# Why might UCINET and R return different results for a QAP Logistic Regression (on the same data)?

I'm trying to run a QAP logistic regression to predict the odds of a tie in a social network (represented as a binary adjacency matrix) given two independent variables (also binary matrices) but am getting opposite results depending on whether I run the analysis in R or UCINET.

All three matrices are rectangular (30 x 75). The 30 rows are people I've interviewed and the 75 columns are the entire population (including the 30 interviewees). All matrices include the person IDs as row and column names.

Running the analysis in R (see code at the bottom of the question), I get the following output:

            Estimate  Exp(b)       Pr(<=b) Pr(>=b) Pr(>=|b|)
(intercept) -5.298525  0.004998961 0.0001  0.9999  0.0001
indep1       1.797138  6.032358591 0.9693  0.0307  0.2393
indep2       3.194162 24.389724184 1.0000  0.0000  0.0030


But after exporting the variables to .csv files and re-running it in UCINET, I get:

                  1       2       3       4       5       6       7       8       9
Coef OddsRat     Sig      SD     Avg     Min     Max   P(ge)   P(le)
------- ------- ------- ------- ------- ------- ------- ------- -------
1 Intercept  -3.931   0.020   0.000   0.540  -2.785  -3.931  -1.783       1   0.000
2    indep1   2.391  10.925   0.003   1.508  -0.239  -5.089  15.437   0.003   0.998
3    indep2   1.458   4.296   0.000   0.504  -0.026 -15.991   1.458   0.000       1


Any ideas why this might be happening?

In case it's important, the (QAP) correlation coefficient between the two independent variables is 0.382

I've only included the 30 interviewees in the matrix rows because they are the only people from whom there might be a tie. The networks and QAP regressions are directed.

Incidentally, if I run the QAP logit using full 75x75 adjacency matrices (all people in the columns also appear as rows), I get the same output in both programs.

I also have a related question... A colleague suggested I could run the analysis using the 75x75 matrices but replace the rows of people I haven't interviewed with NAs. This gives me the same results in R and UCINET. Does this seem like a sensible approach, rather than using rectangular matrices?

Thanks!

Reproducible example in R:

library(sna)

# row and column labels
rowIDs <- c("1",  "2",  "3",  "5",  "9",  "16", "18", "19", "26", "27", "34", "35", "36", "40", "46", "49", "60", "64", "70", "72", "73", "74", "75", "76", "77", "82", "85", "86", "97", "100")
colIDs <- c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "23", "26", "27", "34", "35", "36", "38", "40", "41", "43", "45", "46", "47", "49", "51", "52", "53", "57", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "70", "72", "73", "74", "75", "76", "77", "78", "79", "81", "82", "83", "84", "85", "86", "87", "88", "89", "91", "92", "93", "94", "95", "96", "97", "100", "101")

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# assign row/column names

# set up independent variables

# run the analysis
# (warning, this command takes a bit of time to run with 10,000 reps)
nl <- netlogit(adj.dep, g.indeps, reps=10000, nullhyp="qap")
# print output
summary(nl)


The problem is because the data is rectangular (30 x 75), not square (30x30). netlogit() calls rmperm(). If you look into the code for rmperm, you will see the problem

rmperm function (m) { m <- as.sociomatrix.sna(m) if (is.list(m)) return(lapply(m, rmperm)) if (length(dim(m)) == 2) { o <- sample(1:dim(m)[1]) p <- matrix(data = m[o, o], nrow = dim(m)[1], ncol = dim(m)[2]) } else { p <- array(dim = c(dim(m)[1], dim(m)[2], dim(m)[3])) for (i in 1:dim(m)[1]) { o <- sample(1:dim(m)[2]) p[i, , ] <- array(m[i, o, o]) } } p } <environment: namespace:sna>

See, 'o' assumes that the number of rows equals the number of columns. It certainly does not in your case. The good news is that the code would be easy to rewrite, assigning

o1 <- sample(1:dim(m)[2])

o2 <- sample(1:dim(m)[3])

p[i, , ] <- array(m[i, o1, o2])

I would not assume, however, that UCINET is providing accurate results. We can't check its code to verify that it handles asymmetric matrices responsibly. It's an unusual format and I wouldn't assume the software accommodates it.

• Fair point about UCINET - especially since their QAP Logit is in beta... Do you think it would make more sense to run the analyses with 75x75 matrices (with rows for people I didn't interview coded as missing values) rather than use 30x75 matrices? Sep 10, 2014 at 10:13
• I would overwrite rmperm with the above-mentioned changes, as that would ensure the number of cases in the simulations equals the number of cases in the observed data. (If you use QAP with missing data and casewise deletion, the n will vary and inevitably be less than the observed data.) Alternatively, you could focus on the 30x30 matrices in the QAP logistic regressions and perhaps compare the findings to QAP logistic regressions run on the 75x75 matrices. Sep 10, 2014 at 10:46