Error in if (inputs$clusterID == inputs$panelID) { : argument is of length zero

[jonah-allen]

First of all, thank you for developing a fantastic package! I am having and issue implementing clusters. Could you please provide insight into why this error occurs or suggest any adjustments to handle clustering properly? Thank you for your support!

Description

I encountered an issue when running the logitr() function with the clusterID parameter specified. While the model runs successfully without clusterID, adding it results in an error. The error message is:

Error in if (inputs$clusterID == inputs$panelID) { :
  argument is of length zero

I created a clusterID column specifically to ensure the data type in the version column was not the issue. (The scenario columns are not currently in use but may be in the future).

Reproducible Example

Here is a sample structure of my dataset (wtp_risk):

# A tibble: 180 × 12
   version  risk loss_value id         original_choice scenario_a scenario_b scenario_c alt   choice obsID clusterID
   <fct>   <dbl>      <dbl> <chr>      <fct>                <dbl>      <dbl>      <dbl> <fct>  <dbl> <int>    <int>
 1 CO1         8         0  R_bf8TOsp… c                        2          3          1 a          0    53        1
 2 CO1         4       113. R_bf8TOsp… c                        2          3          1 b          0    53        1
 3 CO1         4       113. R_bf8TOsp… c                        2          3          1 c          1    53        1
 4 CO1         8         0  R_2tnw7mp… a                        1          2          2 a          1    27        2
 5 CO1         4       113. R_2tnw7mp… a                        1          2          2 b          0    27        2
 6 CO1         4       113. R_2tnw7mp… a                        1          2          2 c          0    27        2

Code to Reproduce

# Run without clusterID (successful)
mnl_pref <- logitr(
  data = wtp_risk,
  outcome = "choice",
  obsID = "obsID",
  pars = c("loss_value", "risk")
)

# Run with clusterID (error)
mnl_pref <- logitr(
  data = wtp_risk,
  outcome = "choice",
  obsID = "obsID",
  pars = c("loss_value", "risk"),
  clusterID = "clusterID"
)

Observations

• The wtp_risk data frame does not contain NA values in obsID, clusterID, or version.
• The clusterID was created to ensure correct data type handling.
• The error seems related to how panelID is internally processed in the logitr function, even when panelID is not specified. (This is not panel data).
• I have tried setting panelID = NULL specifically and the error still occurs.

Environment

• R version: 4.2.3
• logitr version: 1.1.2
• macOS: 15.0.1

[jhelvy]

Could you send a small portion of the data so I can replicate this error? Would only need the relevant variables used in the example: "choice", "obsID", "loss_value", "risk", "clusterID"

[jonah-allen]

sample_wtp_risk_data.csv

[jonah-allen]

Just realizing that only has cluster groups 1 and 2 included -- there are 25 cluster groups in my data....I think you can manually change those for replication but let me know if you need a different sample!

[jhelvy]

Okay I just ran this and I can replicate the error. It is perhaps a bug in the code, but I'm not sure if it should occur because I'm questioning the use of clusters here. Usually clustering is suggested when you have panel data. In your case, you have different versions. Is that just different versions of a choice experiment? If so then I'm not sure why you would want to cluster your errors around the version. Basically, I don't think clustering is needed.

If you do want to use clusters, then as a work around you can also set panelID = "clusterID" and it will work. With a MNL model there is no difference in the calculation of the log-likelihood with or without a panelID specified, so this will get you what you want without error. You just need to specify both clusterID and panelID like this:

m2 <- logitr(
  data      = wtp_risk,
  outcome   = "choice",
  obsID     = "obsID",
  pars      = c("loss_value", "risk"),
  clusterID = "clusterID",
  panelID   = "clusterID"
)

[jonah-allen]

Thanks very much, that fixed the issue!

Interesting -- my understanding was that clustering by the survey version is best practice because I have significant variation across survey versions; parameters vary (percent risk & percent profit loss) across three options, and the "source of risk" varies across half the surveys (half are viewed as "climate" and the other is "policy", without going into too much detail). I know that description is very general...but any resources you might be able to share on clustering in this case would be very appreciated!

[jhelvy]

I suppose that's a reasonable assumption. This is in general though an issue that I'll have to deal with because you should be able to use clusters without defining a panelID. This is a workaround for now, but I'll patch this.

[Ales-G]

Hello,
First of all thank you very much for creating this package as well as have widely accessible material to explain how to use it. It is really amazing and helpful for practitioners like myself.

I am writing because I have a similar issue as I try to cluser errors in a mix logit

If I use:

mxl_pref <- logitr(
  data           = dat,
  outcome        = "choice",
  obsID          = "obsID",
  pars           = c("wg","sr_c"),
  drawType = 'sobol',
  #panelID        = "id",
  #clusterID      = "id",
  randPars = c(wg="n",
               sr_c="n"), 
  numMultiStarts = 2)

Setting robust to TRUE since clusters are being used
Running multistart...
  Random starting point iterations: 2
  Number of cores: 10
rsession-arm64(92927) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(92928) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
Done!

I get the following results

summary(mxl_pref)
Summary of 10k Draws for Random Coefficients: 
                      Min.     1st Qu.     Median       Mean   3rd Qu. Max.
wg                    -Inf -0.31226879 0.03066811 0.03023746 0.3735653  Inf
sr_cfirst -Inf  0.09645796 0.28118299 0.28100881 0.4658450  Inf
sr_csecond -Inf  0.90574334 0.94789934 0.94793724 0.9900687  Inf

But if I try to cluster SEs by "id" I get the following error, even if I use the workaround you suggests here.

