text:
@book{deHaan,
  title={Extreme Value Theory: An Introduction},
  author={de Haan, Laurens and Ana Ferreira},
  isbn={9780387239460},
  lccn={2006925909},
  series={Springer Series in Operations Research and Financial Engineering},
  year={2006},
  publisher={Springer},
  address={New York}
}

@article{renyi,
  author={R{\'e}nyi, Alfr{\'e}d},
  title={On the theory of order statistics},
  journal={Acta Mathematica Academiae Scientiarum Hungarica},
  year={1953},
  volume={4},
  number={3},
  pages={191--231},
  issn={1588-2632},
  doi={10.1007/BF02127580},
  url={https://doi.org/10.1007/BF02127580}
}

@book{rosenthal,
  title={A First Look at Rigorous Probability Theory},
  author={Jeffrey S. Rosenthal},
  isbn={9789813101654},
  year={2006},
  publisher={World Scientific Publishing Co.},
  address={Singapore},
  edition={second}
}

@book{lahiri,
  title={Measure Theory and Probability Theory},
  author={Athreya, K.B. and Lahiri, S.N.},
  isbn={9780387329031},
  lccn={2006922767},
  series={Springer Texts in Statistics},
  year={2006},
  publisher={Springer},
  address={New York}
}

@book{resnick,
  title={Heavy-Tail Phenomena: Probabilistic and Statistical Modeling},
  author={Resnick, Sidney I.},
  isbn={9780387242729},
  lccn={2006934621},
  series={Springer Series in Operations Research and Financial Engineering},
  year={2007},
  publisher={Springer},
  address={New York}
}

@article{hill,
  ISSN={00905364},
  URL={http://www.jstor.org/stable/2958370},
  author={Bruce M. Hill},
  journal={The Annals of Statistics},
  number={5},
  pages={1163--1174},
  publisher={Institute of Mathematical Statistics},
  title={A Simple General Approach to Inference About the Tail of a Distribution},
  volume={3},
  year={1975}
}

@article{fisher,
  title={Limiting forms of the frequency distribution of the largest or smallest member of a sample},
  volume={24},
  DOI={10.1017/S0305004100015681},
  number={2},
  journal={Mathematical Proceedings of the Cambridge Philosophical Society},
  publisher={Cambridge University Press},
  author={Fisher, R. A. and Tippett, L. H. C.},
  year={1928},
  pages={180–190}
}

@article{gnedenko,
  ISSN={0003486X},
  URL={http://www.jstor.org/stable/1968974},
  author={B. Gnedenko},
  journal={Annals of Mathematics},
  number={3},
  pages={423--453},
  publisher={Annals of Mathematics},
  title={Sur La Distribution Limite Du Terme Maximum D'Une Serie Aleatoire},
  volume={44},
  year={1943}
}

@article{mason,
  ISSN={00911798},
  URL={http://www.jstor.org/stable/2243383},
  author={David M. Mason},
  journal={The Annals of Probability},
  number={3},
  pages={754--764},
  publisher={Institute of Mathematical Statistics},
  title={Laws of Large Numbers for Sums of Extreme Values},
  volume={10},
  year={1982}
}

@article{ilmonen,
  author={Dominicy, Yves and Ilmonen, Pauliina and Veredas, David},
  title={Multivariate Hill Estimators},
  journal={International Statistical Review},
  volume={85},
  year={2015},
  number={1},
  pages={108-142},
  doi={10.1111/insr.12120},
  url={https://onlinelibrary.wiley.com/doi/abs/10.1111/insr.12120},
  eprint={https://onlinelibrary.wiley.com/doi/pdf/10.1111/insr.12120}
}

@article{pickands,
  author={Pickands III, James},
  doi={10.1214/aos/1176343003},
  journal={The Annals of Statistics},
  month={01},
  number={1},
  pages={119--131},
  publisher={The Institute of Mathematical Statistics},
  title={Statistical Inference Using Extreme Order Statistics},
  url={https://doi.org/10.1214/aos/1176343003},
  volume={3},
  year={1975}
}

@article{dekkers,
 ISSN = {00905364},
 URL = {http://www.jstor.org/stable/2241667},
 author = {A. L. M. Dekkers and J. H. J. Einmahl and L. De Haan},
 journal = {The Annals of Statistics},
 number = {4},
 pages = {1833--1855},
 publisher = {Institute of Mathematical Statistics},
 title = {A Moment Estimator for the Index of an Extreme-Value Distribution},
 volume = {17},
 year = {1989}
}

