2
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I've been trying to figure out how to test (in R) if there are significant differences between the group means of my data because it seems to violate the assumptions of tests that do this (ANOVA, Kruskal-Wallis). The obvious problem I have is that my data have large differences in group variability and relatively small sample sizes by group (11 to 36 observations).

> dput(df_count)
structure(list(Year = c(2018, 2019, 2020, 2017, 2010, 2011, 2013, 
2016, 2021, 2009, 2012), n = c(36L, 34L, 25L, 24L, 12L, 12L, 
12L, 12L, 12L, 11L, 11L)), row.names = c(NA, -11L), class = c("tbl_df", 
"tbl", "data.frame"))

I've read I can't run a Kruskal-Wallis test if I don't have homogeneity of variance or small sample sizes like these. One possible work around I got from a colleague would be to convert my density values to presence absence (anything about 0 gets turned into a 1) and do a chi-square test on the proportion of 0's to 1's, but we weren't sure if that was a good solution. I'd also like to do a pairwise comparison, but again wasn't sure what problem would arise given the properties of this dataset.

My data:

> dput(df)
structure(list(Year = c(2018, 2018, 2018, 2018, 2018, 2018, 2018, 
2018, 2018, 2018, 2018, 2018, 2020, 2020, 2020, 2020, 2020, 2020, 
2020, 2020, 2020, 2020, 2020, 2020, 2020, 2019, 2019, 2019, 2019, 
2019, 2019, 2019, 2019, 2019, 2019, 2019, 2018, 2018, 2018, 2018, 
2018, 2018, 2018, 2018, 2018, 2018, 2018, 2018, 2019, 2019, 2019, 
2019, 2019, 2019, 2019, 2019, 2019, 2019, 2019, 2013, 2013, 2013, 
2013, 2013, 2013, 2013, 2013, 2013, 2013, 2013, 2013, 2009, 2009, 
2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2010, 2010, 
2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 
2011, 2011, 2011, 2011, 2011, 2011, 2011, 2011, 2011, 2011, 2011, 
2012, 2012, 2012, 2012, 2012, 2012, 2012, 2012, 2012, 2012, 2012, 
2016, 2016, 2016, 2016, 2016, 2016, 2016, 2016, 2016, 2016, 2016, 
2016, 2017, 2017, 2017, 2017, 2017, 2017, 2017, 2017, 2017, 2017, 
2017, 2017, 2018, 2018, 2018, 2018, 2018, 2018, 2018, 2018, 2018, 
2018, 2018, 2018, 2019, 2019, 2019, 2019, 2019, 2019, 2019, 2019, 
2019, 2019, 2019, 2019, 2020, 2020, 2020, 2020, 2020, 2020, 2020, 
2020, 2020, 2020, 2020, 2020, 2021, 2021, 2021, 2021, 2021, 2021, 
2021, 2021, 2021, 2021, 2021, 2021, 2017, 2017, 2017, 2017, 2017, 
2017, 2017, 2017, 2017, 2017, 2017, 2017), den = c(0.010339884588578, 
0.00455728179952938, 0.00343679685937641, 0, 0, 0, 0.0026099691969192, 
0.00261493942751616, 0, 0.00758841788700932, 0.00261098669259391, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.00258166076347894, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.00511179097342, 0, 0, 0, 0, 0, 
0, 0, 0.0344957485650341, 0, 0.00260181030586538, 0, 0, 0, 0.0090545203588682, 
0, 0.00264281685601483, 0, 0.0378316032295272, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0.0654230184885466, 0, 0, 0, 0, 0, 0, 0, 0, 0.00183150183150183, 
0, 0.00535045478865704, 0.00260213374967473, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0.00273945867001107, 0, 0, 0, 0, 0.0093124763796496, 
0, 0.0104115475163763, 0.176865881398321, 0, 0.0168260157921274, 
0.00986181407592425, 0.0031893056137876, 0.0254639674849916, 
0, 0, 0, 0, 0, 0, 0.0211521212726769, 0, 0, 0, 0, 0.00516893200484304, 
0, 0, 0.0104424761130064, 0, 0, 0, 0.0421221519735819, 0, 0.00252790953920362, 
0.0206951796482847, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0.00777067045723764, 0.0104825822946628, 0, 0, 0, 0, 0, 0.0129942159892243, 
0, 0, 0, 0.0103953727913794, 0, 0, 0.00259452618256605, 0, 0, 
0, 0, 0.00260317460317461, 0, 0, 0, 0.00260752047062565, 0, 0.00259452618256605, 
0.0026038446052897, 0.0226762329646423, 0, 0.00252708407882677, 
0, 0.00548065139740094, 0, 0, 0, 0.0494424158277803, 0, 0.00748566757311657
)), row.names = c(NA, -201L), class = c("tbl_df", "tbl", "data.frame"
))

