS4Ho=; b=sl42LMbhfNDaD7krJQxiglfSHbgs/wfUmPSMxu86ScgUKIh1dhzStz0QMDjNvnG7PX ts2xFlEMNc2Dl2lT5NAvSIMRMyJFoT3eckHFy1QzYBEp1iPNwoPgBxMyIGLH63lDch3h 2w1uBnkaUHSMlndc2uatFufurAnlUDV745G1H79MBFsyjQQPj0rCr62H0PhFxsc6Jb/q JP2G6s9stHXhxt3hpymKhChLODZ3pZWSfFxqIuQraXA3BmEQRqft3YfVNsAxyZPWV01u UjSS7K5CebwLyByn/OehiHtBeriGrvSp5NA/Vi1Fd23X8yuVEC3oeoES2OssUIXg+Sat bJIA== X-Gm-Message-State: AElRT7HYPJjY4gNLODS4fN+QYMdUUS48SYC5eVHmjW7QBtkuyo/6xLTE 5vw+WGYzamPTZ70HQ2XbC7KEQFF/djL3wqlyTGIC2Q== X-Google-Smtp-Source: AG47ELvURhWE7TlCjsZb5PddvuqJMiewXNasfXlB8qh6gh5o+3HTzisFcPxnroCF/u0po7fZbJ0lDrYZzfDvtxudp/8= X-Received: by 10.107.101.2 with SMTP id z2mr13755820iob.273.1520190206045; Sun, 04 Mar 2018 11:03:26 -0800 (PST) MIME-Version: 1.0 Received: by 10.107.141.70 with HTTP; Sun, 4 Mar 2018 11:03:25 -0800 (PST) From: lookman sanni Date: Sun, 4 Mar 2018 20:03:25 +0100 Message-ID: To: Help for igraph users Content-Type: multipart/alternative; boundary="089e082cd2c838f4d805669add3a" X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2607:f8b0:4001:c06::236 Subject: [igraph] Label Propagation Based Graph Clustering X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 04 Mar 2018 19:03:30 -0000 --089e082cd2c838f4d805669add3a Content-Type: text/plain; charset="UTF-8" Hi Everyone, I am trying the label propagation algorithm in the R igraph package: "cluster_label_prop". Several iterations of run produced different clustering results ( clusters count between 5, 6 or 7). Is this algorithm known to not converge ? The authors stated in the related paper that the mathematical convergence of the algorithm is hard to prove, but that one can observe its convergence after about 5 iterations. Is there any way one can control the iterations count in the igraph implementation ? Thank you -- Lookman SANNI --089e082cd2c838f4d805669add3a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Everyone,

I am trying the label prop= agation algorithm in the R igraph package: "cluster_label_prop". = Several iterations of run produced different clustering results ( clusters = count between 5, 6 or 7). Is this algorithm known to not converge ?

The authors stated in the related paper that the mathemat= ical convergence of the algorithm is hard to prove, but that one can observ= e its convergence after about 5 iterations. Is there any way one can contro= l the iterations count in the igraph implementation ?

<= div>Thank you



-- =
<= div>
Lookman SANNI
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Ip=[152.78.119.52]; Helo=[smtp.soton.ac.uk] X-MS-Exchange-CrossTenant-FromEntityHeader: HybridOnPrem X-MS-Exchange-Transport-CrossTenantHeadersStamped: AM2PR04MB0980 X-MS-Exchange-CrossPremises-AuthAs: Internal X-MS-Exchange-CrossPremises-AuthMechanism: 04 X-MS-Exchange-CrossPremises-AuthSource: SRV00045.soton.ac.uk X-MS-Exchange-CrossPremises-SCL: 1 X-MS-Exchange-CrossPremises-messagesource: StoreDriver X-MS-Exchange-CrossPremises-BCC: X-MS-Exchange-CrossPremises-originalclientipaddress: 152.78.118.247 X-MS-Exchange-CrossPremises-processed-by-journaling: Journal Agent X-MS-Exchange-CrossPremises-TransportTrafficType: Email X-MS-Exchange-CrossPremises-TransportTrafficSubType: X-MS-Exchange-CrossPremises-Antispam-ScanContext: DIR:Originating; SFV:NSPM; SKIP:0; X-OrganizationHeadersPreserved: AM2PR04MB0980.eurprd04.prod.outlook.com X-detected-operating-system: by eggs.gnu.org: Windows 7 or 8 [fuzzy] X-Received-From: 104.47.0.49 Subject: [igraph] FW: R multilevel.community only shows 2 levels X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 06 Mar 2018 11:53:34 -0000 --_004_B877ADDF9C1ECC4AA31BDF02AA5AF68D9C46E830SRV00047sotonac_ Content-Type: multipart/alternative; boundary="_000_B877ADDF9C1ECC4AA31BDF02AA5AF68D9C46E830SRV00047sotonac_" --_000_B877ADDF9C1ECC4AA31BDF02AA5AF68D9C46E830SRV00047sotonac_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Just to let you know that I found a solution to my problem. The function I = was looking for is 'cut_at()'. So the simple line > membership <- cut_at(com, 5) gives me the desired membership for level 5. Hope this will help someone else in the future. Cheers, Thea From: igraph-help [mailto:igraph-help-bounces+dh=3Dgeodata.soton.ac.uk@nong= nu.org] On Behalf Of Heim D. Sent: 04 March 2018 13:08 To: igraph-help@nongnu.org Subject: [igraph] R multilevel.community only shows 2 levels Hi, I am new to Community Detection and to make things harder I am also a begin= ner in R - please keep this in mind when you kindly answer. I have a undirected graph with 2198 nodes and 1380771 edges with weights, I= use the walktrap algorithm to detect communities which will give me 10 com= munities, which is the partitioning with the best modularity value. However= , I want to extract the community membership and the modularity for each le= vel/partition. I believe I need to use the multilevel.communities function,= but it does not seem to give me the expected result. The data I use is here: https://www.dropbox.com/s/833784qseu7ybyc/IntLarger= ZeroFlows.csv?dl=3D0 Current code ### load data and create undirected graph with 2198 nodes and 1380771 edges= with weights > df <- read.csv("C:\\Users\\dh2r15\\Desktop\\Malaria\\CommunityDetection\\= input\\IntLargerZeroFlows.csv", header=3D TRUE, stringsAsFactors =3D FALSE= ) > mylinks <- df[,-1] > colnames(mylinks)[3] <- "weight" #rename pred_seed1 to weight > install.packages("igraph") > library(igraph) # create directed graph from dataframe > directed_graph <- graph.data.frame(mylinks, directed =3D TRUE) # collapse to undirected graph, summing weights > net <- as.undirected(directed_graph, mode =3D "collapse", edge.attr.comb = =3D "sum") ### community detection ### com <- walktrap.community(net, weights =3D E(net)$weight, steps =3D 4, merg= es =3DmTRUE, modularity =3D TRUE) # analyse communities length(com) # number of communities modularity(com) # how modular the graph partitioning is # communities for every level > mlc <- multilevel.community(net, weights=3DE(net)$weight) > write.csv(mlc$memberships, "MultilevelMembership.csv") The resulting MultilevelMembership.csv has 2198 columns, I guess each colum= n represents one node. First question is how can I link these back to my or= iginal node names (e.g. MMR_1)? Second problem is that this table has only 2 rows, each representing one le= vel/partition (I assume). Why are there only 2? I was expecting a table wit= h one row for each level, and as there are 2198 nodes surely there must be = 2198 levels (ranging from just one superlarge community including all nodes= , down to 2198 'communities' where each node is by itself in a community)? Maybe I need to use a totally different function, something along the lines= of createing a dendrogramm and cutting that? Any help on this matter is greatly appreciated, I am trying to solve this f= or weeks now and do not get anywhere. Many thanks for reading, Thea length(com) # number of communities: 10 modularity(com) # how modular the graph partitioning is library(igraph) net <- graph_from_data_frame(d=3Dmylinks, vertices=3Dmynodes, directed=3DT) I then use the walktrap algorithm to create communities: com <- walktrap.community(net, weights =3D E(net)$weight, steps =3D 4, merg= es =3D TRUE, modularity =3D TRUE) Walktrap splits the graph into 10 communities and gives me a modularity sco= re of 0.4819893 (which I think is quite good): length(com) # number of communities: 10 modularity(com) # how modular the graph partitioning is I can plot a dendrogram with the 10 communities on top: dendrogram <- dendPlot(com, mode=3D"hclust") Now my question: I need access to the modularity scores and memberships for= all levels, not just the best cut level with 10 communities. So basically = I want to be able to cut my dendrogram at each level and calculate the modu= larity as well as get the membership. How do I do this best please? I am af= ter something like this: * Level Modularity * 1 ? * 2 ? * 3 ? * ... ... * 10 0.4819893 * ... ... This list should include as many levels as the graph has nodes. Then in add= ition there should be something which shows me the membership for each leve= l. Second Problem The second problem I have is to visualize this graph, as it contains so man= y nodes and edges that one can't really see anything: com_plot <- plot(com, net) plotted graph with communities I would be glad for any ideas and solutions on this front. Thank you for reading all this! -- GeoData University of Southampton Southampton SO17 1BJ Tel: 023 8059 2719 Email: dh@geodata.soton.ac.uk www.geodata.soton.ac.uk Please note office hours Monday to Thursday --_000_B877ADDF9C1ECC4AA31BDF02AA5AF68D9C46E830SRV00047sotonac_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Just to le= t you know that I found a solution to my problem. The function I was lookin= g for is ‘cut_at()’.

So the sim= ple line

> membe= rship <- cut_at(com, 5)

gives me t= he desired membership for level 5.

 = ;

Hope this = will help someone else in the future.

