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Confounder-Adjusted Survival Curves and Cumulative Incidence Functions
Estimate and plot confounder-adjusted survival curves using
either 'Direct Adjustment', 'Direct Adjustment with Pseudo-Values',
various forms of 'Inverse Probability of Treatment Weighting', two
forms of 'Augmented Inverse Probability of Treatment Weighting',
'Empirical Likelihood Estimation' or 'Targeted Maximum Likelihood Estimation'.
Also includes a significance test for the difference
between two adjusted survival curves and the calculation of adjusted
restricted mean survival times. Additionally enables the user to
estimate and plot cause-specific confounder-adjusted cumulative
incidence functions in the competing risks setting using the same
methods (with some exceptions).
For details, see Denz et. al (2023)
Datasets for "Statistics: UnLocking the Power of Data"
Datasets for the third edition of "Statistics: Unlocking the Power of Data" by Lock^5 Includes version of datasets from earlier editions.
Open GenBank Files
Opens complete record(s) with .gb extension from the NCBI/GenBank Nucleotide database and returns a list containing shaped record(s). These kind of files contains detailed records of DNA samples (locus, organism, type of sequence, source of the sequence...). An example of record can be found at < https://www.ncbi.nlm.nih.gov/nuccore/HE799070>.
Imputation of High-Dimensional Count Data using Side Information
Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear Poisson model where main row and column effects, as well as effects of known covariates and interaction terms can be fitted. The estimation procedure is based on the convex optimization of the Poisson loss penalized by a Lasso type penalty and a nuclear norm. LORI returns estimates of main effects, covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure. The methods are described in Robin, Josse, Moulines and Sardy (2019)
Distances on Directed Graphs
Distances on dual-weighted directed graphs using
priority-queue shortest paths (Padgham (2019)
Simulate Data from a DAG and Associated Node Information
Simulate complex data from a given directed acyclic graph and information about each individual node. Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to one of many implemented regressions, such as logistic regression, linear regression, poisson regression and more. Also includes a comprehensive framework for discrete-time simulation, which can generate even more complex longitudinal data.
Variable Selection Using Random Forests
Three steps variable selection procedure based on random forests. Initially developed to handle high dimensional data (for which number of variables largely exceeds number of observations), the package is very versatile and can treat most dimensions of data, for regression and supervised classification problems. First step is dedicated to eliminate irrelevant variables from the dataset. Second step aims to select all variables related to the response for interpretation purpose. Third step refines the selection by eliminating redundancy in the set of variables selected by the second step, for prediction purpose. Genuer, R. Poggi, J.-M. and Tuleau-Malot, C. (2015) < https://journal.r-project.org/archive/2015-2/genuer-poggi-tuleaumalot.pdf>.
The Hyperdirichlet Distribution, Mark 2
A suite of routines for the hyperdirichlet distribution
and reified Bradley-Terry; supersedes the 'hyperdirichlet' package;
uses 'disordR' discipline
Exploratory Data Analysis for the 'spatstat' Family
Functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Interface Between 'GRASS' Geographical Information System and 'R'
An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000)