Ninety-four new packages stuck to CRAN in July. Here are my “Top 40” selections in thirteen categories: Climate Modeling, Computational Methods, Data, Ecology, Genomics, Machine Learning, Mathematics, Medicine, Networks, Proteomics, Statistics, Utilities, and Visualization.
climetrics v1.0-5: Provides a framework that facilitates the spatio-temporal analysis of climate dynamics through exploring and measuring different dimensions of climate change in space and time. See the vignette.
HurreconR v1.0: Implements the HURRECON model which estimates wind speed, wind direction, enhanced Fujita scale wind damage, and duration of EF0 to EF5 winds as a function of hurricane location and maximum sustained wind speed. See Boose et al. (2001) and Boose et al. (2004) for background, and the vignette for an overview.
TrenchR v0.1.0: Provides tools for translating environmental change into organism response. The biophysical modeling tools include both general models for heat flows and specific models to predict body temperatures for a variety of ectothermic taxa. See Gates (1980) for background. There are vignettes on Allometries and conversions, Estimating microclimates, and Estimating body temperatures.
elastes v0.1.6: Provides functions to compute functional elastic shape means over sets of open planar curves using a novel approach where planar curves are treated as complex functions. Also, a full Procrustes mean is estimated from the corresponding smoothed Hermitian covariance surface. See Steyer et al. (2022) and Stöcker et. al. (2022) for background and the vignette for examples.
rgrass v0.3-3: Implements a new interface to the GRASS geographical information system that supports both starting R from within the GRASS environment, or running a free-standing R session in a temporary GRASS location. There is an Introduction and a vignette on object formats.
riverconn v0.3.22: Provides functions to calculate indices for river network connectivity. See Jumani et al. (2021) for a review of the incdices and Baldan et al. (2022) for a list of package capabilities and architecture. Have a look at the vignette for examples.
dcifer v1.1.1: Implements Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. See Gerlovina et al. (2022) for the details, and the vignette for an example.
etree v0.1.0: Provides functions to implement Energy Trees, statistical models that perform classification and regression with structured and mixed-type data. See Giubilei et al. (2022) for a description of Energy Trees and the vignettes eforest and etree for examples.
LDABiplots v0.1.2: Provides tools to extract, explore, analyze, and visualize news published on the web by digital newspapers using Latent Dirichlet and machine learning algorithms. See Ble et al. (2003) and Gabriel (1971) for background. There are English and Spanish versions of the vignette.
mildsvm v0.4.0: Implements a support vector machine classifier for weakly supervised, multiple instance data. See Kent and Yu (2022) and Muandet et al. (2012) for the theory and README for an example.
activeAnalyzer v1.0.4: Provides a tool to analyse Actigraphy accelerometer data using PROactive Physical Activity in COPD (chronic obstructive pulmonary disease) instruments. See the vignette for examples.
pedbp v1.0.0: Provides data and utilities for estimating pediatric blood pressure percentiles by sex, age, and height. See Lo et al. (2013) and Martin et al. (2022) for background, and the vignette for an overview.
ergm.multi v0.1.0: Provides a set of extensions for the
ergm package to fit multilayer, multiplex, and multirelational networks as well as samples of multiple networks. See Krivitsky et al. (2020) and Krivitsky et, al. (2022) for the details and the vignette for an extended example.
Families v1.0.1: Provides tools to study kinship networks, grand parenthood, and double burden (presence of children and oldest old parents) in virtual population produced by
VirtualPop. See the vignette for examples.
promor v0.1.0: Implements a comprehensive set of tools for label-free proteomics data analysis and machine learning modeling including differential expression analysis, predictive modeling and performance assessment. Data from MaxQuant may be used. See the vignette for an introduction.
GPCERF v0.1.0: Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. See Ren et al. (2021). Have a look at the Introduction and the vignettes Full Gaussian Process and Nearest-neighbor Gaussian Process.
lnmCluster v0.3.1: Extends the logistic normal multinomial (LNM) clustering model proposed by Fang and Subedi (2020) to provide LNM clustering for compositional data. Details of model assumptions and interpretation can be found in the papers Tu & Subedi (2021) and Tu & Subedi (2022). See the vignette for an example.
tlars v0.0.1: Provides functions to compute the solution path of the Terminating-LARS (T-LARS) algorithm. See Machkour et al. 2022, Efron et al. (2004) and Tibshirani (1996) for the theory, and the vignette for examples.
datadictionary v0.1.0: Provides tools to creates a data dictionary from any dataset in an R environment. It includes functions to add variable labels and write to Excel.
dtrackr v0.2.4: Provides tools to track and document
dplyr data pipelines. As you filter, mutate, and join your way through a data set, functions seamlessly track data flow and generate publication ready documentation of the data pipeline. See the vignettes Consort statment example, Configuration example, Basic Operation, and Joining data pipelines.
ixplorer v0.2.2: Provides tools to create and view tickets in gitea, a self-hosted
git service, using an RStudio addin. It includes helper functions to publish documentation and use
git. There are several vignettes including ixplorer basics and Credential management.
nextGenShinyApps v1.5: Provides responsive tools for designing and developing
Shiny dashboards and applications. The scripts and style sheets are based on
Bootstrap. See the vignette for examples.
renderthis v0.1.0: Provides tools to render slides to different formats, including
mp4, as well as tool to make a
png file of the first slide of a presentation that is re-sized for sharing on social media. There is an Overview and a vignette on basic usage.
ggpackets v0.2.0: Provides tools to create groups of
ggplot2 layers that can be easily migrated from one plot to another, reducing redundant code and improving the ability to format many plots that draw from the same source. See the Getting Started Guide and the vignettes Composing Templates & Functions and Misc Examples.