 = ;

Cheers,

Thea<= /o:p>

 = ;

 = ;

From: = igraph-help [mailto:igraph-help-bounces+dh=3Dgeodata.soton.ac.uk@nongnu= .org] On Behalf Of Heim D.
Sent: 04 March 2018 13:08
To: igraph-help@nongnu.org
Subject: [igraph] R multilevel.community only shows 2 levels

 

= Hi,

I am new to Community Detection and to make things harder I am= also a beginner in R - please keep this in mind when you kindly answer.&nb= sp;

I have a undirected graph with 2198 nodes and 1380771 edges wi= th weights, I use the walktrap algorithm to detect communities which will g= ive me 10 communities, which is the partitioning with the best modularity value. However, I want to extract the community m= embership and the modularity for each level/partition. I believe I need to = use the multilevel.communities function,but it does not seem to give me the= expected result.

The data I use is here: https:= //www.dropbox.com/s/833784qseu7ybyc/IntLargerZeroFlows.csv?dl=3D0 

 

Current code

### load data and create undirected graph with 2198 nodes and = 1380771 edges with weights

> df <- read.csv("C:\\Users\\dh2r15\\Desktop\\Malar= ia\\CommunityDetection\\input\\IntLargerZeroFlows.csv", header=3D TRUE= ,  stringsAsFactors =3D FALSE)

> mylinks <- df[,-1]

> colnames(mylinks)[3] <- "weight" #rename pre= d_seed1 to weight

 

> install.packages("igraph")

> library(igraph)

 

# create directed graph from dataframe=

> directed_graph <- graph.data.frame(mylinks, directed = =3D TRUE)

# collapse to undirected graph, summing weights

> net <- as.undirected(directed_graph, mode =3D &qu= ot;collapse", edge.attr.comb =3D "sum")

 

### community detection ###

com <- walktrap.community(net, weights =3D E(net)$weight, s= teps =3D 4, merges =3DmTRUE, modularity =3D TRUE)

# analyse communities

length(com) #  number of communities

modularity(com) # how modular the graph partitioning is=

# communities for every level

> mlc <- multilevel.community(net, weights=3DE(net)$weig= ht)

> write.csv(mlc$memberships, "MultilevelMembership.csv= ")

 

The resulting MultilevelMembership.csv has 2198 colu= mns, I guess each column represents one node. First question is how can I l= ink these back to my original node names (e.g. MMR_1)? 

Second problem is that this table has only 2 rows, each repres= enting one level/partition (I assume). Why are there only 2? I was exp= ecting a table with one row for each level, and as there are 2198 nodes surely there must be 2198 levels (ranging from just o= ne superlarge community including all nodes, down to 2198 'communities' whe= re each node is by itself in a community)?

 

Maybe I need to use a totally different function, something al= ong the lines of createing a dendrogramm and cutting that?

 

Any help on this matter is greatly appreciated, I am trying to= solve this for weeks now and do not get anywhere.<= /o:p>

Many thanks for reading,<= /p>

Thea

 

 

 





length=
(com) #  number of communities: 10 
modularity(=
com) # how modular the graph partitioning is

 

 

library(igraph)<=
/pre>
net =
<- graph_from_data_frame(d=3D<=
span style=3D"font-family:"inherit",serif;color:#303336;border:no=
ne windowtext 1.0pt;padding:0cm">mylinks<=
span style=3D"font-family:"inherit",serif;color:#303336;border:no=
ne windowtext 1.0pt;padding:0cm">, vertices=3Dmynodes, directed=3DT) 

I then use the walktrap algorithm to create communities:<= /o:p>

com <- walktrap.communit=
y(net,<=
span class=3D"pln"> weights =3D E(net)$weight, steps =3D 4,=3D<=
o:p>
      &n=
bsp;            =
;     TRUE, modularity =3D TRUE

Walktrap splits the graph into 10 communities and gives me a m= odularity score of 0.4819893 (which I think is quite good):

length=
(com) #  number of communities: 10 
modularity(=
com) # how modular the graph partitioning is

I can plot a dendrogram with the 10 communities on top:

dendrogram <- dendPlot(<=
/span>com, mode=3D"hclust") 

Now my question: I need access to the modularity scores and me= mberships for all levels, not just the best cut level with 10 communities. = So basically I want to be able to cut my dendrogram at each level and calculate the modularity as well as get the membership. = How do I do this best please? I am after something like this:

·       &= nbsp; Level Modularity=

·       &= nbsp; 1 ?

·       &= nbsp; 2 ?

·       &= nbsp; 3 ?

·       &= nbsp; ... ...

·       &= nbsp; 10 0.4819893

·       &= nbsp; ... ...

This list should include as many levels as the graph has nodes= . Then in addition there should be something which shows me the membership = for each level.

Second Problem

The second problem I have is to visualize this graph, as it co= ntains so many nodes and edges that one can't really see anything:

com_plot <- plot<=
/span>(=
com, net) 

plotted graph with communities

I would be glad for any ideas and solutions on this front.

Thank you for reading all this!

 

--

GeoData=

University of Southampton

Southampton

SO17 1BJ

 <= /span>

Tel: 023 8059 2719

 <= /span>

 

Please note office hours Monday to Thur= sday

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X-Received-From: 2a00:1450:400c:c0c::231 Subject: [igraph] status of the Viger-Latapy sampling method for graphs with a given degree sequence X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 06 Mar 2018 13:29:23 -0000 --089e082fd1c4dc84850566be6d70 Content-Type: multipart/alternative; boundary="089e082fd1c4dc84830566be6d6f" --089e082fd1c4dc84830566be6d6f Content-Type: text/plain; charset="UTF-8" Hello everyone, I am looking at the various methods available in igraph to *uniformly* sample random graphs with a given degree sequence. The obvious candidate function is igraph_degree_sequence_game(). http://igraph.org/c/doc/igraph-Generators.html#igraph_degree_sequence_game This function provides three generation methods: "SIMPLE" is explained, and it's clear that the sampling is not uniform. Also, this method allows multigraphs and self-loops. "SIMPLE_NO_MULTIPLE" is explicitly mentioned as not uniform. What remains is the Viger-Latapy method. The link here is broken, but it's easy to google up the original paper, https://arxiv.org/pdf/cs/0502085.pdf, the abstract of which says: "We address here the problem of generating random graphs uniformly from the set of simple connected graphs having a prescribed degree sequence." While I didn't read the entire paper, the abstract suggests that this method should sample uniformly from the set of *connected* simple graphs. However, this does not appear to be the case in a simple test. Consider the degree sequence (1, 2, 1, 2). The only two simple graphs with this degree sequence are: But the Viger-Latapy method, as implemented in igraph, will generate only the second one. Let's look at a more complicated example, the sequence (1, 2, 2, 2, 1). Here's the list of such graphs (one of which is not connected): The Viger-Latapy method generates only these: Within this set, the sampling is indeed uniform, but there are three connected graphs which are never generated. *Question:* Is the Viger-Latapy method known to be flawed, or is there something I'm missing here? There doesn't seem to be a peer-reviewed publication about this. Szabolcs *P.S. *A method that does work in practice is generating a single realization of the degree sequence, then using igraph_rewire() on it. What is unclear in such situations is how many rewiring steps are necessary to approximate uniform sampling. --089e082fd1c4dc84830566be6d6f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello everyone,

I am looking at the various methods= available in igraph to *uniformly* sample random graphs with a given degre= e sequence.=C2=A0 The obvious candidate function is =C2=A0igraph_degree_seq= uence_game().

http://igraph.org/c/doc/igraph-Generators.= html#igraph_degree_sequence_game

This function provides three ge= neration methods:

"SIMPLE" is explained, and it's clea= r that the sampling is not uniform.=C2=A0 Also, this method allows multigra= phs and self-loops.

"SIMPLE_NO_MULTIPLE" is explicitly men= tioned as not uniform.

What remains is the Viger-Latapy method. The = link here is broken, but it's easy to google up the original paper, https://arxiv.org/pdf/cs/0502= 085.pdf, the abstract of which says:

"We address here the p= roblem of generating random graphs uniformly from the set of simple connect= ed graphs having a prescribed degree sequence."

Whi= le I didn't read the entire paper, the abstract suggests that this meth= od should sample uniformly from the set of *connected* simple graphs.=C2=A0= However, this does not appear to be the case in a simple test.
<= br>
Consider the degree sequence (1, 2, 1, 2).=C2=A0 The only two= simple graphs with this degree sequence are:


But the Viger-Latapy me= thod, as implemented in igraph, will generate only the second one.

Let's look at a more complicated example, the sequence= (1, 2, 2, 2, 1). Here's the list of such graphs (one of which is not c= onnected):


The Viger-Latapy method generates = only=C2=A0these:



Within this se= t, the sampling is indeed uniform, but there are three connected graphs whi= ch are never generated.

Question:

Is the Viger-Latapy method known to be flawed, or is= there something I'm missing here?=C2=A0 There doesn't seem to be a= peer-reviewed publication about this.

Szabolcs

P.S. A method that does work in practice is g= enerating a single realization of the degree sequence, then using igraph_re= wire() on it. What is unclear in such situations is how many rewiring steps= are necessary to approximate uniform sampling.



