Sunday, December 21, 2014

Cross-cultural measurement invariance testing in R in 5 simple steps

Here I am presenting a quick crash course to run invariance tests for cross-cultural research in R. R is a free programme and has an expanding list of awesome features that should be of interest to people doing cross-cultural work. 

I am working with RStudio, but there are other options for running R. Here are the basic steps to get you started and run a cross-cultural equivalence test. 

1. Set your working directory

This step is important because it will allow you to call your data file later on repeatedly without listing the whole path of where it is saved. For example, I saved the file that I am working with on my dropbox folder in a folder called 'Stats' that is in my 'PDF' folder. 
I need to type this command:


Two important points: 
a) for some strange reason you need double \\ to set your directory paths with windows.
b) make sure that there are no spaces in any of your file or directory paths. R does not like it and will throw a tantrum if you have a space somewhere. 

2. Read your data into R

The most convenient way to read data into R is using .csv files. Any programme like SPSS or Excel will allow you to save your data as a .csv file. There are a few more things that we need to discuss about saving your data, but I will discuss this below. 

justice <- read.csv("justice.csv", header = TRUE)

R is an object oriented language, which means we will constantly create objects by calling on functions: object <- function. This may seem weird at first, but will allow you to do lots of cool stuff in a very efficient way.

I am using a data that tested a justice scale, so I am calling my object 'justice'. 

3. Deal with missing data

If you have absolutely no missing data in your data file, skip this step. However most mortal researcher souls will have some missing data in their spreadsheet. R is very temperamental with missing data and we need to tell it what missing data is and how to deal with it. Some people (including myself) who are used to SPSS typically leave missing data as a blank cell in the spreadsheet. This will create problems. The best option is to write a little syntax command in spss to recode all blank cells to a constant number. 
For example, I could write something like this in SPSS:

recode variable1 to variable12
(sysmis=9999) (else=copy) into
pj1 pj2 pj3 pj4 ij1 ij2 ij3 ij4 dj1 dj2 dj3 dj4. 

Now I can save those new variables as a .csv file and read into R using the step above.

Once you have executed step 2, you need to define these annoying 9999s as missing values.
The simplest and straightforward option is to write this short command that converts all these offending values into NA - the R form of missing data.

justice[justice==9999] <- NA

Note the square brackets and double ==. If you want to treat only a selected variable, you could write:

justice$pj1[justice$pj1==9999] <- NA

This tells R that you want only the pj1 variable in the dataframe justice to be treated in this way. 

To check that all worked well, type:


You should see something like this:

If all went well, now your minimum and maximum values are within the bounds of your original data and you have a row of NA's a the bottom of each variable column.

4. Loading the analysis packages

R is a very powerful tool because it is constantly expanding. Researchers from around the world are uploading tools and packages that allow you to run fancy new stats all the time. However, the base installation of R does not include them. So we need to tell R which packages we want to use.
For measurement invariance tests, these three are particularly useful: lavaan (the key one) and semTools (important for the invariance tests).

Write this code to download and install the packages on your machine:

install.packages(c("semTools", "lavaan"))

Make sure you have good internet connectivity and you are not blocked by an institutional firewall. I had some problems recently trying to download R packages when accessing it from a university campus with a strong firewall. 

Once all packages are downloaded, you need to call them before you can run any analyses:



Important: You need to call these packages each time that you want to run some analyses, if you have restarted R or RStudio.

5. Running the analyses

R is an object oriented language, as I mentioned before. The analysis can be executed in a couple of steps. First we need to specify the model that we run by creating a new object that contains all the information. Then we tell R what to do with that model. Finally, we have various options for obtaining the results, that is the fit indices and parameter estimates as well as other diagnostic information. 

Let's create the model first:

This creates the model that we can then work with. The '=~' denotes that the items are loading on the latent factor. This is what it looks like:

The next set of commands sets specifies what should be done with the model. In the case of a simple CFA, we can call this function: <-cfa(cfa.justice, data=justice)

To identify the model, lavaan sets the loading of the first item on each latent variable to 1. This is convenient, but may be problematic if the item is not a good indicator. An alternative strategy is to set the variance of the latent variable to 1. This can be done by adding to the fit statement. <-cfa(cfa.justice, data=justice,

This statement runs the analysis, but we still need to request the output.

