Simulate expected equilibrium length composition, yield-per-recruit, and the spawning potential ratio (SPR) using the length-based SPR (LBSPR) model. Fit the LBSPR model to length data to estimate selectivity, relative apical fishing mortality, and the spawning potential ratio for data-limited fisheries. See Hordyk et al (2016) <doi:10.1139/cjfas-2015-0422> for more information about the LBSPR assessment method.

The aim of neo2R is to provide simple and low level connectors for querying neo4j graph databases (<https://neo4j.com/>). The objects returned by the query functions are either lists or data.frames with very few post-processing. It allows fast processing of queries returning many records. And it let the user handle post-processing according to the data model and his needs.

Next-Generation Clustered Heat Maps (NG-CHMs) allow for dynamic exploration of heat map data in a web browser. NGCHM allows users to create both stand-alone HTML files containing a Next-Generation Clustered Heat Map, and .ngchm files to view in the NG-CHM viewer. See Ryan MC, Stucky M, et al (2020) <doi:10.12688/f1000research.20590.2> for more details.

K-nearest neighbor search for projected and non-projected sf spatial layers. Nearest neighbor search uses (1) C code from GeographicLib for lon-lat point layers, (2) function knn() from package nabor for projected point layers, or (3) function st_distance() from package sf for line or polygon layers. The package also includes several other utility functions for spatial analysis.

Provide methods for estimating optimal treatment regimes in survival contexts with Kaplan-Meier-like estimators when no unmeasured confounding assumption is satisfied (Jiang, R., Lu, W., Song, R., and Davidian, M. (2017) <doi:10.1111/rssb.12201>) and when no unmeasured confounding assumption fails to hold and a binary instrument is available (Xia, J., Zhan, Z., Zhang, J. (2022) <arXiv:2210.05538>).

Plot malaria parasite genetic data on two or more episodes. Compute per-person posterior probabilities that each Plasmodium vivax (Pv) recurrence is a recrudescence, relapse, or reinfection (3Rs) using per-person P. vivax genetic data on two or more episodes and a statistical model described in Taylor, Foo and White (2022) <doi:10.1101/2022.11.23.22282669>. Plot per-recurrence posterior probabilities.

Village potential statistics (PODES) collects various information on village potential and challenges faced by villages in Indonesia. Information related to village potential includes economy, security, health, employment, communication and information, sports, entertainment, development, community empowerment, education, socio-culture, transportation in the village. Information related to challenges includes natural disasters, public health, environmental pollution, social problems and security disturbances that occur in the village.

This package provides tools for writing and debugging R code. Provides: %.>% dot-pipe (an S3 configurable pipe), unpack/to (R style multiple assignment/return), build_frame()'/'draw_frame() ('data.frame example tools), qc() (quoting concatenate), := (named map builder), let() (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by gtools::strmacro() and base::bquote()'), and more.

This package provides a visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using ggplot2'. Multiple sequence alignment can easily be combined with other ggplot2 plots, such as phylogenetic tree Visualized by ggtree', boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.

All alleles from the IPD IMGT/HLA <https://www.ebi.ac.uk/ipd/imgt/hla/> and IPD KIR <https://www.ebi.ac.uk/ipd/kir/> database for Homo sapiens. Reference: Robinson J, Maccari G, Marsh SGE, Walter L, Blokhuis J, Bimber B, Parham P, De Groot NG, Bontrop RE, Guethlein LA, and Hammond JA KIR Nomenclature in non-human species Immunogenetics (2018), in preparation.

This package provides methods and tools for estimating, simulating and forecasting of so-called BEKK-models (named after Baba, Engle, Kraft and Kroner) based on the fast Berndtâ Hallâ Hallâ Hausman (BHHH) algorithm described in Hafner and Herwartz (2008) <doi:10.1007/s00184-007-0130-y>. For an overview, we refer the reader to Fülle et al. (2024) <doi:10.18637/jss.v111.i04>.

Distributes Gaussian process calculations across nodes in a distributed memory setting, using Rmpi. The bigGP class provides high-level methods for maximum likelihood with normal data, prediction, calculation of uncertainty (i.e., posterior covariance calculations), and simulation of realizations. In addition, bigGP provides an API for basic matrix calculations with distributed covariance matrices, including Cholesky decomposition, back/forwardsolve, crossproduct, and matrix multiplication.