@article{peng,
  author={de Haan, L. and Peng, L.},
  title={Comparison of tail index estimators},
  journal= {Statistica Neerlandica},
  year={1998},
  volume={52},
  number={1},
  pages={60-70},
  doi={10.1111/1467-9574.00068},
  url={https://onlinelibrary.wiley.com/doi/abs/10.1111/1467-9574.00068},
  eprint={https://onlinelibrary.wiley.com/doi/pdf/10.1111/1467-9574.00068},
}

@article{hausler,
  title={On asymptotic normality of Hill's estimator for the exponent of regular variation},
  ISSN={00905364},
  URL={http://www.jstor.org/stable/2241207},
  author={E. Haeusler and J. L. Teugels},
  journal={The Annals of Statistics},
  number={2},
  pages={743--756},
  publisher={Institute of Mathematical Statistics},
  volume={13},
  year={1985}
}

@book{embrechts,
  title={Modelling Extremal Events for Insurance and Finance},
  author={Embrechts, P. and Kl{\"u}ppelberg, C. and Mikosch, T.},
  isbn={9783540609315},
  lccn={97012308},
  series={Stochastic Modelling and Applied Probability},
  url={https://books.google.fi/books?id=BXOI2pICfJUC},
  year={1997},
  publisher={Springer},
  address={Berlin}
}

@article{haanResnick,
  author={ Laurens   de Haan  and  Sidney   Resnick },
  title={On asymptotic normality of the hill estimator},
  journal={Communications in Statistics. Stochastic Models},
  volume={14},
  number={4},
  pages={849-866},
  year={1998},
  publisher={Taylor & Francis},
  doi={10.1080/15326349808807504},
  URL={https://doi.org/10.1080/15326349808807504},
  eprint = {https://doi.org/10.1080/15326349808807504}
}

@book{bingham,
  title={Regular Variation},
  author={Bingham, N.H. and Goldie, C.M. and Teugels, J.L.},
  number={nro 1},
  isbn={9780521379434},
  lccn={86284221},
  series={Encyclopedia of Mathematics and its Applications},
  url={https://books.google.fi/books?id=VCU5D4jMfiEC},
  year={1989},
  publisher={Cambridge University Press}
}

@article{mcneil,
  title={Estimating the Tails of Loss Severity Distributions Using Extreme Value Theory},
  volume={27},
  DOI={10.2143/AST.27.1.563210},
  number={1},
  journal={ASTIN Bulletin},
  publisher={Cambridge University Press},
  author={McNeil, Alexander J.},
  year={1997},
  pages={117–137}
}

@article{resnickFire,
  title={Discussion of the Danish Data on Large Fire Insurance Losses},
  volume={27},
  DOI={10.2143/AST.27.1.563211},
  number={1},
  journal={ASTIN Bulletin},
  publisher={Cambridge University Press},
  author={Resnick, Sidney I.},
  year={1997},
  pages={139–151}
}

@article{mcneilStock,
  title={Estimation of tail-related risk measures for heteroscedastic financial time series: an extreme value approach},
  journal={Journal of Empirical Finance},
  author={Alexander J. McNeil and Rüdiger Frey},
  volume={7},
  number={3},
  pages={271 - 300},
  year={2000},
  note={Special issue on Risk Management},
  issn={0927-5398},
  doi={https://doi.org/10.1016/S0927-5398(00)00012-8},
  url={http://www.sciencedirect.com/science/article/pii/S0927539800000128}
}

@article{potter,
  author={Potter, H. S. A.},
  title={The Mean Values of Certain Dirichlet Series II},
  journal={Proceedings of the London Mathematical Society},
  volume={47},
  number={1},
  pages={1-19},
  year={1942},
  doi={10.1112/plms/s2-47.1.1},
  url={https://londmathsoc.onlinelibrary.wiley.com/doi/abs/10.1112/plms/s2-47.1.1},
  eprint={https://londmathsoc.onlinelibrary.wiley.com/doi/pdf/10.1112/plms/s2-47.1.1}
}