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-0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=pxO1O4PblRP7YK+JDg/a/uKnLX0f+H4dOdUN6FwbajY=; b=FV4eCpYNtLCrll7dAmOntSlOo+8gwn+hGGVjyml2U8PI7AabFB6/tNVIzgFAX5fRLo cG9HypD8wkOEa/VcKUth28ljtXLt40USNRhDaepJ9bUhNn4G7rS/8yRvdCs/J+0Lt+8R 69SssQzzJuPFaT6UO09o0XgyFW6Mx3KycjLFLnGdaqs/uuHWQ3SGvQOiK4RqWB5ND+bp 83M9mpdf+DLRgYZ4QO/z2KI4cTcdMZlKnsuQeCQ4GvvrejMlCuZ8pUEcHr1tHZOGrRLq i5thhGhZy7C3PmPGMJHxa8KRlKfUXIVTn2cijKd0rflSKLzVfYT8yWXG+bm+mHs4vlBm sE6A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=pxO1O4PblRP7YK+JDg/a/uKnLX0f+H4dOdUN6FwbajY=; b=OSZXhFqCbttcuFIw90rNN7wYInexEBy14SZ980AfibZX2do0KtHgZwTG/hyR0FIDr6 YaiRwEWWiF6AF80eDvZVJZbU1EGTmCq36Y3CuPv8hQVTE7nFS4VbVGeQzHxLWJueAhpk gSsOBTe+i2HCoVs5q/qiG6JqdVyaNh9bDGNwSaO8Pqhu+flnt/+rbN1deJjQ+KF9zPWJ 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X-Received-From: 2a00:1450:4010:c07::229 Subject: [igraph] Preserve Edge Numbering X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 14 Mar 2018 08:37:24 -0000 --0000000000007adcc405675b4820 Content-Type: text/plain; charset="UTF-8" Hi, I am currently removing random nodes from a graph G creating G'. I can preserve the vertex numbering by assigning ids to individual nodes. So in G' I can access the old vertex numbering as usual. But I wanted the same functionality with edges. The get_edgelist function gives the new edge list as it does not depend on my custom id assignment. Does anybody have any idea how to do this? -- Viraj Parimi --0000000000007adcc405675b4820 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
=3D""
Hi,

<= /div>
I am currently removing random nodes from a graph G creating = G'. I can preserve the vertex numbering by assigning ids to indi= vidual nodes. So in G' I can access the old vertex numbering as usual. = But I wanted the same functionality with edges. The get_edgelist function gives the new edge list as it doe= s not depend on my custom id assignment. Does anybody have any idea how to = do this?

--
Viraj Parimi
--0000000000007adcc405675b4820-- From MAILER-DAEMON Mon Mar 19 03:41:50 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1expQU-00018k-KJ for mharc-igraph-help@gnu.org; Mon, 19 Mar 2018 03:41:50 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:37331) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1expQT-00018d-9N for igraph-help@nongnu.org; Mon, 19 Mar 2018 03:41:50 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1expQO-0005XZ-EE for igraph-help@nongnu.org; Mon, 19 Mar 2018 03:41:49 -0400 Received: from mail-wr0-x22c.google.com ([2a00:1450:400c:c0c::22c]:36379) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1expQO-0005VZ-6r for igraph-help@nongnu.org; Mon, 19 Mar 2018 03:41:44 -0400 Received: by mail-wr0-x22c.google.com with SMTP id d10so17505636wrf.3 for ; Mon, 19 Mar 2018 00:41:43 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:content-transfer-encoding:mime-version:subject:message-id:date :to; bh=tPYe5vLjaq0f6gPyw01XK4HfTAz2aDUZMt5kpQCKbPc=; b=n21G5Gg96hJaeLt+lgpgD4QEMLBlXhdBleQQj/3ofpXkq/JM5rolGZG8KY5AtgRhyC k4mcSyN4GP5alSJk4DIgVq22l1at0nMLoS6Cs0KU8GbiuV5Au4gTW0hNuQBHSeEj0QEl BTJY/LrPkTBq7mzZ7tvW26Sk6z43PmLzd9eJKY01ul2Lu0j0GosJHgdH8bJMviHT6B/+ zAzRu/TwOIk97rOorlhy/5HGsN8OekMkPHS0s7r0g8x1Li6mvDItpkEjQtdjXZ8s8YfP 4Z5RiX3bdBmPiIWpd3uvrrbWCUj20LiuCXYZI5PQuqGWa3mHrN1WVFlarGqsFeBooGoy AVtg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:content-transfer-encoding:mime-version :subject:message-id:date:to; bh=tPYe5vLjaq0f6gPyw01XK4HfTAz2aDUZMt5kpQCKbPc=; b=NXjJo7+wwlSb4UC6kVAKXd2eh2XIIF7H31p3IRATqxvtXNBVfmLgd7TN+c0DOWiXx9 zLAPiXbOkwO517I6gAMdJG1uWjAU1qSC18Xv2SI39wfXsxw1OK05Ub66A4eoGJ7j9PuR mgltEpU99w/xfGbb6SEE6PezV1+l1lSD+II6nUBYVmRXS9uUUyPv95n8/uwrdklO9FmU WDQcdgA4c9rPWwBuI11NkhJ7pPDunb06tyMC4vRU0txVz4CbY9ap8RlFgPjbd8E3inw7 Scgy9FoBhsURnPSNbkcOkZunOcNzoDQ2Lp1LzVmjST6GnSUf2uvuloTbdmnycUh2kUgT V83g== X-Gm-Message-State: AElRT7GTFv9BslCgsx0BrufQnycDz6p9zPGMDdDfdKUbN412F/42Au2S WmK59AQF58zONx5xDUAQhHnZYxyW X-Google-Smtp-Source: AG47ELtzgeTDCiMaRIA5t8AV9dZ4wGUv5BgFre4L3Yqn1NRkCclFQjRcERBzQoqRSwMmBFlJws6nHA== X-Received: by 10.223.199.69 with SMTP id b5mr9165480wrh.212.1521445302763; Mon, 19 Mar 2018 00:41:42 -0700 (PDT) Received: from haruns-mbp.kfupm.edu.sa ([212.26.2.2]) by smtp.gmail.com with ESMTPSA id 4sm9918956wmz.31.2018.03.19.00.41.41 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Mon, 19 Mar 2018 00:41:42 -0700 (PDT) From: Harun Pirim Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Mime-Version: 1.0 (Mac OS X Mail 11.2 \(3445.5.20\)) Message-Id: <396897F2-D71B-4501-A223-3BCAE42DF9BA@gmail.com> Date: Mon, 19 Mar 2018 10:41:40 +0300 To: Help for igraph users X-Mailer: Apple Mail (2.3445.5.20) X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:400c:c0c::22c Subject: [igraph] glpk_not_available X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 19 Mar 2018 07:41:50 -0000 Dear All, I ran cluster_optimal() function and got the message: Warning in install.packages : package =E2=80=98GLPK=E2=80=99 is not available (for R version 3.4.4) Any quick fix suggested? thank you, harun =20= From MAILER-DAEMON Mon Mar 19 04:02:50 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1expko-0005Xp-Rt for mharc-igraph-help@gnu.org; Mon, 19 Mar 2018 04:02:50 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:41571) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1expkj-0005VJ-9f for igraph-help@nongnu.org; Mon, 19 Mar 2018 04:02:49 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1expkd-0003CO-TG for igraph-help@nongnu.org; Mon, 19 Mar 2018 04:02:43 -0400 Received: from ppsw-30.csi.cam.ac.uk ([131.111.8.130]:59978) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1expkd-0003Az-ME for igraph-help@nongnu.org; Mon, 19 Mar 2018 04:02:39 -0400 X-Cam-AntiVirus: no malware found X-Cam-ScannerInfo: http://help.uis.cam.ac.uk/email-scanner-virus Received: from mail.mrc-lmb.cam.ac.uk ([131.111.85.9]:40356 helo=mail.lmb.internal) by ppsw-30.csi.cam.ac.uk (ppsw.cam.ac.uk [131.111.8.136]:25) with esmtp id 1expkb-000IwK-eb (Exim 4.89_2) for igraph-help@nongnu.org (return-path ); Mon, 19 Mar 2018 08:02:37 +0000 Received: from [90.253.86.32] (helo=[192.168.1.2]) by mail.lmb.internal with esmtpsa (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256) (Exim 4.90_1) (envelope-from ) id 1expkb-0018lp-Fw for igraph-help@nongnu.org; Mon, 19 Mar 2018 08:02:37 +0000 From: Gregory Jefferis Content-Type: multipart/alternative; boundary=Apple-Mail-5133207B-8936-4083-BDFB-65C3EBA6F256 Content-Transfer-Encoding: 7bit Mime-Version: 1.0 (1.0) Date: Mon, 19 Mar 2018 08:02:37 +0000 Message-Id: <831CBD47-DFB6-4B1D-8A42-BCDA7A409AFB@mrc-lmb.cam.ac.uk> References: <396897F2-D71B-4501-A223-3BCAE42DF9BA@gmail.com> In-Reply-To: <396897F2-D71B-4501-A223-3BCAE42DF9BA@gmail.com> To: Help for igraph users X-Mailer: iPhone Mail (15C202) X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-Received-From: 131.111.8.130 Subject: Re: [igraph] glpk_not_available X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 19 Mar 2018 08:02:49 -0000 --Apple-Mail-5133207B-8936-4083-BDFB-65C3EBA6F256 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable The package is Rgplk not GLPK, so that=E2=80=99s odd. Are you trying to inst= all this manually? If so check the package name. As for installation, it depends on your platform. If you=E2=80=99re on a Mac= , there=E2=80=99s some kind of snafu on the cran mac build machine: https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64/Rglpk-00install= .html Install Rgplk from source if you can. On windows the binary may have been un= available during the R 3.4.3 to 3.4.4 transition. Best, Greg. > On 19 Mar 2018, at 07:41, Harun Pirim wrote: >=20 > Dear All, >=20 > I ran cluster_optimal() function and got the message: >=20 > Warning in install.packages : > package =E2=80=98GLPK=E2=80=99 is not available (for R version 3.4.4) >=20 > Any quick fix suggested? >=20 > thank you, >=20 > harun =20 > _______________________________________________ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help --Apple-Mail-5133207B-8936-4083-BDFB-65C3EBA6F256 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable The package is Rgplk not GLPK, so that=E2=80= =99s odd. Are you trying to install this manually? If so check the package n= ame.

As for installation, it depends on your platform. If= you=E2=80=99re on a Mac, there=E2=80=99s some kind of snafu on the cran mac= build machine:

Install Rgplk from source if you can. On windows the binary may h= ave been unavailable during the R 3.4.3 to 3.4.4 transition. Best,

Greg.

