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  • in reply to: Mixed effects ANOVA for Latin square designs #103

    I had to remove my previous response because most things I said there were kind of incorrect. But I think I this response should be correct now.

    In your design you have realized all 16 combinations of the factors Correction and Narrative. However, not within-subjects, but only across subjects. This means you can estimate fixed effects for their interaction, but no random slopes for it and no within-subjects ANOVA. In fact, the absence of any replicates for any factor on the individual level, precludes basically any calculation of random-slopes. However, following the logic that in your situation the random variability is confounded with the residual variance, the following mixed model should in principle be appropriate (along the lines discussed here):
    mixed(dv ~ Correction*Narrative + Order + (1|participants), data)

    To make sure that the model is in fact not grossly anti-conservative one could run a simulation study from generated data without effect to see if the alpha-levels are within nominal ranges, but this might be outside what could be expected from a masters thesis (but would be pretty cool, see the previous link for some hints how to do it).

    If Order had more than 4 levels, one could probably also treat it like a random-effects grouping factor (e.g., see here). But with 4 levels that seems not really advisable. You can only hope it does not really effect the results.

    I hope that helps. I would probably go with it.

    in reply to: Mixed effects ANOVA for Latin square designs #98

    Where is Correction in your design? Are these the levels within Order? Does this entail that you had only four specific pairings of Correction and Narrative?

    To know how to set up a mixed model it is important to know if you have replicates for each cell of the design and participant. In other words, did each participant only provide one response per Narrative level or several. For mixed models one usually wants/needs several responses per unit of observation and cell of the design (i.e., replicates) to estimate the full random effects structure.

    I think to get more help the best would be to either post a mockup of your data (as in this example) or your data.

    in reply to: Repeated measures ANOVA for Latin Square designs #91

    In general the afex ANOVA functions are for fully factorial designs. If your design is not fully factorial, I guess it is not possible to use the afex ANOVA functions.

    For analyzing completely replicated latin square designs in R see:

    in reply to: Mixed effects ANOVA for Latin square designs #90

    I am not sure I fully understand the nature of your latin square design without actually seeing the design figure/plot (i.e., I do not understand the meaning of treatment factor, column blocking factor, and row blocking factor). It may help to provide it, especially if there are replications (i.e., given that 4 x 4 = 16 and you have 37 participants, that is quite likely). Example here.

    As long as a single unit of observation (i.e., probably participant) provides data for more than one condition, setting up a mixed model is probably doable. For this question it is important to know if one of the factors (Correction or Narrative) is a within-subjects (i.e., repeated-measures) factor or not.

    Even if none of your factors is a repeated-measures factor, setting up a latin square design with mixed models is possible. An example is given here.

    Note that in any case, the presence of interactions makes an analysis using a latin square approach difficult as it assumes no interaction. An interaction in the data thus invalidates the results and suggests the necessity of collecting new data allowing for an interaction, potentially with a reduced design. But I think it would be helpful to first described exactly what each participant saw to evaluate whether or not a simple mixed model analysis is appropriate and one can have a look at the interaction.

    in reply to: ANOVA with occasional missing observations #83

    Great question as I was honestly surprised afex does not do that automatically. I guess I always remove my NAs from the data before running analyses and hadn’t encountered that before.

    Fortunately, the solution is super simple. We can simply pass na.rm=TRUE to the call of the ANOVA function and this will be passed on to mean() which does the automatic aggregation. Then the mean for each participant and cell are calculated excluding NAs:

    aov_ez("id", "response", sk2011.1[ sk2011.1$what == "affirmation",], 
           within = c("inference", "type"), between = "instruction", na.rm=TRUE)
    # Contrasts set to contr.sum for the following variables: instruction
    # Anova Table (Type 3 tests)
    # Response: response
    #                       Effect    df     MSE         F   ges p.value
    # 1                instruction 1, 38 1072.56      0.12  .001     .73
    # 2                  inference 1, 38  995.53  12.68 **   .11    .001
    # 3      instruction:inference 1, 38  995.53 13.07 ***   .11   .0009
    # 4                       type 1, 38  188.61      0.06 .0001     .81
    # 5           instruction:type 1, 38  188.61    3.04 +  .005     .09
    # 6             inference:type 1, 38  499.82 30.59 ***   .13  <.0001
    # 7 instruction:inference:type 1, 38  499.82  11.33 **   .05    .002
    # ---
    # Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘+’ 0.1 ‘ ’ 1
    # Warning message:
    # More than one observation per cell, aggregating the data using mean (i.e, fun_aggregate = mean)! 
    in reply to: mixed parametric bootstrapping with optimx::nlminb #80

