10. When assumptions are violated - data transformation and non-parametric methods
Log-normally distributed data
Log-normal distribution is very common in many kinds of biological data. These are random
variables logarithm of which follows the normal distribution. As a result, log-normal
variables may range from the zero limit (excluding zero itself) to plus infinity – that is pretty
realistic e.g. for dimensions, mass, time, etc. In contrast to the symmetric normal
distribution, log-normal variables are positively skewed and display a positive correlation
between mean and variance (Fig. 10.1). A straightforward suggestion for such data is to
apply log-transformation to the values to obtain normally distributed variables (Figs 10.1,
10.2, Table 10.1). ANOVA applied on non-transformed and transformed data provides quite
different results (Table 10.1.).
Fig. 10.1. Example of a log-normal variable: effect of job on the length of phone calls. The
left panel shows the boxplot on the ordinary linear scale, while the right panel shows the
same values on the log-scaled y-axis.
Table 10.1. Summaries of ANOVA applied on non-transformed and transformed data
displayed in Fig. 10.1.
Analysis R2 F DF p
non-transformed 0.26 4.13 3,36 0.013
log-transformed 0.42 8.72 3,36 0.0002
Fig. 10.2. Diagnostic plots of ANOVA models applied on non-transformed (upper row) and
log-transformed data (lower row). Note the improved normal fit on the QQplot and
homogeneity of variances after transformation (Residuals vs. Fitted and Scale-Location
plots).
Note that log-transformation is not a simple utility procedure it also affects the
interpretation of the analysis. Log-transformation changes the scale from additive to
multiplicative, i.e. we test the null hypothesis stating that the ratio between population
means is 1 (instead of the difference being 0). We also consider different means – analysis
on log-scale implies testing the geometric means on the original scale. The same applies to
regression coefficients, which become relative rather than absolute numbers e.g. the slope
indicates how many times the response variable will change with a change in the predictor.
An example with log-transformation in linear regression is displayed in Fig. 10.3., 10.4. and
Table 10.2.
Log-transformation is sometimes used for data, which are not log-normally distributed but
are just positively skewed. Such data may contain zeros and thus are not log-transformable.
Instead log (x + constant) transformation must be used. Alternatively, square-root
transformation may be considered for such data.
Note that the analysis results do not depend on the logarithm used – natural and decadic
logarithms are used most frequently. Just beware of being consistent in using the same
logarithm throughout the analysis.
Fig. 10.3. Example of a regression with log-normal variable: how grain yield of maize
depends on the amount of fertilizer applied. The left panel shows the scatterplot on the
ordinary linear scale, while the right panel shows the same values on the log-scaled y-axis.
Table 10.2. ANOVA tables of linear models fitted on non-transformed and transformed data
displayed in Fig. 10.3.
Analysis R2 F DF p
non-transformed 0.10 11.0 1,98 0.0013
log-transformed 0.14 16.05 1,98 0.0001
Fig. 10.4. Diagnostic plots of linear models fitted on non-transformed (upper row of plots)
and log-transformed data (lower row of plots). Note improved normal fit on the QQplot and
improved homogeneity of variances after transformation (Scale-Location plot).
Non-parametric tests
Some distributions cannot be approximated by the normal distribution, and simple
transformations may not helpful. This applies e.g. to many data on the ordinal scale such as
school grades, subjective rankings etc. For such cases, non-parametric tests were developed
(Table 10.3.). These tests replace the original values by their order and use the resulting
order values to test differences in central tendencies (which are not precisely means)
between the samples. These tests are still based on the assumption that the samples come
from the same distribution (which, however, is quite reasonable).
Table 10.3. List of parametric tests and their non-parametric counterparts together with
appropriate R functions.
Parametric test Non-parametric test R function
two-sample t-test Mann-Whitney U test wilcox.test
paired t-test Wilcoxon test wilcox.test with
parameter paired=T
One way ANOVA Kruskal-Wallis test* kruskal.test
Pearson correlation Spearman correlation cor.test with parameter
method=”spearman”
* Dunn test may be used for post-hoc comparisons (function dunnTest in package FSA)
Permutation tests
Permutation tests represent valuable alternatives to parametric or non-parametric tests.
First, a statistic of difference from the null hypothesis (between samples) is defined. That
may be the raw or relative difference or an F-ratio if multiple groups are analyzed. This
statistic is computed for observed data (observed statistic). Subsequently, values of the
response variable are repeatedly permuted (reshuffled), and the same statistic is computed
in each permutation. The p-value is then determined by the formula:
𝑝𝑝 =
𝑥𝑥 + 1
𝑛𝑛𝑝𝑝𝑝𝑝𝑝𝑝𝑝𝑝 + 1
where x is the number of permutations in which test statistic was higher than observed test
statistic, and nperm is the total number of permutations.
How to do in R
1. Log-scaling of graph axes:
scale_y_continuous(trans=’log10’). You can also log-scale
x-axis (scale_x_continuous()) or use ‘log2’ to use 2 as
the log-basis.
2. Log-transformation: function log for natural logarithm,
log10 for decadic
3. Non-parametric tests: see Table 10.3.
4. Permutation tests are available in library coin:
a. permutation-based ANOVA: function oneway_test
b. permutation-based correlation: spearman_test
Both functions require this parameter
distribution=approximate(B=number of permutations)
to be set; B is usually set to 999 or 9999.