On 19 Mar 2018, at 07:41, Harun Pirim <= harunpirim@gmail.com> wrote:<= br>
Dear All,
=
I ran cluster_optimal() function and got the message:

Warning in install.packages :
&= nbsp;package =E2=80=98GLPK=E2=80=99 is not available (for R version 3.4.4)

Any quick fix suggested?

thank you,

harun  
_______________________________________________
i= graph-help mailing list
igraph-help@nongnu.org
https://lists.nongnu.org/mailman/list= info/igraph-help
= --Apple-Mail-5133207B-8936-4083-BDFB-65C3EBA6F256-- From MAILER-DAEMON Mon Mar 19 04:19:25 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1exq0r-0000Mv-FI for mharc-igraph-help@gnu.org; Mon, 19 Mar 2018 04:19:25 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:44175) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1exq0p-0000Mc-5A for igraph-help@nongnu.org; Mon, 19 Mar 2018 04:19:24 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1exq0k-0004wo-Sq for igraph-help@nongnu.org; Mon, 19 Mar 2018 04:19:23 -0400 Received: from mail-wm0-x232.google.com ([2a00:1450:400c:c09::232]:37583) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1exq0k-0004wR-IZ for igraph-help@nongnu.org; Mon, 19 Mar 2018 04:19:18 -0400 Received: by mail-wm0-x232.google.com with SMTP id 139so13839462wmn.2 for ; Mon, 19 Mar 2018 01:19:18 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:mime-version:subject:date:references:to:in-reply-to:message-id; bh=e1Cif0AAR3VXdSKqo6CXszvPVcCFo7tvx+6PwW2JSO8=; b=ejAIrpSWh1bAh9xdZngVBi377MbWMBcB1IXd36X9ilmDWqrQrkEjjqQhDZYAPHXIs3 FnK1Xj7Htk3nz5qYAokTr+V2UNhT6+5ktGHjIo72gFqIzDhxpFbAeOrsMlwkzp32voMv KqS9fgcfWZHRzSJw+rjNubLKaJ12Li7/fjZa4iTo4BrEXpd2OFChqHvvS+x2f3gR+vzE 3/uUge+JYUzUJC+TRQdHqOHL8vH3eV3roAPhbG39ORn8Etc/63DvLEkbJ8qJXtJRagTX vHwIGRSLprlPwV4PvjSjdu0EIvLNEs5UZmuOo8JhuZ/wUPtdHla+AdUnIckDWvv8mYcl DB3w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:mime-version:subject:date:references:to :in-reply-to:message-id; bh=e1Cif0AAR3VXdSKqo6CXszvPVcCFo7tvx+6PwW2JSO8=; b=lve0yUNtXv4Ejb7JUqNjwM4Ml7U+xKoN+CAmNeGFP7EIgMQcoR1QBs9AhInBBi1Fs9 dPr9wTBNUKjaJ1jMWDpQDys3rlZpsmPbWm0U8yUpi5uVL+NGPF5FUp27DN8fTJztnLfm LWs/D4FcdrBGp40cHMqWWGZPVwTq3opei1RVIG+RZQ+zjU5g67XA9//zJeT3GqwWSPBJ Z33yVghqY/aa5qWo9Ahf315StNJUyo9k1UMlinXO2nR4UIDFQ6EaWfswQDBc2jvMV6So TdDEzIuLtWT/aU915APDQ0XS7xnSuRQjT6yszhpw7r7T1Fd6cqOrRaM6UM3FJarV3Aq9 UfBw== X-Gm-Message-State: AElRT7GAj7X3sGRUDl1nrVVbRVi2dj3aMWIwV/37HcF10WoorqryIh5S Py3ozXlJbz7VoKkIdPs5gzNZjQ8d X-Google-Smtp-Source: AG47ELsLZ4+wyMWWiuOsGpAecPeumu6qwzuZPnruqkIiBaiKjsBEONpEqra/ghiEVGq+JqIVg9Z2xw== X-Received: by 10.28.64.193 with SMTP id n184mr7143834wma.4.1521447557207; Mon, 19 Mar 2018 01:19:17 -0700 (PDT) Received: from haruns-mbp.kfupm.edu.sa ([212.26.2.2]) by smtp.gmail.com with ESMTPSA id m9sm12664016wrg.79.2018.03.19.01.19.16 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Mon, 19 Mar 2018 01:19:16 -0700 (PDT) From: Harun Pirim Content-Type: multipart/alternative; boundary="Apple-Mail=_1844B9BD-DE14-47EE-ABF9-CBF33C3F4E9D" Mime-Version: 1.0 (Mac OS X Mail 11.2 \(3445.5.20\)) Date: Mon, 19 Mar 2018 11:19:15 +0300 References: <396897F2-D71B-4501-A223-3BCAE42DF9BA@gmail.com> <831CBD47-DFB6-4B1D-8A42-BCDA7A409AFB@mrc-lmb.cam.ac.uk> To: Help for igraph users In-Reply-To: <831CBD47-DFB6-4B1D-8A42-BCDA7A409AFB@mrc-lmb.cam.ac.uk> Message-Id: X-Mailer: Apple Mail (2.3445.5.20) X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:400c:c09::232 Subject: Re: [igraph] glpk_not_available X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 19 Mar 2018 08:19:24 -0000 --Apple-Mail=_1844B9BD-DE14-47EE-ABF9-CBF33C3F4E9D Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Thank you Gregory for the reply. I didn=E2=80=99t install manually. The function used to work with an = older version of R. It seems an issue with transition to R 3.4.4. I tried installing Rgplk using install.packages() which gave the error: * installing *source* package =E2=80=98Rglpk=E2=80=99 ... ** package =E2=80=98Rglpk=E2=80=99 successfully unpacked and MD5 sums = checked ** libs /bin/sh: line 0: cd: GLPK: No such file or directory make: *** [GLPK.ts] Error 1 ERROR: compilation failed for package =E2=80=98Rglpk=E2=80=99 * removing = =E2=80=98/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rg= lpk=E2=80=99 Warning in install.packages : installation of package =E2=80=98Rglpk=E2=80=99 had non-zero exit = status I may try installing from source, however cluster_optimal() function = will not be connected to the Rgplk package right away I guess. Regards, Harun > On 19 Mar 2018, at 11:02, Gregory Jefferis = wrote: >=20 > The package is Rgplk not GLPK, so that=E2=80=99s odd. Are you trying = to install this manually? If so check the package name. >=20 > As for installation, it depends on your platform. If you=E2=80=99re on = a Mac, there=E2=80=99s some kind of snafu on the cran mac build machine: >=20 > = https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64/Rglpk-00insta= ll.html = >=20 > Install Rgplk from source if you can. On windows the binary may have = been unavailable during the R 3.4.3 to 3.4.4 transition. Best, >=20 > Greg. >=20 > On 19 Mar 2018, at 07:41, Harun Pirim > wrote: >=20 >> Dear All, >>=20 >> I ran cluster_optimal() function and got the message: >>=20 >> Warning in install.packages : >> package =E2=80=98GLPK=E2=80=99 is not available (for R version = 3.4.4) >>=20 >> Any quick fix suggested? >>=20 >> thank you, >>=20 >> harun =20 >> _______________________________________________ >> igraph-help mailing list >> igraph-help@nongnu.org >> https://lists.nongnu.org/mailman/listinfo/igraph-help = > _______________________________________________ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help --Apple-Mail=_1844B9BD-DE14-47EE-ABF9-CBF33C3F4E9D Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Thank= you Gregory for the reply.

I didn=E2=80=99t install manually. The function used to work = with an older version of R. It seems an issue with transition to R = 3.4.4.

I tried = installing Rgplk using install.packages() which gave the = error:

* installing *source* package =E2=80=98Rglpk=E2=80=99 = ...
** package =E2=80=98Rglpk=E2=80=99 successfully = unpacked and MD5 sums checked
** libs
/bin/sh: line 0: cd: GLPK: No such file or = directory
make: *** [GLPK.ts] Error 1
ERROR: compilation failed for package =E2=80=98Rglpk=E2=80=99
* removing = =E2=80=98/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rg= lpk=E2=80=99
Warning in install.packages = :
  installation of package =E2=80=98Rglpk=E2=80= =99 had non-zero exit status


I = may try installing from source, however cluster_optimal() function will = not be connected to the Rgplk package right away I guess.

Regards,

Harun

On 19 = Mar 2018, at 11:02, Gregory Jefferis <jefferis@mrc-lmb.cam.ac.uk> wrote:

The package is Rgplk not GLPK, = so that=E2=80=99s odd. Are you trying to install this manually? If so = check the package name.

As for installation, it depends on your platform. If you=E2=80=99= re on a Mac, there=E2=80=99s some kind of snafu on the cran mac build = machine:


Install Rgplk from source if you can. On = windows the binary may have been unavailable during the R 3.4.3 to 3.4.4 = transition. Best,

Greg.

On 19 Mar = 2018, at 07:41, Harun Pirim <harunpirim@gmail.com> wrote:

Dear All,

I ran = cluster_optimal() function and got the message:

Warning in = install.packages :
 package = =E2=80=98GLPK=E2=80=99 is not available (for R version 3.4.4)

Any = quick fix suggested?

thank you,

harun  
_______________________________________________
igraph-help mailing list
igraph-help@nongnu.org
https://lists.nongnu.org/mailman/listinfo/igraph-help

__________________________= _____________________
igraph-help mailing list
igraph-help@nongnu.org
https://lists.nongnu.org/mailman/listinfo/igraph-help