> mxl_pref <- logitr(
+   data           = dat,
+   outcome        = "choice",
+   obsID          = "obsID",
+   pars           = c("wg","sr_c"),
+   drawType = 'sobol',
+   panelID        = "wrkid",
+   clusterID      = "wrkid",
+   randPars = c(wg="n",
+                sr_c="n"), 
+   numMultiStarts = 2)
Setting robust to TRUE since clusters are being used
Running multistart...
  Random starting point iterations: 2
  Number of cores: 10
rsession-arm64(92951) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(92952) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
Done!
> summary(mxl_pref)
Error in matrix(t(matrix(X, mx, nx * n)), mx * m, nx * n, byrow = T) : 
  invalid 'nrow' value (too large or NA)

Do you know what may be causing the error, and how can I calculate my WTP using clustering for the mixed logit?

thank you very much in advance.

[jhelvy]

Thanks for checking out logitr @Ales-G. Just like my response to the prior question in this issue, it would really help if you could send a sample of the data so I can inspect how you have this set up. I don't know what wrkid looks like, which you use in your example as the panelID.

[Ales-G]

Dear @jhelvy,

thanks so much for your kind reply. I am attaching a example dataset that encounters my issue.

If I run my mixed logit in WTP space with no clustering, I get my results, but if I add clustering I get the following error: Error in matrix(t(matrix(X, mx, nx * n)), mx * m, nx * n, byrow = T) : invalid 'nrow' value (too large or NA). One thing to note is that I included in the dataset a variable called diff that indicates that some wrkid2 have completed more tasks (more observations), than others. This appears to be the source of the problem I think.

Below an example of what I am doing

> mxl_wtp <- logitr(
+   data           = df,
+   outcome        = "choice",
+   obsID          = "obsID",
+   pars           = "brand",
+   scalePar       = "wg",
+   drawType = 'sobol',
+   #panelID        = "wrkid2",
+   #clusterID      = "wrkid2",
+   randPars = c(brand="n"), 
+   numMultiStarts = 100)
Running multistart...
  Random starting point iterations: 100
  Number of cores: 10
rsession-arm64(73575) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73576) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73577) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73578) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73579) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73580) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73581) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73582) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73583) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73584) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
Done!
> summary(mxl_wtp)

=================================================

Model estimated on: Thu Jun 19 15:58:30 2025 

Using logitr version: 1.1.2 

Call:
logitr(data = samp_fin, outcome = "choice", obsID = "obsID", 
    pars = "brand", scalePar = "wg", randPars = c(brand = "n"), 
    numMultiStarts = 100, drawType = "sobol")

Frequencies of alternatives:
      1       2 
0.51136 0.48864 

Summary Of Multistart Runs:
    Log Likelihood Iterations Exit Status
1        -120.9131         54           3
2        -120.9120         59           3
......
99       -120.9097         61           3
100      -120.9135         53           3

Use statusCodes() to view the meaning of each status code

Exit Status: 3, Optimization stopped because ftol_rel or ftol_abs was reached.
                                 
Model Type:           Mixed Logit
Model Space:   Willingness-to-Pay
Model Run:              14 of 100
Iterations:                    54
Elapsed Time:         0h:0m:0.36s
Algorithm:         NLOPT_LD_LBFGS
Weights Used?:              FALSE
Robust?                     FALSE

Model Coefficients: 
                 Estimate  Std. Error z-value Pr(>|z|)
scalePar      -2.4611e-02  1.7201e-02 -1.4308   0.1525
brandbeta      8.3530e+02  1.1631e+04  0.0718   0.9427
brandgamma     3.2199e+02  3.5017e+03  0.0920   0.9267
sd_brandbeta  -7.1535e+03  4.2324e+04 -0.1690   0.8658
sd_brandgamma  9.8206e+02  1.0804e+04  0.0909   0.9276
                                     
Log-Likelihood:         -119.17994460
Null Log-Likelihood:    -121.99390378
AIC:                     248.35988920
BIC:                     264.21230000
McFadden R2:               0.02306639
Adj McFadden R2:          -0.01791926
Number of Observations:  176.00000000

Summary of 10k Draws for Random Coefficients: 
           Min.   1st Qu.   Median     Mean   3rd Qu. Max.
brandbeta  -Inf -3981.933 840.7686 845.3176 5665.1169  Inf
brandgamma -Inf  -340.749 321.6741 321.0787  983.8869  Inf

> mxl_wtp_cls <- logitr(
+   data           = df,
+   outcome        = "choice",
+   obsID          = "obsID",
+   pars           = "brand",
+   scalePar       = "wg",
+   drawType = 'sobol',
+   panelID        = "wrkid2",
+   clusterID      = "wrkid2",
+   randPars = c(brand="n"), 
+   numMultiStarts = 100)
Setting robust to TRUE since clusters are being used
Running multistart...
  Random starting point iterations: 100
  Number of cores: 10
rsession-arm64(73593) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73594) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73595) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73596) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73597) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73598) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73599) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73600) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73601) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
rsession-arm64(73602) MallocStackLogging: can't turn off malloc stack logging because it was not enabled.
Done!
> summary(mxl_wtp_cls)
Error in matrix(t(matrix(X, mx, nx * n)), mx * m, nx * n, byrow = T) : 
  invalid 'nrow' value (too large or NA)

sampdata.csv

Thanks a lot in advance for your support on this. Again, the package, and the explanations are amazing!

Best