Design of Experiments and Factorial Plans Utilities

A number of functions to create and analyze factorial plans according to the Design of Experiments (DoE) approach, with the addition of some utility function to perform some statistical analyses. DoE approach follows the approach in "Design and Analysis of Experiments" by Douglas C. Montgomery (2019, ISBN:978-1-119-49244-3). The package also provides utilities used in the course "Analysis of Data and Statistics" at the University of Trento, Italy.

A Crew Launcher Plugin for AWS Batch

In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'crew.aws.batch' package extends the 'mirai'-powered 'crew' package with a worker launcher plugin for AWS Batch. Inspiration also comes from packages 'mirai' by Gao (2023) < https://github.com/r-lib/mirai>, 'future' by Bengtsson (2021) , 'rrq' by FitzJohn and Ashton (2023) < https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) ), and 'batchtools' by Lang, Bischl, and Surmann (2017). .

Similarity-Based Segmentation of Multidimensional Signals

A dynamic programming solution to segmentation based on maximization of arbitrary similarity measures within segments. The general idea, theory and this implementation are described in Machne, Murray & Stadler (2017) . In addition to the core algorithm, the package provides time-series processing and clustering functions as described in the publication. These are generally applicable where a `k-means` clustering yields meaningful results, and have been specifically developed for clustering of the Discrete Fourier Transform of periodic gene expression data (`circadian' or `yeast metabolic oscillations'). This clustering approach is outlined in the supplemental material of Machne & Murray (2012) ), and here is used as a basis of segment similarity measures. Notably, the time-series processing and clustering functions can also be used as stand-alone tools, independent of segmentation, e.g., for transcriptome data already mapped to genes.

Compute Decision Interval and Average Run Length for CUSUM Charts

Computation of decision intervals (H) and average run lengths (ARL) for CUSUM charts. Details of the method are seen in Hawkins and Olwell (2012): Cumulative sum charts and charting for quality improvement, Springer Science & Business Media.

Asymptotic Classification Theory for Cognitive Diagnosis

Cluster analysis for cognitive diagnosis based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; ). Given the sample statistic of sum-scores, cluster analysis techniques can be used to classify examinees into latent classes based on their attribute patterns. In addition to the algorithms used to classify data, three labeling approaches are proposed to label clusters so that examinees' attribute profiles can be obtained.

Crew Launcher Plugins for Traditional High-Performance Computing Clusters

In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'crew.cluster' package extends the 'mirai'-powered 'crew' package with worker launcher plugins for traditional high-performance computing systems. Inspiration also comes from packages 'mirai' by Gao (2023) < https://github.com/r-lib/mirai>, 'future' by Bengtsson (2021) , 'rrq' by FitzJohn and Ashton (2023) < https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) ), and 'batchtools' by Lang, Bischl, and Surmann (2017). .

'FASTA' ML and ‘altall’ Sequences from IQ-TREE .state Files

Takes a .state file generated by IQ-TREE as an input and, for each ancestral node present in the file, generates a FASTA-formatted maximum likelihood (ML) sequence as well as an ‘AltAll’ sequence in which uncertain sites, determined by the two parameters thres_1 and thres_2, have the maximum likelihood state swapped with the next most likely state as described in Geeta N. Eick, Jamie T. Bridgham, Douglas P. Anderson, Michael J. Harms, and Joseph W. Thornton (2017), "Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty" .

Data sets from Devore's "Prob and Stat for Eng (7th ed)"

Data sets and sample analyses from Jay L. Devore (2008), "Probability and Statistics for Engineering and the Sciences (7th ed)", Thomson.

Efficient Determination of Sample Size in Balanced Design of Experiments

For a balanced design of experiments, this package calculates the sample size required to detect a certain standardized effect size, under a significance level. This package also provides three graphs; detectable standardized effect size vs power, sample size vs detectable standardized effect size, and sample size vs power, which show the mutual relationship between the sample size, power and the detectable standardized effect size. The detailed procedure is described in R. V. Lenth (2006-9) < https://homepage.divms.uiowa.edu/~rlenth/Power/>, Y. B. Lim (1998), M. A. Kastenbaum, D. G. Hoel and K. O. Bowman (1970) , and Douglas C. Montgomery (2013, ISBN: 0849323312).

Forest Yield Tables for Northwest Germany and their Application

The new yield tables developed by the Northwest German Forest Research Institute (NW-FVA) provide a forest management tool for the five main commercial tree species oak, beech, spruce, Douglas-fir and pine for northwestern Germany. The new method applied for deriving yield tables combines measurements of growth and yield trials with growth simulations using a state-of-the-art single-tree growth simulator. By doing so, the new yield tables reflect the current increment level and the recommended graduated thinning from above is the underlying management concept. The yield tables are provided along with methods for deriving the site index and for interpolating between age and site indices and extrapolating beyond age and site index ranges. The inter-/extrapolations are performed traditionally by the rule of proportion or with a functional approach.