= --Apple-Mail=_1844B9BD-DE14-47EE-ABF9-CBF33C3F4E9D-- From MAILER-DAEMON Mon Mar 19 04:29:45 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1exqAr-000213-Sa for mharc-igraph-help@gnu.org; Mon, 19 Mar 2018 04:29:45 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:45867) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1exqAo-00020I-P1 for igraph-help@nongnu.org; Mon, 19 Mar 2018 04:29:43 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1exqAn-0004Hc-LP for igraph-help@nongnu.org; Mon, 19 Mar 2018 04:29:42 -0400 Received: from mail-wm0-x233.google.com ([2a00:1450:400c:c09::233]:54916) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1exqAn-0004GN-EZ for igraph-help@nongnu.org; Mon, 19 Mar 2018 04:29:41 -0400 Received: by mail-wm0-x233.google.com with SMTP id h76so13472448wme.4 for ; Mon, 19 Mar 2018 01:29:41 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:in-reply-to:references:from:date:message-id:subject:to; bh=2lWNPS7n+uYQy92I0GliVCsCsk29KetMSeZytMLX6U0=; b=suuf5WykmbGs9XTCc1WXMgv0J12hLXTcPctflRxlbVe7a6qY3i8fQ1eoziqaKWF8Sn yehrBOc9LikGsLl1tZ1kLyOahfSSmvQc5TVXwc+xBeG8FvfwWySbzEuKiwbCpXNvvD6I pYriO4oHGUdgFP3B4egB0/R8ZdmmVgMqVQnACsQ/ikGOuXKdfA7rStj+/xalDJfMhwKJ l4vQrUULOiUHsiVWXzCh/glHI12rU88iA5t2j3VBTwNtkfHG9d6hZR7fvcGrqOVs0VA/ 6337gxTkjFVrS4kHH+dYyl9LYK9C16WC2TYPprqb2ySiXAlMGARurvlpCfKnJuqd4GpA 5vHA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:in-reply-to:references:from:date :message-id:subject:to; bh=2lWNPS7n+uYQy92I0GliVCsCsk29KetMSeZytMLX6U0=; b=U8qOJXnd9UPZ3Yh4S3lSW1kMFgmra4xBhVhUPeYsJJjWXhmLDyN/MX2re4nk+JCiYh FhHe7w+3bFRyijXhtL//q4V5NHVU4DfWaOCRZpgyWgJpil/P2djsIQEO7LfchzFMLmBy s6tFv/GGVAr6W9er3PLqZ/Dn8RjkVwFXCTgHNpgRzc2n+NVww/LiRW3pfL6ApKLIz41x rUj4y3eajW6k1Sxxp6i4r2isFrJLpJeGb5jDJ9Xba3LmQWvO7BzqK2mDG+yT1UPNu/1u HVgn6bGOnI15kPBBNyr42gUUWcCHYydI0rE3LbAPoYHaw4qLSsxJ4Pa4XDv5k4OhTvFf vnLA== X-Gm-Message-State: AElRT7FaNywpfGdUMMptn0xioH1CNUoiqTHrTzielaXrK6t2J4IPcY1i EMk3DQcq5UHSZo207qspFo++O0gASBp8mao61cB7bjXi X-Google-Smtp-Source: AG47ELvSfFAh/czCmj22v4AIc9VVV8iu8YtLCs1OAuIX5Kiaz61Vp0MeMIjhYJUEOAvJR86cCag3xtqObmQ+9jP7JUk= X-Received: by 10.28.231.24 with SMTP id e24mr790843wmh.123.1521448179747; Mon, 19 Mar 2018 01:29:39 -0700 (PDT) MIME-Version: 1.0 Received: by 10.223.149.3 with HTTP; Mon, 19 Mar 2018 01:29:19 -0700 (PDT) In-Reply-To: <396897F2-D71B-4501-A223-3BCAE42DF9BA@gmail.com> References: <396897F2-D71B-4501-A223-3BCAE42DF9BA@gmail.com> From: =?UTF-8?Q?Szabolcs_Horv=C3=A1t?= Date: Mon, 19 Mar 2018 09:29:19 +0100 Message-ID: To: Help for igraph users Content-Type: multipart/alternative; boundary="089e082f9ec44c50d10567bfc297" X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:400c:c09::233 Subject: Re: [igraph] glpk_not_available X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 19 Mar 2018 08:29:43 -0000 --089e082f9ec44c50d10567bfc297 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable There is a note for igraph 1.2.1: https://cran.r-project.org/web/packages/igraph/news.html "The GLPK library is optional, if it is not available, then the cluster_optimal() function does not work. Unfortunately we cannot bundle the GLPK library into igraph on CRAN any more, because CRAN maintainers forbid the pragmas in its source code." Gregory: I do not think this refers to Rglpk. The underlying igraph function is implemented in C (not R!), and relies on an (older) bundled version of the GLPK C library. The release notes seem to say that this can no longer be included in build hosted on CRAN. On 19 March 2018 at 08:41, Harun Pirim wrote: > Dear All, > > I ran cluster_optimal() function and got the message: > > Warning in install.packages : > package =E2=80=98GLPK=E2=80=99 is not available (for R version 3.4.4) > > Any quick fix suggested? > > thank you, > > harun > _______________________________________________ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help > --089e082f9ec44c50d10567bfc297 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
There is a note for igraph 1.2.1:


"The GL= PK library is optional, if it is not available, then the cluster_optimal() = function does not work. Unfortunately we cannot bundle the GLPK library int= o igraph on CRAN any more, because CRAN maintainers forbid the pragmas in i= ts source code."

Gregory: I do not think this refer= s to Rglpk. The underlying igraph function is implemented in C (not R!), an= d relies on an (older) bundled version of the GLPK C library. The release n= otes seem to say that this can no longer be included in build hosted on CRA= N.

On = 19 March 2018 at 08:41, Harun Pirim <harunpirim@gmail.com> wrote:
Dear All,

I ran cluster_optimal() function and got the message:

Warning in install.packages :
=C2=A0 package =E2=80=98GLPK=E2=80=99 is not available (for R version 3.4.4= )

Any quick fix suggested?

thank you,

harun
_______________________________________________
igraph-help mailing list
igraph-help@nongnu.org
https://lists.nongnu.org/mailman/listinfo/= igraph-help