    After contacting pbkrtest author Søren Højsgaard he told me that it was actually a bug in lme4::refit. So I looked into it and wrote a bug fix that was just merged into lme4:

    So either you wait until the new version of lme4 appears on CRAN (and I have no idea when this might be) or you install the development version: library("devtools"); install_github("lme4/lme4",dependencies=TRUE)
    Note that installing the development version might require other dependencies depending on your OS (e.g., RTools on Windows or XCode on Mac).

    in reply to: mixed parametric bootstrapping with optimx::nlminb #79

    The problem appears to be in the function calculating the parametric bootstrap pbkrtest::PBmodcomp:

    ## Linear mixed effects model:
    data(beets, package="pbkrtest")
    sug   <- lmer(sugpct ~ block + sow + harvest + (1|block:harvest), data=beets, REML=FALSE, control =lmerControl(optimizer = "optimx",optCtrl = list(method = "nlminb", starttests = FALSE, kkt = FALSE)))
    sug.h <- update(sug, .~. -harvest)
    PBmodcomp(sug, sug.h, nsim=50)
    # Error in optwrap(object@optinfo$optimizer, ff, x0, lower = lower, control = control$optCtrl,  : 
    #   must specify 'method' explicitly for optimx

    I will contact the author and let you know what comes out of it. I can do little at the time.

    in reply to: mixed parametric bootstrapping with optimx::nlminb #77

    Does it help to load optimx at the clusters before running the code?
    clusterEvalQ(my.cluster, library(optimx))

    If not, please let me know and I will investigate this further.

    in reply to: asymmetrical mixed anova? #73

    In principle mixed models have the same constraint as all statistical models that you cannot estimate parameters for cells or conditions where you have no data at all (i.e., structurally missing). For example, when your control condition does not interact with one other factor (e.g., for your factor A, the control condition only exists for level a1 and not for level a2) then you cannot have an interaction of A with control.

    As far as I understand your design you have 5 between-subjects or independent-samples groups. For each unit of observation in this group you furthermore have pre-test and post-test observations. This would allow to model the data as a 5 x 2 design with factors group and test_time: ~ group*test_time + (test_time|id) (note that the random effects structure assumes that you have replicates for each unit of observation and test_time condition, which you probably should have)

    The problem with this approach is obviously that it flattens out the 2 x 2 design underlying 4 of your 5 groups. I do not see a way how to incorporate this structure with the control in one model. I think there are two ways to address the 2 x 2 structure subsequently, once you have run the initial model and have determined how the control group relates to the other 4 groups. You could either test the 2 x 2 design from the initial model using lsmeans (using a combination of lsmeans, contrast, and test) or run a second model on the reduced data that has a 2 x 2 x 2 design (i.e., your 4 groups times the repeated-measures factor). The second approach seems somewhat more straight forward to implement.

    • This reply was modified 7 years ago by henrik. Reason: clarified ranom effects structure
    in reply to: Significance of random effects #68

    This is not a simple question, but the short answer is that afex does not have a function for automatically testing whether or not a certain random effects term accounts for a significant portion of the variance. The reason for the absence of this functionality is that following Barr, Levy, Scheepers, and Tily (2013) and Schielzeth and Forstmeier (2009) including all possible random effects (i.e., ‘the maximal random effects structure justified by the design’) is the conservative thing to do. So random effects that are part of the design should in principle be included (and there are rumors that reviewers require this).

    A slightly different perspective on this question comes from lme4 author Doug Bates, Harald Baayen, Reinhold Kliegl and others (Bates, Kliegl, Vasishth, & Baayen, 2015; Matuschek, Kliegl, Vasishth, Baayen, & Bates, 2017) who highlight that an overparameterized model (i.e., models that contain more random effects than can be estimated given the current data) may be prone to failing to converge and exhibit reduced statistical power. Note that these authors nevertheless agree that removing random effects for which there is actually random variation is potentially dangerous (in terms of increasing the Type 1 error rate). So the question then becomes what is the threshold for which we want to say that a random effects term is large enough or ‘significant’. In Matuschek et al., they suggest a downward procedure (i.e., beginning with the maximal model and beginning with the largest effect) with alpha = .2 (instead of the more common alpha = .05). Again, the idea is to avoid situations in which a random effects term is reduced that actually shows random variability.