This package provides access to consolidated information from the Brazilian Federal Government Payment Card. Includes functions to retrieve, clean, and organize data directly from the Transparency Portal <https://portaldatransparencia.gov.br/download-de-dados/cpgf/> and a curated dataset hosted on the Open Science Framework <https://osf.io/z2mxc/>. Useful for public spending analysis, transparency research, and reproducible workflows in auditing or investigative journalism.

Fast C++'-backed tools for computing conspecific and total neighborhood basal area in mapped forest plots. Includes unweighted and distance-weighted neighborhoods, multiple radii, decay kernels, and basic edge correction. Outputs are model-ready covariates for forest competition, growth, and survival models, following neighborhood modeling workflows commonly used in spatial ecology (e.g., Hülsmann et al. 2024 <doi:10.1038/s41586-024-07118-4>).

This package provides functions to impute large gaps within time series based on Dynamic Time Warping methods. It contains all required functions to create large missing consecutive values within time series and to fill them, according to the paper Phan et al. (2017), <DOI:10.1016/j.patrec.2017.08.019>. Performance criteria are added to compare similarity between two signals (query and reference).

Estimation of the total population size from capture-recapture data efficiently and with low bias implementing the methods from Das M, Kennedy EH, and Jewell NP (2021) <arXiv:2104.14091>. The estimator is doubly robust against errors in the estimation of the intermediate nuisance parameters. Users can choose from the flexible estimation models provided in the package, or use any other preferred model.

Gene regulatory network constructed using combined score obtained from individual network inference method. The combined score measures the significance of edges in the ensemble network. Fisher's weighted method has been implemented to combine the outcomes of different methods based on the probability values. The combined score follows chi-square distribution with 2n degrees of freedom. <doi:10.22271/09746315.2020.v16.i3.1358>.

R companion to Tsay (2005) Analysis of Financial Time Series, second edition (Wiley). Includes data sets, functions and script files required to work some of the examples. Version 0.3-x includes R objects for all data files used in the text and script files to recreate most of the analyses in chapters 1-3 and 9 plus parts of chapters 4 and 11.

This package provides two new layer types for displaying image data as layers within the Grammar of Graphics framework. Displays images using either a rectangle interface, with a fixed bounding box, or a point interface using a central point and general size parameter. Images can be given as local JPEG or PNG files, external resources, or as a list column containing raster image data.

Collection of tools that facilitates data access and workflow for spatial analysis of Argentina. Includes historical information from censuses, administrative limits at different levels of aggregation, location of human settlements, among others. Since it is expected that the majority of users will be Spanish-speaking, the documentation of the package prioritizes this language, although an effort is made to also offer annotations in English.

Analysis of plant pathogen pathotype survey data. Functions provided calculate distribution of susceptibilities, distribution of complexities with statistics, pathotype frequency distribution, as well as diversity indices for pathotypes. This package is meant to be a direct replacement for Herrmann, Löwer and Schachtel's (1999) <doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, HaGiS', previously used for pathotype analysis.

Implementation of icosahedral grids in three dimensions. The spherical-triangular tessellation can be set to create grids with custom resolutions. Both the primary triangular and their inverted penta-hexagonal grids can be calculated. Additional functions are provided that allow plotting of the grids and associated data, the interaction of the grids with other raster and vector objects, and treating the grids as a graphs.

These functions calculate the taxonomic measures presented in Miranda-Esquivel (2016). The package introduces Jack-knife resampling in evolutionary distinctiveness prioritization analysis, as a way to evaluate the support of the ranking in area prioritization, and the persistence of a given area in a conservation analysis. The algorithm is described in: Miranda-Esquivel, D (2016) <DOI:10.1007/978-3-319-22461-9_11>.

The kernel ridge regression and the gradient matching algorithm proposed in Niu et al. (2016) <https://proceedings.mlr.press/v48/niu16.html> and the warping algorithm proposed in Niu et al. (2017) <DOI:10.1007/s00180-017-0753-z> are implemented for parameter inference in differential equations. Four schemes are provided for improving parameter estimation in odes by using the odes regularisation and warping.