--089e082f9ec44c50d10567bfc297-- From MAILER-DAEMON Mon Mar 19 05:05:57 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1exqjt-0002Xo-8G for mharc-igraph-help@gnu.org; Mon, 19 Mar 2018 05:05:57 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:53279) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1exqjq-0002Vc-V7 for igraph-help@nongnu.org; Mon, 19 Mar 2018 05:05:56 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1exqjp-0008SS-6r for igraph-help@nongnu.org; Mon, 19 Mar 2018 05:05:54 -0400 Received: from mail-lf0-x22d.google.com ([2a00:1450:4010:c07::22d]:39198) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1exqjo-0008SB-VX for igraph-help@nongnu.org; Mon, 19 Mar 2018 05:05:53 -0400 Received: by mail-lf0-x22d.google.com with SMTP id p142-v6so1530984lfd.6 for ; Mon, 19 Mar 2018 02:05:52 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:in-reply-to:references:from:date:message-id:subject:to :content-transfer-encoding; bh=HlWm3oNZi864oUpUa9HNXvIJSMSFwd59XbeEKiQ+huI=; b=Fjdk/BMNQtWCToV1/XKVlDqhRoIaCxHJBE2yF66sZGCYuEr4lKboun3UF7dPWuSL1m OLJC0HMSKXG3X4rlLNrzbJr152VwIth9VPb7pCEuHM91I1E9UT/NY88uQEgVDpeXeDXZ 5tsOOgV1+TGyZNvLbN01rdBjnqOt9ToG992lubmby8MMh2ntcQxafo07qs6SXOgOi2cc 7li9rrpNfsxfc5IYFCP+qi+WQTa0omhR1kENkBAK2OMpCZX6awfuDL6kJgNHU+z2ZlMU xj36CaM4Dpk8b37faMXkyss802Gyj3DDo+HJOgKEtO545Qm03zebiGixPpyS0zbKDwCR MbYQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:in-reply-to:references:from:date :message-id:subject:to:content-transfer-encoding; bh=HlWm3oNZi864oUpUa9HNXvIJSMSFwd59XbeEKiQ+huI=; b=qW+GUWhZkbsZrPGfo59b1yWtOIOzHTPc0stERM3TNvkCAs/jcY6XyDuMikWcOEqHs3 5eK87m9MWXo4KiknBWDxfbDt4ko+bkimOQGK5TgRSwB2Ry8+kzcSPDx3BPhbG8P8YGD9 /gFh9qAXW6aX5FG5Ms1iJfO3DFt2pYRgjYwm/SYBLJfD7jntbgqdjjpcGJr188mmYX3U ZRNX7wCO9xNgERAN5IQsU7pzOG+2H2H++T6JVfXYhHb4QXM/hqmU5b26MJnwxtaAnKnS zwkue06o0RuzgYKK0nJ2R9rWj9PxO3mgVMDZ2/6Zjn7VC1sPhGiDlBo+e2QxJbnKckXQ SSEg== X-Gm-Message-State: AElRT7HWPQxPWspvRbgPcsfTAphhtz74wsuL0GVljN/jtjOhp1OharWe FuHJ5d6vDo5F5SiyagwsMiNcCUMTSBSBI5XB4tk= X-Google-Smtp-Source: AG47ELux1jT/HxWQpYeyDye8n9ya8Nu/ycouIL3eaBw4181PgTQwrQzSZ2q7mFWf6znp8Z82L/PZg32GhFx8HAYXY/k= X-Received: by 10.46.156.204 with SMTP id g12mr7747143ljj.95.1521450350977; Mon, 19 Mar 2018 02:05:50 -0700 (PDT) MIME-Version: 1.0 Received: by 2002:a19:d9d3:0:0:0:0:0 with HTTP; Mon, 19 Mar 2018 02:05:50 -0700 (PDT) In-Reply-To: <396897F2-D71B-4501-A223-3BCAE42DF9BA@gmail.com> References: <396897F2-D71B-4501-A223-3BCAE42DF9BA@gmail.com> From: =?UTF-8?B?R8OhYm9yIENzw6FyZGk=?= Date: Mon, 19 Mar 2018 09:05:50 +0000 Message-ID: To: Help for igraph users Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:4010:c07::22d Subject: Re: [igraph] glpk_not_available X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 19 Mar 2018 09:05:56 -0000 I suspect that you are on macOS. CRAN macOS machines do not have the GLPK library, so igraph cannot link to it. igraph used to have a built-in GLPK library, but that is not allowed any more on CRAN. For now you need to compile the package for yourself I am afraid. This will cause a lot of problems in the future, so I am investigating other solutions, e.g. hosting the package in another repository. G. On Mon, Mar 19, 2018 at 7:41 AM, Harun Pirim wrote: > Dear All, > > I ran cluster_optimal() function and got the message: > > Warning in install.packages : > package =E2=80=98GLPK=E2=80=99 is not available (for R version 3.4.4) > > Any quick fix suggested? > > thank you, > > harun > _______________________________________________ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help From MAILER-DAEMON Mon Mar 19 07:44:11 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1extD1-0002z4-Hw for mharc-igraph-help@gnu.org; Mon, 19 Mar 2018 07:44:11 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:32914) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ext6d-0001Jf-EN for igraph-help@nongnu.org; Mon, 19 Mar 2018 07:37:36 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ext6a-0002KO-7h for igraph-help@nongnu.org; Mon, 19 Mar 2018 07:37:35 -0400 Received: from mail-wr0-x230.google.com ([2a00:1450:400c:c0c::230]:40356) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1ext6a-0002Jd-1m for igraph-help@nongnu.org; Mon, 19 Mar 2018 07:37:32 -0400 Received: by mail-wr0-x230.google.com with SMTP id z8so8512292wrh.7 for ; Mon, 19 Mar 2018 04:37:31 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:content-transfer-encoding:mime-version:subject:message-id:date :to; bh=UfZZzHM4N4JbFIioBd0gTgmF3c7mCorbmomOzg6c4lU=; b=mMSl4Rlw5662DeRxhxNtKRlMBD+y5B216QyXylLpRXIXuKhX6sauqdLaY0lLFZdKOQ VWbJktxOtBSSVSDiV2XzxjlhdMiejncQk82LjdwhD2kax50+fvYwtUR6JzNIKnhup6Fl xnlRAeOaB1XrAM2KsA9ducq6Cjc2RB4eax/LDJFM/N4s5P3e7a/pyc0Qbcku0mEbjnxR AgxS/yEF9F2/hzeRk4jQRf5Ud5UBRNi8EeL7GrLOLqYU3nVMtGfO63/MtwSKkm217Cca IyBuBVlgA3fYoZrKk6i61kAyiiwkvHFRoORgdQ819HMwj0lUz3TGrb3RertH7uCNv5wO CskQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:content-transfer-encoding:mime-version :subject:message-id:date:to; bh=UfZZzHM4N4JbFIioBd0gTgmF3c7mCorbmomOzg6c4lU=; b=G6Xz7Kk99UPgrBnd6DKj7Q/Q29XGjGU7qI10+1zf6V3xa0TGl23OWJKL0/Y3a8iHFD bqtz5OUgJaES6ha5bTevpumX0piCQR6TIllVhNAZIgvG9eW1sICkVGuTS2dAJaqdtYFm aoRovMTKq/ar71qS+TyWAQy0OAaRA94OR/cN7LtdrUNBpPt8qeLg/8RdoHlsYPv3bqwG Pbx5DskcX9x8SYpuf6n7fMkSgzXCJjGVP4fRvxfVBbVnDIHn5+ChTZbBUN15zsJkrblZ FOk0sp+jh67YadOa9YjM9LznM6vVELrYNfmhtSPqVM8bwFjtWAye8E5w9YZ6xxi63rVM MStA== X-Gm-Message-State: AElRT7HfQYTm/P8scbh1InpTDDRB0viNHOyy87YrP29G5iVF6NTDSMEs 0Rv8tJUpEap538F7C9iJurCZklx9 X-Google-Smtp-Source: AG47ELu5iljYrTfSvd40ixXptc8kPTyhOxG6Ix52w60isIQ/aMO6aVCyZxaPPxU8E62bUz8lRcXSwQ== X-Received: by 10.223.172.236 with SMTP id o99mr4116539wrc.36.1521459450353; Mon, 19 Mar 2018 04:37:30 -0700 (PDT) Received: from [192.168.1.8] ([151.29.252.194]) by smtp.gmail.com with ESMTPSA id x18sm181316wmc.2.2018.03.19.04.37.29 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Mon, 19 Mar 2018 04:37:29 -0700 (PDT) From: Simone Gabbriellini Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable Mime-Version: 1.0 (Mac OS X Mail 11.2 \(3445.5.20\)) Message-Id: <26907FE6-E5B2-459B-A56E-8D16E82A7E1E@gmail.com> Date: Mon, 19 Mar 2018 12:37:28 +0100 To: Help for igraph users X-Mailer: Apple Mail (2.3445.5.20) X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:400c:c0c::230 X-Mailman-Approved-At: Mon, 19 Mar 2018 07:44:09 -0400 Subject: [igraph] Watts_Strogatz() generator with equal degree for each node X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 19 Mar 2018 11:37:36 -0000 Hi list, I am using K_Regular() to generate random graph with fixed degree, and I = am wondering if there is anything similar to generate Small World = networks where each node has the same degree. Right now I am managing the creation of a Lattice and then I am rewiring = the links on my own... just wanted to be sure I am not missing anything = in the docs. Best, Simone From MAILER-DAEMON Thu Mar 22 15:56:54 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1ez6KU-0004Uy-An for mharc-igraph-help@gnu.org; Thu, 22 Mar 2018 15:56:54 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:52870) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ez6KT-0004Un-Cx for igraph-help@nongnu.org; Thu, 22 Mar 2018 15:56:54 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ez6KQ-0000aA-AB for igraph-help@nongnu.org; Thu, 22 Mar 2018 15:56:53 -0400 Received: from smtp5-g21.free.fr ([212.27.42.5]:48522) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1ez6KQ-0000ZN-3l for igraph-help@nongnu.org; Thu, 22 Mar 2018 15:56:50 -0400 Received: from [IPv6:2a01:cb00:17a:a000:cdc2:6f3c:de30:b8f4] (unknown [IPv6:2a01:cb00:17a:a000:cdc2:6f3c:de30:b8f4]) (Authenticated sender: beugnet.vincent@free.fr) by smtp5-g21.free.fr (Postfix) with ESMTPSA id 00BCC5FF67 for ; Thu, 22 Mar 2018 20:56:46 +0100 (CET) Date: Thu, 22 Mar 2018 20:56:43 +0100 Message-ID: X-Android-Message-ID: From: Vincent Beugnet To: igraph-help@nongnu.org Importance: Normal X-Priority: 3 X-MSMail-Priority: Normal MIME-Version: 1.0 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: base64 X-detected-operating-system: by eggs.gnu.org: Windows NT kernel [generic] [fuzzy] X-Received-From: 212.27.42.5 Subject: [igraph] Sorting vertices by degree with igraph C library X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 22 Mar 2018 19:56:54 -0000 PGRpdiBkaXI9J2F1dG8nPkhlbGxvLDxkaXYgZGlyPSJhdXRvIj5JJ2QgbGlrZSB0byBzb3J0IGFs bCB2ZXJ0aWNlcyBmcm9tIGEgZ3JhcGggKHVuZGlyZWN0ZWQpIGJ5IGRlY3JlYXNpbmcgZGVncmVl IGFuZCBwcmludCB0aGVpciBpZHMgd2l0aCB0aGlzIG9yZGVyLiBCdXQgYXMgdGhlIHZlY3RvciBp biBpZ3JhcGhfZGVncmVlIGlzIG5vdCByZWxhdGVkIHdpdGggdGhlIGdyYXBoLCBJIGRvbid0IGtu b3cgaG93IHRvIGdldCB0aGUgb3JkZXJlZCBpZHMuIENhbiBzb21lb25lIGhlbHAgbWUgPzwvZGl2 PjxkaXYgZGlyPSJhdXRvIj48YnI+PC9kaXY+PGRpdiBkaXI9ImF1dG8iPlRoYW5rczwvZGl2Pjxk aXYgZGlyPSJhdXRvIj48YnI+PC9kaXY+PGRpdiBkaXI9ImF1dG8iPlAuUzogSSdtIHVzaW5nIHRo ZSBDIGxpYnJhcnk8L2Rpdj48L2Rpdj4= From MAILER-DAEMON Thu Mar 22 17:36:42 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1ez7t4-0005hR-MP for mharc-igraph-help@gnu.org; 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boundary="001a114b3c4436b25c0568071af2" X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:400c:c0c::230 Subject: Re: [igraph] Sorting vertices by degree with igraph C library X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 22 Mar 2018 21:36:41 -0000 --001a114b3c4436b25c0568071af2 Content-Type: text/plain; charset="UTF-8" Hello Vincent, Normally you would have to program this yourself. E.g. you can generate a vector of increasing integers (vertex indices), write a custom comparison function that compares v1 and v2 through degrees[v1] and degrees[v2], then use this to sort the indices (e.g. through the qsort() C standard library function, or much more easily with std::sort() in C++) Luckily, this is already done in igraph, though not documented. The function is igraph_vector_qsort_ind() You'll find its description in the vector.pmt file. On 22 March 2018 at 20:56, Vincent Beugnet wrote: > Hello, > I'd like to sort all vertices from a graph (undirected) by decreasing > degree and print their ids with this order. But as the vector in > igraph_degree is not related with the graph, > The degree vector is related with the graph in that the degree of the nth vertex is the nth entry in the vector. > I don't know how to get the ordered ids. Can someone help me ? > > Thanks > > P.S: I'm using the C library > > _______________________________________________ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help > > --001a114b3c4436b25c0568071af2 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Vincent,

Normally you would have = to program this yourself. E.g. you can generate a vector of increasing inte= gers (vertex indices), write a custom comparison function that compares v1 = and v2 through degrees[v1] and degrees[v2], then use this to sort the indic= es (e.g. through the qsort() C standard library function, or much more easi= ly with std::sort() in C++)

Luckily, this is already do= ne in igraph, though not documented. The function is=C2=A0 igraph_vector_qs= ort_ind()=C2=A0 You'll find its description in the vector.pmt file.
On 22 March 2018 at 2= 0:56, Vincent Beugnet <beugnet.vincent@free.fr> wrote:=
Hello,
I'd like to sort all vertices from a graph (undirected) by decreasing= degree and print their ids with this order. But as the vector in igraph_de= gree is not related with the graph,

=
The degree vector is related with the graph in that the degree of the = nth vertex is the nth entry in the vector.
=C2=A0
I don't know = how to get the ordered ids. Can someone help me ?
Thanks