    To gather information about the size of a random effect (irrespective of significance), one can simply call summary on mixed objects:

    sk2_aff <- droplevels(sk2011.2[sk2011.2$what == "affirmation",])
    sk_m1 <- mixed(response ~ instruction*inference*type+(inference*type|id), sk2_aff)

    Which gives:

    Linear mixed model fit by REML ['merModLmerTest']
    Formula: response ~ instruction * inference * type + (inference * type |      id)
       Data: sk2_aff
    REML criterion at convergence: 10393.7
    Scaled residuals: 
        Min      1Q  Median      3Q     Max 
    -3.9241 -0.3314  0.0654  0.3796  3.7675 
    Random effects:
     Groups   Name             Variance Std.Dev. Corr                         
     id       (Intercept)      141.84   11.910                                
              inference1       158.83   12.603   -0.71                        
              type1             39.81    6.310   -0.24 -0.09                  
              type2             10.43    3.230    0.43  0.23 -0.41            
              inference1:type1  54.38    7.374   -0.05 -0.33 -0.55 -0.42      
              inference1:type2   4.33    2.081   -0.39  0.50  0.16 -0.31 -0.31
     Residual                  443.39   21.057                                
    Number of obs: 1134, groups:  id, 63

    The size of the random effects is given by the variance or standard deviation of the parameters (and the variances can be related to the residual variance also given). Note that summary is an lme4 function and no afex function so the output is given in terms of the model parameters and not the factors. So for type, which is a factor with three levels, we have two parameters where neither can be easily mapped to the three factor levels and should be considered jointly (the same is true for the inference:type interaction).
    We can now fit another model for which we remove the highest order random effect, the inference:type interaction. Then we can compare the model fit of the two models using the anova function:

    sk_m2 <- mixed(response ~ instruction*inference*type+(inference+type|id), sk2_aff)
    anova(sk_m1, sk_m2)

    This gives:

    Data: sk2_aff
    sk_m2: response ~ instruction * inference * type + (inference + type | 
    sk_m2:     id)
    sk_m1: response ~ instruction * inference * type + (inference * type | 
    sk_m1:     id)
          Df   AIC   BIC  logLik deviance  Chisq Chi Df Pr(>Chisq)    
    sk_m2 23 10496 10612 -5225.1    10450                             
    sk_m1 34 10462 10633 -5196.9    10394 56.568     11  3.997e-08 ***
    Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

    Here the likelihood ratio tests performed by anova indicates that removing the highest order effect leads to a significant reduction in model fit with chi^2 (11) = 56.57, p < .0001.

    Note that for afex versions prior to 0.17 (which will arrive on CRAN shortly), there was an error in the model labels when calling anova in which case the following produces the same output:
    anova(sk_m1$full_model, sk_m2$full_model, refit = FALSE)

    – Bates, D., Kliegl, R., Vasishth, S., & Baayen, H. (2015). Parsimonious Mixed Models. arXiv:1506.04967 [Stat]. Retrieved from
    – Barr, D. J., Levy, R., Scheepers, C., & Tily, H. J. (2013). Random effects structure for confirmatory hypothesis testing: Keep it maximal. Journal of Memory and Language, 68(3), 255–278.
    – Matuschek, H., Kliegl, R., Vasishth, S., Baayen, H., & Bates, D. (2017). Balancing Type I error and power in linear mixed models. Journal of Memory and Language, 94, 305–315.
    – Schielzeth, H., & Forstmeier, W. (2009). Conclusions beyond support: overconfident estimates in mixed models. Behavioral Ecology, 20(2), 416–420.

    in reply to: Citing afex #61

    The suggested citation at the time of writing is:
    Henrik Singmann, Ben Bolker, Jake Westfall and Frederik Aust (2016). afex: Analysis of Factorial Experiments. R package version 0.16-1.

    However, this changes with any update of afex and the easiest way to find out the current suggestion is to call:

    This produces:

    To cite package ‘afex’ in publications use:
      Henrik Singmann, Ben Bolker, Jake Westfall and Frederik Aust (2016). afex: Analysis of Factorial
      Experiments. R package version 0.16-1.
    A BibTeX entry for LaTeX users is
        title = {afex: Analysis of Factorial Experiments},
        author = {Henrik Singmann and Ben Bolker and Jake Westfall and Frederik Aust},
        year = {2016},
        note = {R package version 0.16-1},
        url = {},

    Btw, citation("package") works for any package and also without any package to learn how to cite R.

    • This reply was modified 7 years, 2 months ago by henrik.
    • This reply was modified 7 years, 2 months ago by henrik.
Viewing 11 posts - 76 through 86 (of 86 total)