Allows identification of palettes derived from LTER (Long Term Ecological Research) photographs based on user criteria. Also facilitates extraction of palettes from users photos directly.

Create maps made of lines. The package contains one function: linemap(). linemap() displays a map made of lines using a raster or gridded data.

L-systems or Lindenmayer systems are parallel rewriting systems which can be used to simulate biological forms and certain kinds of fractals. Briefly, in an L-system a series of symbols in a string are replaced iteratively according to rules to give a more complex string. Eventually, the symbols are translated into turtle graphics for plotting. Wikipedia has a very good introduction: en.wikipedia.org/wiki/L-system This package provides basic functions for exploring L-systems.

Lights Out is a puzzle game consisting of a grid of lights that are either on or off. Pressing any light will toggle it and its adjacent lights. The goal of the game is to switch all the lights off. This package provides an interface to play the game on different board sizes, both through the command line or with a visual application. Puzzles can also be solved using the automatic solver included. View a demo online at <https://daattali.com/shiny/lightsout/>.

This package provides methods for estimation and statistical inference on directional and fluctuating selection in age-structured populations.

Fit the log binomial regression model (LBM) by Exact method. Limited parameter space of LBM causes trouble to find admissible estimates and fail to converge when MLE is close to or on the boundary of space. Exact method utilizes the property of boundary vectors to re-parametrize the model without losing any information, and fits the model on the standard fitting algorithm with no convergence issues.

Create small multiples of several leaflet web maps with (optional) synchronised panning and zooming control. When syncing is enabled all maps respond to mouse actions on one map. This allows side-by-side comparisons of different attributes of the same geometries. Syncing can be adjusted so that any combination of maps can be synchronised.

Perform pairwise likelihood inference in latent autoregressive count models. See Pedeli and Varin (2020) for details.

Generate a local library copy with relevant packages. All packages currently found within the search path - except base packages - will be copied to the directory provided and can be used later on with the .libPaths() function.

An implementation of list comprehensions as purely syntactic sugar with a minor runtime overhead. It constructs nested for-loops and executes the byte-compiled loops to collect the results.

An emulator designed for rapid sequential emulation (e.g., Markov chain Monte Carlo applications). Works via extension of the laGP approach by Gramacy and Apley (2015 <doi:10.1080/10618600.2014.914442>). Details are given in Rumsey et al. (2023 <doi:10.1002/sta4.576>).

This package performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is provided. Wrapper routines for blackbox optimization under mixed equality and inequality constraints via an augmented Lagrangian scheme, and for large scale computer model calibration, are also provided. For details and tutorial, see Gramacy (2016 <doi:10.18637/jss.v072.i01>.

Log-analytic methods intended for testing multiplicative effects.

This package provides a high level interface for torch providing utilities to reduce the the amount of code needed for common tasks, abstract away torch details and make the same code work on both the CPU and GPU'. It's flexible enough to support expressing a large range of models. It's heavily inspired by fastai by Howard et al. (2020) <doi:10.48550/arXiv.2002.04688>, Keras by Chollet et al. (2015) and PyTorch Lightning by Falcon et al. (2019) <doi:10.5281/zenodo.3828935>.

This package provides a set of functions to locate some programs available on the user machine. The package provides functions to locate Node.js', npm', LibreOffice', Microsoft Word', Microsoft PowerPoint', Microsoft Excel', Python', pip', Mozilla Firefox and Google Chrome'. User can test the availability of a program with eventually a version and call it with function system2() or system(). This allows the use of a single function to retrieve the path to a program regardless of the operating system and its configuration.

Recursive partition algorithms designed for fitting survival trees with left-truncated and right-censored (LTRC) data, as well as interval-censored data. The LTRC trees can also be used to fit survival trees with time-varying covariates.

Determine a Prototype from a number of runs of Latent Dirichlet Allocation (LDA) measuring its similarities with S-CLOP: A procedure to select the LDA run with highest mean pairwise similarity, which is measured by S-CLOP (Similarity of multiple sets by Clustering with Local Pruning), to all other runs. LDA runs are specified by its assignments leading to estimators for distribution parameters. Repeated runs lead to different results, which we encounter by choosing the most representative LDA run as prototype.

An implementation of logistic normal multinomial (LNM) clustering. It is an extension of LNM mixture model proposed by Fang and Subedi (2020) <arXiv:2011.06682>, and is designed for clustering compositional data. The package includes 3 extended models: LNM Factor Analyzer (LNM-FA), LNM Bicluster Mixture Model (LNM-BMM) and Penalized LNM Factor Analyzer (LNM-FA). There are several advantages of LNM models: 1. LNM provides more flexible covariance structure; 2. Factor analyzer can reduce the number of parameters to estimate; 3. Bicluster can simultaneously cluster subjects and taxa, and provides significant biological insights; 4. Penalty term allows sparse estimation in the covariance matrix. Details for model assumptions and interpretation can be found in papers: Tu and Subedi (2021) <arXiv:2101.01871> and Tu and Subedi (2022) <doi:10.1002/sam.11555>.

Offers a variety of color palettes inspired by art, nature, and personal inspirations. Each palette is accompanied by a unique backstory, enriching the understanding and significance of the colors.

Translates R help documentation on the fly by using a Large Language model of your choice. If you are using RStudio or Positron the translated help will appear in the help pane.

Estimate and confidence/credible intervals for an unknown regressor x0 given an observed y0.

This package provides flexible but lightweight logging facilities for R scripts. Supports priority levels for logs and messages, flagging messages, capturing script output, switching logs, and logging to files or connections.

This package implements bootstrap methods for linear regression models with errors following a time-varying process, focusing on approximating the distribution of the least-squares estimator for regression models with locally stationary errors. It enables the construction of bootstrap and classical confidence intervals for regression coefficients, leveraging intensive simulation studies and real data analysis.

An interface for NetLogo <https://www.netlogo.org> that enables programmatic setup and execution of simulations. Designed to facilitate integrating NetLogo models into reproducible workflows by creating and running BehaviorSpace experiments and retrieving their results.