Plot of mean density +-standard error bars enter image description here

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2
  • $\begingroup$ Kruskal Wallis is not a test of group means. The usual thing would be Welch(-Satterthwaite) ANOVA (but the small sample size means that your significance level would be sensitive to non-normality). However, I think a big issue is likely to be the assumption of independence you need no matter which of the more usual tests you consider. $\endgroup$
    – Glen_b
    Commented May 11, 2022 at 23:37
  • $\begingroup$ Each value is also associated with the location in which it was collected (“den” = no. of shrimp/area surveyed at each site and season/year sampled without replacement - nothing thrown back). $\endgroup$
    – Nate
    Commented May 12, 2022 at 2:18

1 Answer 1

3
$\begingroup$

Kruskal-Wallis is a non-parametric rank-based test. Under its null hypothesis observations in one group are not larger than observations in any other group. This means that Kruskal-Wallis compares medians, not means.

The issue with using Kruskal-Wallis on your data is that it contains 77% zeros and so there are a lot of ties. The p-value has to be corrected for all those ties.

Note: Variance is not an appropriate summary for your data because it consists mostly of zeros and the distribution of the densities is very skewed. Tests that are sensitive to non-normaliity are not appropriate and symmetric confidence intervals as shown in your plot don't make much sense either.

kruskal.test(den ~ Year, data = data)
#> 
#>  Kruskal-Wallis rank sum test
#> 
#> data:  den by Year
#> Kruskal-Wallis chi-squared = 29.435, df = 10, p-value = 0.001059
# p-value adjusted for ties

However, why treat time (in years) as a categorical variable? You have observations from 11 consecutive years. A better plot of your data shows that the proportion of distribution of non-zero data points increases between 2016 and 2018 and then declines again.

This suggests to treat time as continuous and to model its effect with a smooth nonlinear function. Here is an analysis using proportional odds regression with restricted cubic splines as implemented in the rms package.

Note: Proportional odds regression generalizes the Kruskal-Wallis test [1].

library("rms")

anova(orm(den ~ rcs(Year, 4), data = data))
#>                 Wald Statistics          Response: den 
#> 
#>  Factor     Chi-Square d.f. P     
#>  Year       10.04      3    0.0182
#>   Nonlinear  9.26      2    0.0098
#>  TOTAL      10.04      3    0.0182

[1] Biostatistics for Biomedical Research course notes. Available online.


R code to make the small multiples plot above.

data %>%
  mutate(
    den = round(den, 3)
  ) %>%
  ggplot(
    aes(den)
  ) +
  geom_bar(
    width = 0.001
  ) +
  facet_wrap(
    ~Year,
    ncol = 4
  )
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21
  • 1
    $\begingroup$ And if you are interested in pairwise comparisons, it will still be better to fit the regression model. This will give you model-based p-values for the comparisons (also called contrasts). If you compare pairs of years separately, you'll have to make multiplicity adjustment for multiple tests. $\endgroup$
    – dipetkov
    Commented May 11, 2022 at 22:54
  • 1
    $\begingroup$ Imagine there are two tests you're choosing between, on the basis of what you find in the sample you want to run your test on. The frequentist properties of the tests you run are no longer what you want them to be. For example, the actual significance level for both tests will tend to shift away from the level you chose. The problem is related to this issue: en.wikipedia.org/wiki/Testing_hypotheses_suggested_by_the_data but in a somewhat less direct form. $\endgroup$
    – Glen_b
    Commented May 12, 2022 at 0:47
  • 1
    $\begingroup$ Some of the posts/comments at stats.stackexchange.com/questions/2492/… are also relevant - for example Harvey Motulsky's answer there is short but on point. I have some much longer answers in other threads but I don't wish to labor the point. It's not about heteroskedasticity but on the usefulness of testing the comments largely carry over. $\endgroup$
    – Glen_b
    Commented May 12, 2022 at 1:00
  • 2
    $\begingroup$ Confidence intervals don't have to be symmetric. Many CIs have the form mean +/- 2 SD, so are symmetric but that's not a requirement. I'm not sure CIs make sense for your data which is bounded below by 0 and so most measurements are 0s. But you could consider asking a new question explicitly about CIs. No-one else is reading such a long thread of comments.... $\endgroup$
    – dipetkov
    Commented May 14, 2022 at 18:19
  • 3
    $\begingroup$ Last comment from me also: Bootstrapping is a good idea, but you'd run into another issue. To estimate a CI with bootstrapping you need to estimate quantiles. In your case [0, X95] where X95 is the 95th quantile seems a reasonable CI. The issue is that for each year you have few observations, so it's hard to see how you can bootstrap the value such that Pr{X < X95} = .95. Limits are harder to estimate than central quantities like mean and median. Need more observations to estimate what's happening in the tails, so to speak. $\endgroup$
    – dipetkov
    Commented May 14, 2022 at 18:34

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