partitions, DescTools, gmp, mvp, multicool, JuliaConnectoR,
Ryacas, gmpoly

A Swift, Versatile Phylogenomic and High-Throughput Sequencing
Simulator
person(c("Lucas", "A."), "Nell", email = "lucas@lucasnell.com",
role = c("cph", "aut", "cre"),
comment = c(ORCID = "0000-0003-3209-0517"))
Simply and efficiently
simulates (i) variants from reference genomes and (ii) reads from both Illumina
<https://www.illumina.com/>
and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms.
It can either read reference genomes from FASTA files or simulate new ones.
Genomic variants can be simulated using summary statistics, phylogenies,
Variant Call Format (VCF) files, and coalescent simulations—the latter of which
can include selection, recombination, and demographic fluctuations.
'jackalope' can simulate single, paired-end, or mate-pair Illumina reads,
as well as PacBio reads.
These simulations include sequencing errors, mapping qualities, multiplexing,
and optical/polymerase chain reaction (PCR) duplicates.
Simulating Illumina sequencing is based on ART
by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>.
PacBio sequencing simulation is based on
SimLoRD  by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>.
All outputs can be written to standard file formats.
ape, R6, Rcpp (>= 0.12.11), RcppProgress (>= 0.1), zlibbioc
Rcpp, RcppArmadillo, RcppProgress, Rhtslib, zlibbioc

coala, knitr, markdown, rmarkdown, scrm, testthat

Jackknife estimates of Kaplan-Meier estimators or integrals.
The package is for computing both the original and
modified jackknife estimates of Kaplan-Meier estimators.

Jackknife Estimates of Kaplan-Meier Estimators or Integrals
The package is for computing both the original and modified jackknife estimates of Kaplan-Meier estimators.

Computing the original and modified jackknife estimates of Kaplan-Meier estimators.

Correcting Nonparametric Frontier Measurements for Outliers
c(
person("Kleber Morais de","Sousa", role = c("aut", "cre"), email = "kleberfinancas@gmail.com"),
person("Maria da Conceicao Sampaio de", "Sousa", role = c("aut"), email = "csampaiodesousa@gmail.com"),
person("Paulo Aguiar do", "Monte", role = c("aut"), email = "pauloaguiardomonte@gmail.com")
)
Kleber Morais de Sousa [aut, cre],
Maria da Conceicao Sampaio de Sousa [aut],
Paulo Aguiar do Monte [aut]
Kleber Morais de Sousa <kleberfinancas@gmail.com>
Provides method used to check whether data have outlier in efficiency measurement
of big samples with data envelopment analysis (DEA). In this jackstrap method, the package
provides two criteria to define outliers: heaviside and k-s test. The technique was developed
by Sousa and Stosic (2005) "Technical Efficiency of the Brazilian Municipalities: Correcting
Nonparametric Frontier Measurements for Outliers." <doi:10.1007/s11123-005-4702-4>.
fBasics, Benchmarking, dplyr, ggplot2, foreach, doParallel,
reshape, tidyr, scales, parallel, graphics, plyr, rlang, utils