The simplest way is to use summary again. Here is an option that prints both the fit indices and the standardized parameters.

summary(, fit.measures= TRUE, standardized=TRUE)

Here is a truncated and annotated version of the output:

lavaan (0.5-17) converged normally after  39 iterations
                                                                  Used       Total
  Number of observations                          2518        2634
# The following shows the estimator and the Chi square stats. As can be seen, we have 51 df's, but the model does not fit that well.
  Estimator                                                  ML 
Minimum Function Test Statistic              686.657 
Degrees of freedom                                   51 
P-value (Chi-square)                                 0.000

Model test baseline model:
  Minimum Function Test Statistic            20601.993 
Degrees of freedom                                 66 
P-value                                                     0.000
#The incremental fit indices are in contrast quite good. The CFI and TLI should be ideally be above .95 (or at least .90). So this model does look good.
User model versus baseline model:
  Comparative Fit Index (CFI)                    0.969 
Tucker-Lewis Index (TLI)                       0.960

Loglikelihood and Information Criteria:
  Loglikelihood user model (H0)             -44312.277 
Loglikelihood unrestricted model (H1)     -43968.949
  Number of free parameters                         27
#The AIC and BIC are useful for comparing models, especially non-nested models. Not the case right now.
  Akaike (AIC)                               88678.555 
Bayesian (BIC)                             88835.998 
Sample-size adjusted Bayesian (BIC)        88750.212
#The RMSEA should be small. Values smaller than .08 are deemed acceptable, below .05 are good. We are doing ok-ish with this one here.
Root Mean Square Error of Approximation:
  RMSEA                                          0.070 
90 Percent Confidence Interval          0.066  0.075  
P-value RMSEA <= 0.05                          0.000
#Another useful lack of fit index. The SRMR should be below .05 if possible. This is looking good.
Standardized Root Mean Square Residual:
  SRMR                                           0.037
#Now we have a print out of all the parameter estimates, including the standardized loadings, variances and  covariances. Here it is important to check whether loadings are relatively even and strong, and that the variances and covariances are reasonable (e.g., we want to avoid very high correlations between latent variables). It is looking ok overall. Item ij4 may need some careful attention.
Parameter estimates:
  Information             Expected  Standard Errors                             Standard
                   Estimate  Std.err  Z-value  P(>|z|)  Std.all
Latent variables: 
pj =~    pj1   1.000                                           1.202    0.789   
pj2               1.009    0.027   38.005    0.000    1.213    0.790   
pj3               0.769    0.025   31.003    0.000    0.924    0.643   
pj4               0.802    0.024   33.244    0.000    0.963    0.687 
ij =~    ij1   1.000                                             1.256    0.879   
ij2               1.064    0.014   75.039    0.000    1.335    0.957   
ij3               1.015    0.015   68.090    0.000    1.274    0.910   
ij4               0.808    0.022   37.412    0.000    1.014    0.644 
dj =~    dj1 1.000                                              1.211    0.821   
dj2               1.013    0.019   51.973    0.000    1.227    0.871   
dj3               1.056    0.020   52.509    0.000    1.279    0.877   
dj4               1.014    0.021   48.848    0.000    1.228    0.834
pj ~~    ij    0.828    0.041   20.435    0.000    0.549    0.549   
dj                0.817    0.040   20.187    0.000    0.562    0.562 
ij ~~    dj    0.711    0.037   19.005    0.000    0.467    0.467
pj1               0.874    0.036                      0.874    0.377   
pj2               0.889    0.036                      0.889    0.377 
pj3               1.213    0.039                      1.213    0.587   
pj4               1.040    0.035                      1.040    0.528   
ij1               0.464    0.016                      0.464    0.227   
ij2               0.164    0.011                      0.164    0.084   
ij3               0.336    0.013                      0.336    0.172   
ij4               1.448    0.042                      1.448    0.585   
dj1               0.709    0.025                      0.709    0.326   
dj2               0.479    0.019                      0.479    0.242   
dj3               0.489    0.020                      0.489    0.230   
dj4               0.662    0.024                      0.662    0.305   
pj                1.444    0.066                      1.000    1.000   
ij                1.576    0.057                      1.000    1.000   
dj                1.466    0.060                      1.000    1.000

However, we want to do an invariance analysis. Right now we collapsed the samples and ran an analysis across all groups. This can create problems, especially if the samples have different means (see my earlier blogpost for an explanation of this problem). 

