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Data analysis – which data departed from normality?
All data departed from normality and were therefore log10 transformed.
Effects on performance and pupil data departed from previous findings, and self-reported assessments suggested that positive mood was difficult to sustain.
Because the data departed from multivariate normality (see Table 2) we used full information maximum likelihood parameter estimates with standard errors that are robust to non-normality (i.e., MLR).
Because the molecular data departed from clock-like evolution, a Bayesian analysis implemented with BEAST ver. 1.4.7 [ 72] was used under a log-normal relaxed molecular clock [ 73] and a Yule pure birth model of speciation to estimate the times of divergence and their credibility intervals in the genus Alnus.
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A further step would be to examine the impact of the survival rates used to generate the synthetic data departing from those assumed in the estimation model, as well as propagating uncertainty in the assumptions about natural history in the estimation procedure.
Before estimating divergence times, likelihood ratio tests were performed using PAUP* 4.0b10s [ 46] to determine if the cyt- b sequence data departed significantly from clocklike behavior.
Before estimating divergence times, a likelihood ratio test was performed on the louse 3-gene data set using PAUP* 4.0b10 [ 62] to determine if the sequence data departed significantly from clocklike behavior.
To test whether the number of rate shifts inferred under the RLC model using the real data departed significantly from the null expectation (zero shifts, i.e. a strict molecular clock), we ran priors-only analyses (i.e. without data) and compared overlap between the two distributions for this parameter [cf. 9].
This is perhaps unsurprising as our data departed in several ways from the ideal conditions for the fitting of standard factor models with maximum likelihood.
Where the spline-interpolated data departed (both positively and negatively) from the Fourier fit by more than a user-specified threshold (see Table 1) the data were again considered unreliable, removed and linearly interpolated from adjacent, reliable values in the spline-fitted series.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com