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My igraph library doesn't recognize "graph_from_incidence_matrix() and graph_from_adjacency_matrix()" anymore (Everything else from igraph works fine). I've uninstalled and reinstalled igraph but still no luck. Here is an example:

library(igraph)
inc <- matrix(sample(0:1, 15, repl=TRUE), 3, 5)
colnames(inc) <- letters[1:5]
rownames(inc) <- LETTERS[1:3]
graph_from_incidence_matrix(inc)
Error: could not find function "graph_from_incidence_matrix"

Any help is appreciated. UPDATE: Here is my session info:

`R version 3.1.3 (2015-03-09)
 Platform: x86_64-apple-darwin10.8.0 (64-bit)
 Running under: OS X 10.10.5 (Yosemite)

 locale:
 [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     

 other attached packages:
 [1] qgraph_1.3.1   R.matlab_3.2.0 igraph_0.7.1  

 loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3     cluster_2.0.1     colorspace_1.2-6             corpcor_1.6.7      
 [5] d3Network_0.5.2.1   digest_0.6.8        ellipse_0.3-8          fdrtool_1.2.14     
 [9] foreign_0.8-63      Formula_1.2-1       ggm_2.3              ggplot2_1.0.1      
[13] glasso_1.8          grid_3.1.3          gridExtra_0.9.1     gtable_0.1.2       
[17] gtools_3.4.2        Hmisc_3.16-0        huge_1.2.6          jpeg_0.1-8         
[21] lattice_0.20-31     latticeExtra_0.6-26 lavaan_0.5-18       magrittr_1.5       
[25] MASS_7.3-40         Matrix_1.2-0        matrixcalc_1.0-3    mnormt_1.5-2       
[29] munsell_0.4.2       nnet_7.3-9          parallel_3.1.3      pbivnorm_0.6.0     
[33] plyr_1.8.2          png_0.1-7           proto_0.3-10        psych_1.5.4        
[37] quadprog_1.5-5      R.methodsS3_1.7.0   R.oo_1.19.0         R.utils_2.0.2      
[41] RColorBrewer_1.1-2  Rcpp_0.11.6         reshape2_1.4.1      rjson_0.2.15       
[45] rpart_4.1-9         scales_0.2.4        sem_3.1-5           sna_2.3-2          
[49] splines_3.1.3       stats4_3.1.3        stringi_0.4-1       stringr_1.0.0      
[53] survival_2.38-1     tools_3.1.3         whisker_0.3-2 `
mathlover
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    Very likely you have either forgotten to use `library(igraph)` or have overwritten the functions somehow - if the latter you can try using `igraph:::graph_from_incidence_matrix` – user20650 Aug 26 '17 at 12:53
  • @user20650 No, I haven't forgotten library(igraph). igraph:::graph_from_incidence_matrix didn't work either. As I mentioned , everything else works from igraph. This function also used to work a couple of months ago. Here is a screenshot: http://imgur.com/a/mG4RU – mathlover Aug 26 '17 at 17:55
  • Update: it seems that graph.incidence() is doing the same thing and that works, so I'm using it instead. But I'm still curious why graph_from_incidence_matrix() doesn't work anymore. – mathlover Aug 26 '17 at 18:25
  • mathlover, after starting a new r session , can you load igraph, and then edit your question to post the results of `sessionInfo()` - perhaps its a version issue. PS when you restart R does it load a previous r workspace? - have a look at ls() after restarting. – user20650 Aug 26 '17 at 18:59
  • ah, from your screenshot, it seems you are using igraph version 0.7.1. Im currently on 1.0.1 - cant remember when, but igraph changed the syntax a while ago from things like graph(dot)incidence to using underscores, so perhaps your version does not support this . – user20650 Aug 26 '17 at 19:03
  • okay, yo follow up on the version. looking at the code of [Version 0.7.1](https://cran.r-project.org/src/contrib/Archive/igraph/), specificall the R code under `structure.generators.R` you can see the `graph.incidence` function is defined but not `graph_from_incidence_matrix` . Neweer igraph version has this new syntax see https://github.com/igraph/rigraph/blob/dev/R/incidence.R , although previous syntax is still supported – user20650 Aug 26 '17 at 19:14
  • @user20650 Wow, how is it possible that when I install igraph from Rstudio, it installs Version 0.7.1 instead of the newest version? – mathlover Aug 26 '17 at 20:51
  • depends on several things: operating system, versions etc. Pls add sessionInfo to question – user20650 Aug 26 '17 at 21:04
  • ah ok , you are using a mac - I cant help, however, your R version is quite behind - current version is 3.4.1. So try updating and then try reinstalling igraph. if you have difficulties you should add a new question specific to this. – user20650 Aug 27 '17 at 00:56

1 Answers1

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are you sure you loaded the library correctly? at the moment there is a ' infront of the row 

library(igraph)

remove that and run your code again. after the library()-statement you should get something similar to this one:

Attach paket: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

After running the rest of your code I get the following output: 

IGRAPH 6798dd1 UN-B 8 6 -- 
+ attr: type (v/l), name (v/c)
+ edges from 6798dd1 (vertex names):
[1] A--a A--b A--c A--e B--b C--e
Jan
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  • that ' was left from my attempt to put it in the code format. I removed igraph and run my code again but still no luck. I don't get that "Attach paket: ‘igraph’...". message. As I mentioned above, anything else from graph works except these two functions. Here is a screenshot http://imgur.com/a/mG4RU – mathlover Aug 26 '17 at 17:42