@article{geluk,
  title={Second-order regular variation, convolution and the central limit theorem},
  journal={Stochastic Processes and their Applications},
  volume={69},
  number={2},
  pages={139 - 159},
  year={1997},
  issn={0304-4149},
  doi={https://doi.org/10.1016/S0304-4149(97)00042-2},
  url={http://www.sciencedirect.com/science/article/pii/S0304414997000422},
  author={J. Geluk and L. de Haan and S. Resnick and C. Stărică}
}


text:
package testbed

var _ EntityInterface = &PutInterfaceTest{}

type EntityInterface interface {
	Kind() string
	ID() string
}

type PutInterfaceTest struct {
	kind string
	id   string
}

func (e *PutInterfaceTest) Kind() string {
	return e.kind
}
func (e *PutInterfaceTest) ID() string {
	return e.id
}

repository: mercari/datastore

license_type: permissive

repo_name: mercari/datastore

branch_name: refs/heads/master

gha_license_id: MIT

gha_language: Go

extension: go


text:
package main

import (
	"flag"
	"log"
	"net/http"
	"time"

	"github.com/valyala/fasthttp"
	"github.com/zerodha/fastglue"
)

var (
	addr = flag.String("addr", ":8080", "TCP address to listen to")
)

func main() {
	flag.Parse()

	g := fastglue.New()
	g.GET("/", handleIndex)

	s := &fasthttp.Server{
		Name:         "Decode",
		ReadTimeout:  5 * time.Second,
		WriteTimeout: 5 * time.Second,
	}
	if err := g.ListenAndServe(*addr, "", s); err != nil {
		log.Fatalf("Error in ListenAndServe: %s", err)
	}
}

type request struct {
	Name     string `json:"name" url:"name"`
	EMail    string `json:"email" url:"email"`
	DOB      string `json:"date_of_birth" url:"dob"`
	Location string `json:"location" url:"location"`
}

func handleIndex(r *fastglue.Request) error {
	var (
		req request
	)

	if err := r.Decode(&req, "url"); err != nil {
		return r.SendErrorEnvelope(http.StatusBadRequest, "decode failed", err.Error(), "InputError")
	}

	return r.SendEnvelope(req)
}

license: MIT

repository: GKLeong/fastglue

repo_name: GKLeong/fastglue


text:
// Copyright 2021 Saferwall. All rights reserved.
// Use of this source code is governed by Apache v2 license
// license that can be found in the LICENSE file.

package s3

import (
	"context"
	"io"
	"time"

	"github.com/aws/aws-sdk-go/aws"
	"github.com/aws/aws-sdk-go/aws/credentials"
	"github.com/aws/aws-sdk-go/aws/session"
	awss3 "github.com/aws/aws-sdk-go/service/s3"
	"github.com/aws/aws-sdk-go/service/s3/s3manager"
)

// Service provides abstraction to cloud object storage.
type Service struct {
	// S3 uploader.
	uploader *s3manager.Uploader
}

// New generates new s3 object storage service.
func New(region, accessKey, secretKey string) (Service, error) {

	// The session the S3 Uploader will use.
	creds := credentials.NewStaticCredentials(accessKey, secretKey, "")
	sess, err := session.NewSession(&aws.Config{Region: aws.String(region),
		Credentials: creds})
	if err != nil {
		return Service{}, nil
	}

	// S3 service client the Upload manager will use.
	s3Svc := awss3.New(sess)

	// Create an uploader with S3 client and custom options
	uploader := s3manager.NewUploaderWithClient(s3Svc, func(u *s3manager.Uploader) {
		u.PartSize = 5 * 1024 * 1024 // 5MB per part
		u.LeavePartsOnError = true   // Don't delete the parts if the upload fails.
	})

	return Service{uploader}, nil
}

// Upload upload an object to s3.
func (s Service) Upload(bucket, key string, file io.Reader, timeout int) error {

	// Create a context with a timeout that will abort the upload if it takes
	// more than the passed in timeout.
	ctx := context.Background()
	var cancelFn func()
	if timeout > 0 {
		ctx, cancelFn = context.WithTimeout(ctx, time.Duration(timeout))
	}

	// Ensure the context is canceled to prevent leaking.
	// See context package for more information, https://golang.org/pkg/context/
	if cancelFn != nil {
		defer cancelFn()
	}

	// Upload input parameters
	upParams := &s3manager.UploadInput{
		Bucket: &bucket,
		Key:    &key,
		Body:   file,
	}