The grouping variable should be a factor, that is a string variable that has the labels. You can also use continuous variables, but then you will need to remember what each number means. In this example, I have data from three samples:

> summary(justice$nation)
     Brazil        NZ         Philippines 

        794        1146         694 

It would be informative to see whether the item loadings are similar in each group. To do this, we only need to add group="nation" to our cfa statement. <-cfa(cfa.justice, data=justice, group="nation")

We can then print the results by using the summary statement again (remember that we have to call the new object for this analysis):

summary(, fit.measures= TRUE, standardized=TRUE) 

I am not printing the output.

Of course, this is not giving us the info that we want, namely whether the model really fits. In addition, we could ask for equal loadings, intercepts, unique variances, etc. I can't go into details about the theory and importance of each of these parameters. I hope to find some time soon to describe this. In the meantime, have a look at this earlier article. 

In R, running these analyses is really straightforward and easy. A single command line will give us all the relevant stats. Pretty amazing!!!!!

To run a full-blown invariance analysis, all you need is to type this simple command:


You can write it as a single line. I just put it on separate lines to show what it actually entails. First, we call the model that we specified above, then we link it to the data that we want to analyze. After that, we specify the grouping variable (nation). The final line requests strict invariance, that is we want to get estimates for a model where loadings, intercepts and unique variances are constrained as well as a model in which we constrain the latent means to be equal. If we don't specify the last line, we will not get the constraints in unique variances. 

Here is the output, but without the strict invariance lines:

Measurement invariance tests:
Model 1: configural invariance:
    chisq        df    pvalue       cfi     rmsea       bic
  992.438   153.000     0.000     0.962     0.081 86921.364
Model 2: weak invariance (equal loadings):
    chisq        df    pvalue       cfi     rmsea       bic
 1094.436   171.000     0.000     0.958     0.080 86882.400
[Model 1 versus model 2]
  delta.chisq      delta.df delta.p.value     delta.cfi
      101.998        18.000         0.000         0.004
Model 3: strong invariance (equal loadings + intercepts):
    chisq        df    pvalue       cfi     rmsea       bic
 1253.943   189.000     0.000     0.952     0.082 86900.945
[Model 1 versus model 3]
  delta.chisq      delta.df delta.p.value     delta.cfi
      261.505        36.000         0.000         0.010
[Model 2 versus model 3]
  delta.chisq      delta.df delta.p.value     delta.cfi
      159.507        18.000         0.000         0.006
Model 4: equal loadings + intercepts + means:
    chisq        df    pvalue       cfi     rmsea       bic
 1467.119   195.000     0.000     0.942     0.088 87067.134
[Model 1 versus model 4]
  delta.chisq      delta.df delta.p.value     delta.cfi
      474.681        42.000         0.000         0.020
[Model 3 versus model 4]
  delta.chisq      delta.df delta.p.value     delta.cfi
      213.176         6.000         0.000         0.009

How do we make sense of this?

Model 1 is the most lenient model, no constraints are imposed on the model and separate CFA's are estimated in each group. The CFI is pretty decent. The RMSEA is borderline. 
Model 2 constraints the factor loadings to be equal. The CFI is still pretty decent, the RMSEA actually improves slightly. This is due to the fact that we have now more df's and RMSEA punishes models with lots of free parameters. The important info comes in the line entitled Model 1 versus model 2. Here we find the difference stats. The X2 difference test is significant and we would need to reject model 2 as significant worse. However, due to the problems with the X2 difference test, many researchers treat this index with caution and examine other fit indices. One commonly examined fit index of the difference is Delta CFI, that is the difference in CFI fit from one model to the next. It should not be larger than .01. In our case, it is borderline - the delta CFI is .01.
We can then compare the other models. The next model constraints both loadings and intercepts (strong invariance). The model fit is pretty decent, we can probably assume that both loadings and intercepts are invariant across these three groups. 
In contrast, constraining the latent means shows some larger problems. The latent means are likely to be different. 

6. Further statistics 

In this particular case, the model fits pretty well. However, often we run into problems. If there is misfit, we either trim the parameter (drop parameters or variables from the model) or we can add parameters. To see which parameters would be useful to add, we can request modification indices. 
This can be done using this command:
mi <- modificationIndices(

The second line (mi) will print the modification indices. It gives you the expected drop in X2 as well as what the parameter estimates would be like if they were freed.

If we want to print only those modification indices above a certain threshold, let's say 10, we could add the following line:
subset (mi, mi>10)

This will give us modification indices for the overall model. If we want to see modification indices for any of the constrained models, we can request them after estimating the respective model.