P.S: I'm using the C library

_________________= ______________________________
igraph-help mailing list
igraph-help@non= gnu.org
https://lists.nongnu.org/mailman/listinfo/= igraph-help


--001a114b3c4436b25c0568071af2-- From MAILER-DAEMON Sat Mar 24 10:53:18 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1ezkXm-0002rM-5M for mharc-igraph-help@gnu.org; Sat, 24 Mar 2018 10:53:18 -0400 Received: from eggs.gnu.org ([208.118.235.92]:47613) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ezkWh-0001HS-Dd for igraph-help@nongnu.org; Sat, 24 Mar 2018 10:53:17 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ezkT9-0001o7-GU for igraph-help@nongnu.org; Sat, 24 Mar 2018 10:49:37 -0400 Received: from smtp3-g21.free.fr ([212.27.42.3]:46450) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1ezkT9-0001mj-8v for igraph-help@nongnu.org; Sat, 24 Mar 2018 10:48:31 -0400 Received: from spooler2-g27.priv.proxad.net (unknown [172.20.243.240]) by smtp3-g21.free.fr (Postfix) with ESMTP id 3FEF013F86E for ; Sat, 24 Mar 2018 15:48:29 +0100 (CET) Date: Sat, 24 Mar 2018 15:48:29 +0100 (CET) From: Vincent Beugnet Reply-To: Vincent Beugnet To: Help for igraph users Message-ID: <909738473.56502494.1521902909111.JavaMail.root@spooler2-g27.priv.proxad.net> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_56502493_1823834817.1521902909110" X-Originating-IP: [88.186.168.225] X-Mailer: Zimbra 7.2.0-GA2598 (ZimbraWebClient - FF3.0 (Win)/7.2.0-GA2598) X-Authenticated-User: beugnet.vincent@free.fr X-detected-operating-system: by eggs.gnu.org: Windows NT kernel [generic] [fuzzy] X-Received-From: 212.27.42.3 Subject: Re: [igraph] Sorting vertices by degree with igraph C library X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 24 Mar 2018 14:53:17 -0000 ------=_Part_56502493_1823834817.1521902909110 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit Thank you very much ! Last question: is there a stable sort already implemented in igraph ? ------=_Part_56502493_1823834817.1521902909110 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 7bit
Thank you very much !

Last question: is there a stable sort already implemented in igraph ?
------=_Part_56502493_1823834817.1521902909110-- From MAILER-DAEMON Sat Mar 24 12:56:21 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1ezmSr-00032Y-G7 for mharc-igraph-help@gnu.org; Sat, 24 Mar 2018 12:56:21 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:39331) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ezmPO-0001uu-06 for igraph-help@nongnu.org; Sat, 24 Mar 2018 12:56:20 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ezmOI-000597-BF for igraph-help@nongnu.org; Sat, 24 Mar 2018 12:52:44 -0400 Received: from mail-wm0-x234.google.com ([2a00:1450:400c:c09::234]:36535) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1ezlzw-0005x0-RU for igraph-help@nongnu.org; Sat, 24 Mar 2018 12:26:29 -0400 Received: by mail-wm0-x234.google.com with SMTP id x82so8439945wmg.1 for ; Sat, 24 Mar 2018 09:26:28 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:in-reply-to:references:from:date:message-id:subject:to; bh=6cFiF67Y3szMakjuGYx7sO9QH7nO4sv2GQo3ou2yWvk=; b=o3uCBAl9tXc0QH0WwC5dquMSsaVXz2DHNm0FTD8Mm1DchILxSQbTbAla6TcZUFVbrY VWivYko7I49/RsSESnI91TP9oUce19GiYC0QHeIVL1ybjI7srpe+nABMzGSTUlQdlKT8 N/GTSiAq8Fdz2Geb6m7BZ8UdESs/Fd+d+1rIoxOs+WMor6ENwIJMGwKWzHloF4EMMEAB QjrweRMX2FaHtGtAZIQYhA3r1ykA1HB0Nn7Z8sV40/Z7f+pAMTh1cjapZtOKo05+TevY RvhUvrqfcu6f72CFQwzVm/PLZUDgK0EM3pgTqbzNT2ErQJ5i5kFB7R48UfsDYrZDK8Uk WrCg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:in-reply-to:references:from:date :message-id:subject:to; bh=6cFiF67Y3szMakjuGYx7sO9QH7nO4sv2GQo3ou2yWvk=; b=lp4UD03KpEkv0Zf1JoWDQxs0NmxaKpEmtuX/gud+puhz+rJDSXHkHCaoqdGq2yevPV FsWUNQEJTbYfb2rYMSbC/UAwGbm39fWNGIl1ogQTKPQDX6YxAnKGFM3r5Hm44lKCve8H TnWOIDinVlRCajxh+oZQaGVmIBtVD5ekmsBIgVHHC5W+gZeNcBpAi0ac62GF6yM10Cov i0GRiqeVftEvPT5kW0yznVunMeuztg4uT30OTw63TWL/3gBT9+exTRv9CkHedwduRbAp 6avXF89l2LrRpfPOSHw5eorkoIvoL8MsslwptjcLb0BRoEoC1iB1BPDzxo4mm752JMrx 0S+g== X-Gm-Message-State: AElRT7Hj2qUcIWI8+CwRMD9/LOXXPPyq7tJ815pj9rbilw7iPCGKHA1/ kTVpSk0NbWRFWccdT0ks7le3d8qYt7/9EBBBFo4= X-Google-Smtp-Source: AG47ELuOAYWgFBvx0es8Q6jrUMo6WhtLKNsiXCnG/MljYzZH1JzD+/zPUwBFgE0lDO/ULcmZD9IWOHPF5cXOJvTEwH0= X-Received: by 10.28.179.194 with SMTP id c185mr10714278wmf.89.1521908787805; Sat, 24 Mar 2018 09:26:27 -0700 (PDT) MIME-Version: 1.0 Received: by 10.223.149.3 with HTTP; Sat, 24 Mar 2018 09:26:07 -0700 (PDT) In-Reply-To: References: <909738473.56502494.1521902909111.JavaMail.root@spooler2-g27.priv.proxad.net> From: =?UTF-8?Q?Szabolcs_Horv=C3=A1t?= Date: Sat, 24 Mar 2018 17:26:07 +0100 Message-ID: To: Vincent Beugnet , Help for igraph users Content-Type: multipart/alternative; boundary="001a1145395ead83c705682b0019" X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:400c:c09::234 Subject: Re: [igraph] Sorting vertices by degree with igraph C library X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 24 Mar 2018 16:56:20 -0000 --001a1145395ead83c705682b0019 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable To give a concrete example, you could sort an igraph vector 'vec' using std::stable_sort(vec.stor_begin, vec.stor_end); To stick to the documented API (might be a good idea), you can use std::stable_sort(VECTOR(vec), VECTOR(vec) + igraph_vector_size(&vec)); http://en.cppreference.com/w/cpp/algorithm/stable_sort You don't need to use any other C++ features in your program if you don't like C++. You can keep it as C. Compiling as C++ will only impose minor restrictions. On 24 March 2018 at 17:20, Szabolcs Horv=C3=A1t wrote: > I do not know. I believe that the documented ones in igraph are not > stable. > > Personally, I would just use std::stable_sort() from the C++ standard > library. Is there any reason why you don't want to use that, and want > something from igraph instead? > > On 24 March 2018 at 15:48, Vincent Beugnet > wrote: > >> Thank you very much ! >> >> Last question: is there a stable sort already implemented in igraph ? >> >> _______________________________________________ >> igraph-help mailing list >> igraph-help@nongnu.org >> https://lists.nongnu.org/mailman/listinfo/igraph-help >> >> > --001a1145395ead83c705682b0019 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
To give a concrete example, you could sort an igraph vecto= r 'vec' using

std::stable_sort(vec.stor_begin, v= ec.stor_end);

To stick to the documented API (migh= t be a good idea), you can use

std::stable_sort(VE= CTOR(vec), VECTOR(vec) + igraph_vector_size(&vec));


=
You don't need to use any other C++ features in your program= if you don't like C++. You can keep it as C.=C2=A0 Compiling as C++ wi= ll only impose minor restrictions.
On 24 March 2018 at 17:20, Szabolcs Horv=C3=A1= t <szhorvat@gmail.com> wrote:
I do not know.=C2=A0 I believe that the documented on= es in igraph are not stable.

Personally, I would just us= e std::stable_sort() from the C++ standard library. Is there any reason why= you don't want to use that, and want something from igraph instead?

On 24 March 2018 at 15:48, Vincent Beugnet <<= a href=3D"mailto:beugnet.vincent@free.fr" target=3D"_blank">beugnet.vincent= @free.fr> wrote:
Thank you very much !

Last question: is there a stable= sort already implemented in igraph ?