	// Perform an upload.
	_, err := s.uploader.UploadWithContext(ctx, upParams)

	return err
}

repository: SavoBit/saferwall-api

repo_name: SavoBit/saferwall-api

branch_name: refs/heads/main


text:
add_web_client_test(
    flow "${PROJECT_SOURCE_DIR}/plugins/flow/web_external/tests/spec/flowSpec.js"
    PLUGIN flow
    BASEURL "/static/built/plugins/flow/testEnvFlow.html")

repository: Kitware/flow

repo_name: Kitware/flow

gha_language: Python

extension: cmake


text:
package token

import "bytes"

var give = []byte(`Give`)

// IsGive checks for keyword break
func IsGive(word []byte) bool {
	return bytes.Equal(word, give)
}

repository: young-steveo/thrash

repo_name: young-steveo/thrash


text:
DESCRIPTION = "Libdivecomputer is a cross-platform and open source library for communication with dive computers from various manufacturers."
HOMEPAGE = "http://www.divesoftware.org/libdc/"

LICENSE = "LGPLv2.1"
LIC_FILES_CHKSUM = "file://COPYING;md5=fbc093901857fcd118f065f900982c24"

DEPENDS = "libusb1"

inherit autotools pkgconfig

PV = "0.0.0"
PR = "r1"

SRCREV = "b7a6be15ca58cc8f89fbc8fa1a4c840e13d51092"
SRC_URI = "git://libdivecomputer.git.sourceforge.net/gitroot/libdivecomputer/libdivecomputer \
file://fix-ar.patch"
S = "${WORKDIR}/git"

repository: ExorEmbedded/exor-workspace

repo_name: ExorEmbedded/exor-workspace

extension: bb


text:
package pgo_cli_test

/*
 Copyright 2020 Crunchy Data Solutions, Inc.
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at

      http://www.apache.org/licenses/LICENSE-2.0

 Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
*/

import (
	"testing"
	"time"

	"github.com/stretchr/testify/require"
)

// TC115 ✓
// TC116 ✓
// TC119 ✓
func TestClusterDelete(t *testing.T) {
	t.Parallel()

	withNamespace(t, func(namespace func() string) {
		t.Run("delete cluster", func(t *testing.T) {
			t.Run("removes data and backups", func(t *testing.T) {
				t.Parallel()
				withCluster(t, namespace, func(cluster func() string) {
					requireClusterReady(t, namespace(), cluster(), time.Minute)
					require.NotEmpty(t, clusterPVCs(t, namespace(), cluster()), "expected data to exist")

					output, err := pgo("delete", "cluster", cluster(), "--no-prompt", "-n", namespace()).Exec(t)
					require.NoError(t, err)
					require.Contains(t, output, "deleted")

					gone := func() bool {
						return len(clusterPVCs(t, namespace(), cluster())) == 0
					}
					requireWaitFor(t, gone, time.Minute, time.Second,
						"timeout waiting for data of %q in %q", cluster(), namespace())

					output, err = pgo("show", "cluster", cluster(), "-n", namespace()).Exec(t)
					require.NoError(t, err)
					require.NotContains(t, output, cluster())
				})
			})

			t.Run("can keep backups", func(t *testing.T) {
				t.Parallel()
				withCluster(t, namespace, func(cluster func() string) {
					requireClusterReady(t, namespace(), cluster(), time.Minute)
					require.NotEmpty(t, clusterPVCs(t, namespace(), cluster()), "expected data to exist")

					output, err := pgo("delete", "cluster", cluster(), "--keep-backups", "--no-prompt", "-n", namespace()).Exec(t)
					require.NoError(t, err)
					require.Contains(t, output, "deleted")

					gone := func() bool {
						return len(clusterPVCs(t, namespace(), cluster())) == 1
					}
					requireWaitFor(t, gone, time.Minute, time.Second,
						"timeout waiting for data of %q in %q", cluster(), namespace())

					pvcs := clusterPVCs(t, namespace(), cluster())
					require.NotEmpty(t, pvcs)
					require.Contains(t, pvcs[0].Name, "pgbr-repo")

					output, err = pgo("show", "cluster", cluster(), "-n", namespace()).Exec(t)
					require.NoError(t, err)
					require.NotContains(t, output, cluster())
				})
			})

			t.Run("can keep data", func(t *testing.T) {
				t.Parallel()
				withCluster(t, namespace, func(cluster func() string) {
					requireClusterReady(t, namespace(), cluster(), time.Minute)
					require.NotEmpty(t, clusterPVCs(t, namespace(), cluster()), "expected data to exist")

					output, err := pgo("delete", "cluster", cluster(), "--keep-data", "--no-prompt", "-n", namespace()).Exec(t)
					require.NoError(t, err)
					require.Contains(t, output, "deleted")

