Description: RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method. We develop a data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source RNA-seq dataset provided by the user. Users control the proportion of genes simulated to be differentially expressed (DE) and can provide a vector of weights to control the distribution of effect sizes. The algorithm requires a matrix of RNA-seq read counts with large sample sizes in at least two treatment groups. Many datasets are available that fit this standard.

Title: Simulate Survival Time and Markers
Description: Provides functions to simulate from joint survival and marker
models. The user can specific all basis functions of time, random or
deterministic covariates, random or deterministic left-truncation and
right-censoring times, and model parameters.
Suggests: testthat (>= 2.1.0), splines, R.rsp

Suggests: testthat (>= 2.1.0), splines, R.rsp, Matrix

Author: Benjamin Christoffersen [cre, aut]

Title: Test Surveys by Simulating Spatially-Correlated Populations
person("Paul", "Regular", email = "Paul.Regular@dfo-mpo.gc.ca",
person("Jonathan", "Babyn", email = "Jonathan.Babyn@dfo-mpo.gc.ca",
person("Greg", "Robertson", email = "Greg.Robertson@dfo-mpo.gc.ca",
Description: Simulate age-structured populations that vary in space and time and
explore the efficacy of a range of built-in or user-defined sampling
protocols to reproduce the population parameters of the known population.
(See Regular et al. (2020) <doi.org/10.1371/journal.pone.0232822> for more
Imports: sp, raster, igraph, rgeos, data.table, magrittr, progress,
doParallel, parallel, foreach, plotly, rlang
Suggests: fields, rmarkdown, flexdashboard, shiny, crosstalk,
htmltools, viridis, lme4, ggplot2, INLA, knitr
Author: Paul Regular [aut, cre] (<https://orcid.org/0000-0003-0318-2615>),