For example, if we want to see the modification indices after constraining the loadings to be similar, we can run the following line:

metric <-cfa(cfa.justice, 

This will now give us the modification indices for this particular model. 

There are more options for running constrained models. For example, this line gives the scalar invariant model: 

scalar <-cfa(cfa1,
                   group.equal=c("loadings", "intercepts"))

As you can see, these models are replicating the models implied in the overall analysis that we got with the measurementInvariance command above. 


I hope I have convinced you that measurement invariance in R using lavaan and semTools is a piece of cake. It is an awesome resource, allows you to run lots of models in no time whatsoever and of course it is free!!!!! Once you get into R, you can do even more fancy stuff and run everything from simple stats to complex SEM and ML models in a single programme. 

More info on lavaan can be found here (including a pdf tutorial). 

I am still in the process of learning how to navigate this awesome programme. If you have some suggestions for simplifying any of the steps or if you spot some mistakes or have any other suggestions... please get in touch and let me know :)
If there are some issues that are unclear or confusing, let me know too and I will try and clarify!
Look forward to hearing from you and hope you find this useful!

Wednesday, December 17, 2014

The beauty of black and white

Marcel Cesar, a friend of mine, nominated me for a five-day black and white challenge on FB. The task was to post one picture per day, for five days. He posted some pretty amazing ones and seeing some of those amazing pictures by him and others, I thought I would try to match their brilliance. 
It had been ages since I last took BW photos. I had been trained to do all the processing in a darkroom when I was a kid, but after I switched to digital, I hardly used BW settings or converted pictures to BW afterwards. However, when experimenting in the evenings with some shots that I liked or had taken a while ago, I started to remember what had drawn me to photography as a kid. Pictures in BW have this timeless quality, simple shots are rendered art and captured history at the same time. Simple moments that would pass in a flash suddenly feel like they carry bigger significance, being transformed into instant classics. 

I just wanted to give a bit of background to those five pictures that I had selected. For me good photography (and photos) tell stories. I want to capture a moment that appears significant or beautiful or both. I have memories and thoughts attached to most photos that I take and I want to share a bit of how I see the world. When I see photos taken by others, I also try to find the stories that they capture or the thoughts that the photographer may have had when taking the shot. We probably all see different stories unfold in these frozen moments, but this is the fun to decipher somebody else's mind and see the world through their eyes. 

This is a portrait of Gi, a great friend of mine. We always catch up with each other when I happen to pass through Brazil and we have done a few photo shots over the years. This was on a hot Saturday afternoon in Lapa, the bohemian centre of Rio de Janeiro. Lapa, even though dizzily crowded with party-goers at night and with people hurrying about their business during weekdays, is eerily empty on weekends during the heat of the midday sun. We were just crossing the sun-bleached square in front of the arcs when I snapped this picture. For me, the smile and the sun capture two of the most iconic features of Rio. 

This was the finishing moment of one of the dance performances during the 2014 Diwali celebration in Wellington. Diwali in NZ has turned into a celebration of Indian culture, with dance and music performances by Indian school and community groups, arts and craft shops and lots of food stalls. It is secular public ritual and has quite a different vibe and atmosphere compared to Diwali in India. I like this shot because of its ephemeral grace and humbleness in the gestures of the dancers. 

The sky over Kaikora was breathtaking. We were preparing for some weekend tramp in the mountains around Kaikora and walked out to this spot by the beach to enjoy the sun. Some seals were playing in the water and lots of people were out and about on this sunny autumn day. I had a Canon 10D and was playing around with different tone options at that time. Being shot in sepia, for me, this shot captures the simplicity and timeless beauty of NZ. 

This is a deeply spiritual picture. I snapped this moment at the end of the street procession during the Vegetarian Festival, a Taoist celebration in Thailand. A spirit medium (ma song) is about to awake from trance and the priest (huat kua) is performing the rites to bring the human back. The incense has a deep spiritual significance here, because the central god takes the form of incense smoke. 

This photo was originally shot in BW. It is a scene from a market on the outskirts of the old city in Damascus. I was teaching in Beirut, Lebanon in 2005 and went to Damascus for a weekend. Meandering aimlessly through the maze of 5,000 year old streets, I came out to this little square where neighbors had organized a small fair with very simple carousels and stalls. These kids happily showed me the goldfish that they had just bought. Simple happiness and pleasures. It is sad to know that these peaceful places have disappeared in the bitter brutality of a civil war.