					gone := func() bool {
						return len(clusterPVCs(t, namespace(), cluster())) == 1
					}
					requireWaitFor(t, gone, time.Minute, time.Second,
						"timeout waiting for data of %q in %q", cluster(), namespace())

					pvcs := clusterPVCs(t, namespace(), cluster())
					require.NotEmpty(t, pvcs)
					require.Equal(t, cluster(), pvcs[0].Name)
				})
			})
		})
	})
}


text:
inherit gnomebase

SRC_URI[archive.md5sum] = "d6f2a43589480d2315672da0b5839b56"
SRC_URI[archive.sha256sum] = "20d1e7466ca4c83c92e29f9e8dfcc8e5721fdf1337f53157bed97be3b73b32a8"

LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://COPYING;md5=751419260aa954499f7abaabaa882bbe"

BBCLASSEXTEND = "native"

repository: astarche/meta-openembedded

repo_name: astarche/meta-openembedded

branch_name: refs/heads/nilrt/master/sumo


text:
@Manual{R-base,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2020},
  url = {https://www.R-project.org/},
}

@Manual{R-Biobase,
  title = {Biobase: Base functions for Bioconductor},
  author = {R. Gentleman and V. Carey and M. Morgan and S. Falcon},
  year = {2020},
  note = {R package version 2.48.0},
}

@Manual{R-BiocGenerics,
  title = {BiocGenerics: S4 generic functions used in Bioconductor},
  author = {The Bioconductor Dev Team},
  year = {2020},
  note = {R package version 0.34.0},
}

@Manual{R-BiocStyle,
  title = {BiocStyle: Standard styles for vignettes and other Bioconductor documents},
  author = {Andrzej Oles and Martin Morgan and Wolfgang Huber},
  year = {2020},
  note = {R package version 2.16.0},
  url = {https://github.com/Bioconductor/BiocStyle},
}

@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2020},
  note = {R package version 0.20},
  url = {https://CRAN.R-project.org/package=bookdown},
}

@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel {
             Henry} and Kirill Müller},
  year = {2020},
  note = {R package version 1.0.2},
  url = {https://CRAN.R-project.org/package=dplyr},
}

@Manual{R-DSI,
  title = {DSI: 'DataSHIELD' Interface},
  author = {Yannick Marcon},
  year = {2020},
  note = {R package version 1.1.0},
  url = {https://CRAN.R-project.org/package=DSI},
}

@Manual{R-DSOpal,
  title = {DSOpal: 'DataSHIELD' Implementation for 'Opal'},
  author = {Yannick Marcon},
  year = {2020},
  note = {R package version 1.1.0},
  url = {https://CRAN.R-project.org/package=DSOpal},
}

@Manual{R-forcats,
  title = {forcats: Tools for Working with Categorical Variables (Factors)},
  author = {Hadley Wickham},
  year = {2020},
  note = {R package version 0.5.0},
  url = {https://CRAN.R-project.org/package=forcats},
}

@Manual{R-GenomeInfoDb,
  title = {GenomeInfoDb: Utilities for manipulating chromosome names, including modifying
them to follow a particular naming style},
  author = {Sonali Arora and Martin Morgan and Marc Carlson and H. Pagès},
  year = {2020},
  note = {R package version 1.24.2},
}

@Manual{R-GenomicRanges,
  title = {GenomicRanges: Representation and manipulation of genomic intervals},
  author = {P. Aboyoun and H. Pagès and M. Lawrence},
  year = {2020},
  note = {R package version 1.40.0},
}

@Manual{R-ggplot2,
  title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
  author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington},
  year = {2020},
  note = {R package version 3.3.2},
  url = {https://CRAN.R-project.org/package=ggplot2},
}

@Manual{R-httr,
  title = {httr: Tools for Working with URLs and HTTP},
  author = {Hadley Wickham},
  year = {2020},
  note = {R package version 1.4.2},
  url = {https://CRAN.R-project.org/package=httr},
}

@Manual{R-IRanges,
  title = {IRanges: Foundation of integer range manipulation in Bioconductor},
  author = {H. Pagès and P. Aboyoun and M. Lawrence},
  year = {2020},
  note = {R package version 2.22.2},
}

@Manual{R-kableExtra,
  title = {kableExtra: Construct Complex Table with 'kable' and Pipe Syntax},
  author = {Hao Zhu},
  year = {2020},
  note = {R package version 1.2.1},
  url = {https://CRAN.R-project.org/package=kableExtra},
}