_______________________________________________
igraph-help mailing list
igraph-help@non= gnu.org
https://lists.nongnu.org/mailman/listinfo/= igraph-help



--001a1145395ead83c705682b0019-- From MAILER-DAEMON Sat Mar 24 14:09:19 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1eznbT-0002Wu-J9 for mharc-igraph-help@gnu.org; Sat, 24 Mar 2018 14:09:19 -0400 Received: from eggs.gnu.org ([208.118.235.92]:33834) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1eznXd-0001C6-JB for igraph-help@nongnu.org; Sat, 24 Mar 2018 14:09:18 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1eznWZ-0007Nb-JE for igraph-help@nongnu.org; Sat, 24 Mar 2018 14:05:21 -0400 Received: from mail-wr0-x229.google.com ([2a00:1450:400c:c0c::229]:36638) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1ezluI-0002ot-OO for igraph-help@nongnu.org; Sat, 24 Mar 2018 12:20:38 -0400 Received: by mail-wr0-x229.google.com with SMTP id d10so14906504wrf.3 for ; Sat, 24 Mar 2018 09:20:38 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:in-reply-to:references:from:date:message-id:subject:to; bh=tNbSiqbkj+mOMRYFhSz4GxpD0oiPOHKhPfWkFMW9W70=; b=Vw48el9ZxGl2q4gLym+Ha924RUitqUdONvP4R8lokOGjAFzMmhCC4WrzxM0Djbs4JC zD5a7XljXN3XQgrfQbKcoWhQaq5ea4lN+2FPLFAsK9lZ3v/Iirm2DA51fsrvI+3j0f+s Bpv/y1DPUZn1qp7dUVijbDT6huV0nUCjPQoV7h5ld0niYjm0dvwzoHxr4z7Hojj+5GrU BXx7FQohmU6Y+6QqOCXtAfa/ffjLCtPqVWATu7Yf5j5XkRYgN3vvlOssVWXqV1HQPMF2 Yi2XINNisgzs9DwVpI6pzxr6ac1QDTBBgPl4sliFqU9dxw9gSqWh2z4rN+LvYyQe9vBp gzRA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:in-reply-to:references:from:date :message-id:subject:to; bh=tNbSiqbkj+mOMRYFhSz4GxpD0oiPOHKhPfWkFMW9W70=; b=NaGj/C58sYr5mNPw0nG3evh28bLdPpXUEwtB2Yfsy0KMQNoLnInVnscWcNy1udkDgE JPlII9EtXLKH1Oa3rzxTBoUHqc4DqJw7xB6TXRSJoh828ahR/DOe/q73ftRRREkLFVPw VEUikkmN9p4vMVvnsLZ72e5ZJu5sMbuPDuhAPBUFCJU73sxBQozc+/6O1xiVgIMOghlh d/CkgBv6GkzkeHfR0POHqACTClyj4QKOLEUF9ZlkMkG4k29euVqZc4Kw0JxreWYIkcQa UAgPv/1X7uXkSsV+5hMl5ekcPB4cPa5jrzQb0PXdlTMzlb0E+gJHXXKpgqu2j44INnPx AQVA== X-Gm-Message-State: AElRT7FebmuwYP8GANjzcW05/2q/ThaUyjUevyXyb7m105/sMZiPaNQt HTcKTV43tqnmtycUAWjJzjY0ooINGOzfFO2gOHo= X-Google-Smtp-Source: AG47ELs/S3ieKLqQLCJFtqW/OXR/b4NKa+1x9/M7PwoeOqhEB34d4s7LD8BIX7fLGR4n2LWFm8mECvS7LukgX5YuJqY= X-Received: by 10.223.227.74 with SMTP id n10mr4327179wrj.235.1521908437468; Sat, 24 Mar 2018 09:20:37 -0700 (PDT) MIME-Version: 1.0 Received: by 10.223.149.3 with HTTP; Sat, 24 Mar 2018 09:20:17 -0700 (PDT) In-Reply-To: <909738473.56502494.1521902909111.JavaMail.root@spooler2-g27.priv.proxad.net> References: <909738473.56502494.1521902909111.JavaMail.root@spooler2-g27.priv.proxad.net> From: =?UTF-8?Q?Szabolcs_Horv=C3=A1t?= Date: Sat, 24 Mar 2018 17:20:17 +0100 Message-ID: To: Vincent Beugnet , Help for igraph users Content-Type: multipart/alternative; boundary="883d24f24ac0cbca4d05682aeb37" X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:400c:c0c::229 Subject: Re: [igraph] Sorting vertices by degree with igraph C library X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 24 Mar 2018 18:09:18 -0000 --883d24f24ac0cbca4d05682aeb37 Content-Type: text/plain; charset="UTF-8" I do not know. I believe that the documented ones in igraph are not stable. Personally, I would just use std::stable_sort() from the C++ standard library. Is there any reason why you don't want to use that, and want something from igraph instead? On 24 March 2018 at 15:48, Vincent Beugnet wrote: > Thank you very much ! > > Last question: is there a stable sort already implemented in igraph ? > > _______________________________________________ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help > > --883d24f24ac0cbca4d05682aeb37 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I do not know.=C2=A0 I believe that the documented ones in= igraph are not stable.

Personally, I would just use std= ::stable_sort() from the C++ standard library. Is there any reason why you = don't want to use that, and want something from igraph instead?

On 24 March 2= 018 at 15:48, Vincent Beugnet <beugnet.vincent@free.fr> wrote:
Thank you very much !

Las= t question: is there a stable sort already implemented in igraph ?

_______________________________________________
igraph-help mailing list
igraph-help@nongnu.org
https://lists.nongnu.org/mailman/listinfo/= igraph-help


--883d24f24ac0cbca4d05682aeb37-- From MAILER-DAEMON Wed Mar 28 12:54:19 2018 Received: from list by lists.gnu.org with archive (Exim 4.71) id 1f1EL5-0006Kp-Bi for mharc-igraph-help@gnu.org; Wed, 28 Mar 2018 12:54:19 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:47720) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from <2016triplea@gmail.com>) id 1f1EL2-0006K4-F5 for igraph-help@nongnu.org; Wed, 28 Mar 2018 12:54:17 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from <2016triplea@gmail.com>) id 1f1EL1-00083q-Go for igraph-help@nongnu.org; Wed, 28 Mar 2018 12:54:16 -0400 Received: from mail-qk0-x236.google.com ([2607:f8b0:400d:c09::236]:40684) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from <2016triplea@gmail.com>) id 1f1EL1-00083V-AY for igraph-help@nongnu.org; Wed, 28 Mar 2018 12:54:15 -0400 Received: by mail-qk0-x236.google.com with SMTP id o64so3086013qkl.7 for ; Wed, 28 Mar 2018 09:54:15 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=i1WA9CPcST9W1wNCqFjPwYMRgyzJsqFviWqqxepIusY=; b=cJtctqf2XSrYgoQny2LodLIgS62AMSs1lsQ8vegWnhJoiduuc+cW2LS7Q3nahJS2Xv +Z4f0KIAR5zTIH3LFVN/DSJy50P5SOXet6y9iBoeHQ5Uhrpu3a+MT9ehb1mjjKuQWk4P wR5bgP4u5OYt03RchkOHZRTEnC2yt6kZrT80SHEsPFiQCms/X37wszO71RVf9qlypgfM 2+m5CFm1V87as2DdbRbbMpiKDN0QXF450DOTJu6xr2MZjuJ07kEoMRg60kXoK87mFXbU 25f3TgaVmP0vPmhHael0sAG4OTmc0ho2bVUZV8twK5arybRDzbUr6UDLRrassSxC3fkp Xjyw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=i1WA9CPcST9W1wNCqFjPwYMRgyzJsqFviWqqxepIusY=; b=jNacnoh1zRQLB3rnyOvZMYa/oNYTtbkKNeb6irES6zHSz2A4lCUiLE5GqAA8usxj9X /TZnREBEyONpK3hnf7mnxGrIBkX/7ZmTIKbsGEToalbsFaVZBW8asmIjgKW6pTtfvW4c TJp2/jG9o4dbGTpgMQbPySSELu2KQewsRFompeKaY45KDXQP6Ss0LhiG1cve2PoW70GW CWUbUuek1hnW49NTlDnQehpm7sMtGII40XhgKpj9rKQeVv4yhxAAm4BoAj454Jasw9kB yi1iCj7VMWa8AU5YWZQchC/2QxcqAkuOXnyUegxQMEWufq/sB64lD5MObtNd0SeQlQAT RVTQ== X-Gm-Message-State: ALQs6tAaOw7R2FmFdjHmLCJ8NKn9GdnbvbCfpECKVpZeSBpjq4ADzOY0 CXReb/5KJ92bigorWHfOSjzUi538YsbRPjOYpQDlDw== X-Google-Smtp-Source: AIpwx49K7qoVPPF0ecaySXctTIL31SHG2j8mm+jn7d+gK7s68kYKPiyJrMY9Mq+IVNZgzYom2TcsWLUAaMHqT4BhSkA= X-Received: by 10.55.158.137 with SMTP id h131mr5893393qke.330.1522256054325; Wed, 28 Mar 2018 09:54:14 -0700 (PDT) MIME-Version: 1.0 Received: by 10.12.212.226 with HTTP; Wed, 28 Mar 2018 09:54:13 -0700 (PDT) From: Triple A <2016triplea@gmail.com> Date: Wed, 28 Mar 2018 09:54:13 -0700 Message-ID: To: igraph-help@nongnu.org Content-Type: multipart/alternative; boundary="94eb2c061cd860156605687bdbe1" X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2607:f8b0:400d:c09::236 Subject: [igraph] Python igraph weighted centrality error: unhandled type X-BeenThere: igraph-help@nongnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Help for igraph users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 28 Mar 2018 16:54:17 -0000 --94eb2c061cd860156605687bdbe1 Content-Type: text/plain; charset="UTF-8" Dear all, I am calculating weighted centrality measures using python-igraph. from igraph import * g = Graph.Read_Ncol("sample.txt",names=True,directed=False,weights=True)print (g.vs["name"])print (g.es["weight"]) Below are two lists of the vertices and edge weights in my network: ['a', 'b', 'c', 'd', 'e'][4.0, 2.0, 3.0, 4.0, 4.0] I am using following codes calculating weighted centrality: print (g.strength(weights=True))print (g.betweenness(weights=True)) Below is the error message I got: TypeError: unhandled type Can anyone let me know what went wrong? Thank you! Claire --94eb2c061cd860156605687bdbe1 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear all,

I am calculating weighted centrality measures usi= ng python-igraph.

from igraph import *
g =3D Graph.Read_Ncol("sample.txt&qu=
ot;,names=3DTrue,directed=3DFalse,weights=3D=
True)
print (g.vs["name"])
print (g.es["weight"])

Below are two lists of the vertices and edge weights in my network:=

['a', 'b', 'c', 'd', 'e']
[4=
.0,=
 2.0, 3.0, 4.0, 4.0]

I a= m using following codes calculating weighted centrality:

print (g.strength(weights=3DTrue))
print (g.betweenness(weights=3DTrue))=

Below is the error message I got:

TypeErro=
r: =
unhandled type

Can anyone let me know what went wro= ng? Thank you!

Claire
--94eb2c061cd860156605687bdbe1--