Correction: A statistical test and sample size recommendations for comparing community composition following PCA.
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ABSTRACT:
SUBMITTER: Skalski JR
PROVIDER: S-EPMC8409637 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Many investigations of anthropogenic and natural impacts in ecological systems attempt to detect differences in ecological variables or community composition. Frequently, ordination procedures such as principal components analysis (PCA) or canonical correspondence analysis (CCA) are used to simplify such complex data sets into a set of primary factors that express the variation across the original variables. Scatterplots of the first and second principal components are then used to visually inspect for differences in community composition between treatment groups. We present a multidimensional extension of analysis of variance based on an analysis of distance (ANODIS) that can be used to formally test for differences in community composition using 1, 2, or more dimensions of a PCA or CCA of the original sample observations. The statistical tests of significance are based on F-statistics adapted for the analysis of this multidimensional data. Because the analysis is parametric, power and sample size calculations useful in the design of field studies can be readily computed. The use of ANODIS is illustrated using bivariate PCA scatterplots from three published studies. Statistical power calculations using the noncentral F-distribution are illustrated.
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Project description:Growth reference centile charts are widely used in child health to assess weight, height and other age-varying measurements. The centiles are easy to construct from reference data, using the LMS method or GAMLSS (Generalised Additive Models for Location Scale and Shape). However, there is as yet no clear guidance on how to design such studies, and in particular how many reference data to collect, and this has led to study sizes varying widely. The paper aims to provide a theoretical framework for optimally designing growth reference studies based on cross-sectional data. Centiles for weight, height, body mass index and head circumference, in 6878 boys aged 0-21 years from the Fourth Dutch Growth Study, were fitted using GAMLSS. The effect on precision of varying the sample size and the distribution of measurement ages (sample composition) was explored by fitting a series of GAMLSS models to simulated data. Sample composition was defined as uniform on the ageλ scale, where λ was chosen to give constant precision across the age range. Precision was measured on the z-score scale, and was the same for all four measurements, with a standard error of 0.041 z-score units for the median and 0.066 for the 2nd and 98th centiles. Compared to a naïve calculation, the process of smoothing the centiles increased the notional sample size two- to threefold by 'borrowing strength'. The sample composition for estimating the median curve was optimal for λ=0.4, reflecting considerable over-sampling of infants compared to children. However, for the 2nd and 98th centiles, λ=0.75 was optimal, with less infant over-sampling. The conclusion is that both sample size and sample composition need to be optimised. The paper provides practical advice on design, and concludes that optimally designed studies need 7000-25,000 subjects per sex.
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Project description:BackgroundMargin Reflex Distance 1(MRD 1) only describes the central height of upper eyelid and relies on the examiner's experience and disregards eyelid contour abnormalities. Therefore MRD 1 may not be sufficient for an acceptable result to evaluate the outcomes of ptosis surgery. The primary purpose of this study was to assess outcomes of unilateral ptosis correction based on parameters including degree of symmetry, MRD 1, peak height of the upper lid, temporal and nasal ocular surface area, and temporal/nasal area ratio with an objective, quantitative, and repeatable method.MethodsThis study was designed as a retrospective non-randomized case-control study. Medical records of the patients with unilateral ptosis between October 2015 and December 2020 were reviewed. Patients with unilateral ptosis who underwent surgical correction and levator function of 5 mm or greater were included in the study. Two groups were defined; ptotic eye was case group and contralateral eye was control group. Data analysis was performed Image J and Matlab softwares.ResultsThirty-four patients were included in the study. Mean age of patients was 58.8 ± 12.7 years (range 15-75 years). Mean follow-up time was 19.5 ± 7.3 months (range 8-40 months). Four patients were diagnosed with congenital ptosis and 30 patients aponeurotic ptosis. Mean preoperative degree of symmetry for overall eyelid contour was 36.6 ± 27.5% (range 1-92%). Mean postoperative degree of symmetry for overall eyelid contour was 72.4 ± 16.5% (range 55-92%). Temporal/Nasal (T/N) area ratios for contralateral normal eye was 1.19 pre-postoperative, and it was 1.11 preoperatively, 1.15 postoperatively for operated ptotic eye.ConclusionsThis study primarily demonstrated a quantitative, objective, and repeatable method to investigate the degree of symmetry after eyelid surgeries. Secondly, this study suggested that T/N ratio may not be a reliable parameter to evaluate the eyelid symmetry.
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Project description:Background: Since the early 2010s, the neuroimaging field has paid more attention to the issue of false positives. Several journals have issued guidelines regarding statistical thresholds. Three papers have reported the statistical analysis of the thresholds used in fMRI literature, but they were published at least 3 years ago and surveyed papers published during 2007-2012. This study revisited this topic to evaluate the changes in this field. Methods: The PubMed database was searched to identify the task-based (not resting-state) fMRI papers published in 2017 and record their sample sizes, inferential methods (e.g., voxelwise or clusterwise), theoretical methods (e.g., parametric or non-parametric), significance level, cluster-defining primary threshold (CDT), volume of analysis (whole brain or region of interest) and software used. Results: The majority (95.6%) of the 388 analyzed articles reported statistics corrected for multiple comparisons. A large proportion (69.6%) of the 388 articles reported main results by clusterwise inference. The analyzed articles mostly used software Statistical Parametric Mapping (SPM), Analysis of Functional NeuroImages (AFNI), or FMRIB Software Library (FSL) to conduct statistical analysis. There were 70.9%, 37.6%, and 23.1% of SPM, AFNI, and FSL studies, respectively, that used a CDT of p ? 0.001. The statistical sample size across the articles ranged between 7 and 1,299 with a median of 33. Sample size did not significantly correlate with the level of statistical threshold. Conclusion: There were still around 53% (142/270) studies using clusterwise inference that chose a more liberal CDT than p = 0.001 (n = 121) or did not report their CDT (n = 21), down from around 61% reported by Woo et al. (2014). For FSL studies, it seemed that the CDT practice had no improvement since the survey by Woo et al. (2014). A few studies chose unconventional CDT such as p = 0.0125 or 0.004. Such practice might create an impression that the threshold alterations were attempted to show "desired" clusters. The median sample size used in the analyzed articles was similar to those reported in previous surveys. In conclusion, there seemed to be no change in the statistical practice compared to the early 2010s.
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