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Processing and Analysing Animal Trajectories
Tools to handle, manipulate and explore trajectory data, with an emphasis on data from tracked animals. The package is designed to support large studies with several million location records and keep track of units where possible. Data import directly from 'movebank' < https://www.movebank.org/cms/movebank-main> and files is facilitated.
Longitudinal Targeted Maximum Likelihood Estimation
Targeted Maximum Likelihood Estimation ('TMLE') of treatment/censoring specific mean outcome or marginal structural model for point-treatment and longitudinal data.
Tools for Linear Dimension Reduction
Linear dimension reduction subspaces can be uniquely defined using orthogonal projection matrices. This package provides tools to compute distances between such subspaces and to compute the average subspace. For details see Liski, E.Nordhausen K., Oja H., Ruiz-Gazen A. (2016) Combining Linear Dimension Reduction Subspaces
Spatio-Temporal Autologistic Regression Model
Estimates the coefficients of the two-time centered autologistic regression model based on Gegout-Petit A., Guerin-Dubrana L., Li S. "A new centered spatio-temporal autologistic regression model. Application to local spread of plant diseases." 2019.
AI-Driven Code Generation, Explanation and Execution for Data Analysis
Employing artificial intelligence to convert data analysis questions into executable code, explanations, and algorithms. The self-correction feature ensures the generated code is optimized for performance and accuracy. 'mergen' features a user-friendly chat interface, enabling users to interact with the AI agent and extract valuable insights from their data effortlessly.
Compare the Goodness of Fit of Benford's and Blondeau Da Silva's Digit Distributions to a Given Dataset
Allows to compare the goodness of fit of Benford's and Blondeau Da Silva's digit distributions in a dataset. It is used to check whether the data distribution is consistent with theoretical distributions highlighted by Blondeau Da Silva or not (through the dat.distr() function): this ideal theoretical distribution must be at least approximately followed by the data for the use of Blondeau Da Silva's model to be well-founded. It also enables to plot histograms of digit distributions, both observed in the dataset and given by the two theoretical approaches (with the digit.ditr() function). Finally, it proposes to quantify the goodness of fit via Pearson's chi-squared test (with the chi2() function).
Longitudinal Graphical Lasso
For high-dimensional correlated observations, this package carries out the L_1 penalized maximum likelihood
estimation of the precision matrix (network) and the correlation parameters. The correlated data can be
longitudinal data (may be irregularly spaced) with dampening correlation or clustered data with uniform correlation.
For the details of the algorithms, please see the paper Jie Zhou et al. Identifying Microbial Interaction Networks Based on Irregularly Spaced
Longitudinal 16S rRNA sequence data
Yeast-Proteome Secondary-Structure Calculator
An extension for 'NetSurfP-2.0' (Klausen et al. (2019)
Find Related Items and Lexical Dimensions in a Lexicon
Implements code to identify lexical competitors in a given list
of words. We include many of the standard competitor types used in spoken word
recognition research, such as functions to find cohorts, neighbors, and
rhymes, amongst many others. The package includes documentation for using a
variety of lexicon files, including those with form codes made up of multiple
letters (i.e., phoneme codes) and also basic orthographies. Importantly, the
code makes use of multiple CPU cores and vectorization when possible, making
it extremely fast and able to handle large lexicons. Additionally, the package
contains documentation for users to easily write new functions, allowing
researchers to examine other relationships within a lexicon.
Preprint: < https://osf.io/preprints/psyarxiv/8dyru/>. Open access:
Functions Related to ICES Advice
A collection of functions that facilitate computational steps related to advice for fisheries management, according to ICES guidelines. These include methods for calculating reference points and model diagnostics.