@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2020},
  note = {R package version 1.29},
  url = {https://CRAN.R-project.org/package=knitr},
}

@Manual{R-Matrix,
  title = {Matrix: Sparse and Dense Matrix Classes and Methods},
  author = {Douglas Bates and Martin Maechler},
  year = {2019},
  note = {R package version 1.2-18},
  url = {https://CRAN.R-project.org/package=Matrix},
}

@Manual{R-opalr,
  title = {opalr: 'Opal' Data Repository Client and 'DataSHIELD' Utils},
  author = {Yannick Marcon},
  year = {2020},
  note = {R package version 1.5.1},
  url = {https://CRAN.R-project.org/package=opalr},
}

@Manual{R-progress,
  title = {progress: Terminal Progress Bars},
  author = {Gábor Csárdi and Rich FitzJohn},
  year = {2019},
  note = {R package version 1.2.2},
  url = {https://CRAN.R-project.org/package=progress},
}

@Manual{R-purrr,
  title = {purrr: Functional Programming Tools},
  author = {Lionel Henry and Hadley Wickham},
  year = {2020},
  note = {R package version 0.3.4},
  url = {https://CRAN.R-project.org/package=purrr},
}

@Manual{R-R6,
  title = {R6: Encapsulated Classes with Reference Semantics},
  author = {Winston Chang},
  year = {2019},
  note = {R package version 2.4.1},
  url = {https://CRAN.R-project.org/package=R6},
}

@Manual{R-readr,
  title = {readr: Read Rectangular Text Data},
  author = {Hadley Wickham and Jim Hester and Romain Francois},
  year = {2018},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=readr},
}

@Manual{R-rmarkdown,
  title = {rmarkdown: Dynamic Documents for R},
  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
  year = {2020},
  note = {R package version 2.3},
  url = {https://CRAN.R-project.org/package=rmarkdown},
}

@Manual{R-S4Vectors,
  title = {S4Vectors: Foundation of vector-like and list-like containers in
Bioconductor},
  author = {H. Pagès and M. Lawrence and P. Aboyoun},
  year = {2020},
  note = {R package version 0.26.1},
}

@Manual{R-snpStats,
  title = {snpStats: SnpMatrix and XSnpMatrix classes and methods},
  author = {David Clayton},
  year = {2020},
  note = {R package version 1.38.0},
}

@Manual{R-stringr,
  title = {stringr: Simple, Consistent Wrappers for Common String Operations},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=stringr},
}

@Manual{R-survival,
  title = {survival: Survival Analysis},
  author = {Terry M Therneau},
  year = {2020},
  note = {R package version 3.2-3},
  url = {https://CRAN.R-project.org/package=survival},
}

@Manual{R-tibble,
  title = {tibble: Simple Data Frames},
  author = {Kirill Müller and Hadley Wickham},
  year = {2020},
  note = {R package version 3.0.3},
  url = {https://CRAN.R-project.org/package=tibble},
}

@Manual{R-tidyr,
  title = {tidyr: Tidy Messy Data},
  author = {Hadley Wickham},
  year = {2020},
  note = {R package version 1.1.2},
  url = {https://CRAN.R-project.org/package=tidyr},
}

@Manual{R-tidyverse,
  title = {tidyverse: Easily Install and Load the 'Tidyverse'},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 1.3.0},
  url = {https://CRAN.R-project.org/package=tidyverse},
}

@Article{Biobase2015,
  author = {W. Huber and V. J. Carey and R. Gentleman and S. Anders and M. Carlson and B. S. Carvalho and H. C. Bravo and S. Davis and L. Gatto and T. Girke and R. Gottardo and F. Hahne and K. D. Hansen and R. A. Irizarry and M. Lawrence and M. I. Love and J. MacDonald and V. Obenchain and A. K. {Ole's} and H. {Pag`es} and A. Reyes and P. Shannon and G. K. Smyth and D. Tenenbaum and L. Waldron and M. Morgan},
  title = {{O}rchestrating high-throughput genomic analysis with {B}ioconductor},
  journal = {Nature Methods},
  year = {2015},
  volume = {12},
  number = {2},
  pages = {115--121},
  url = {http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html},
}

@Article{BiocGenerics2015,
  author = {{Huber} and {W.} and {Carey} and V. J. and {Gentleman} and {R.} and {Anders} and {S.} and {Carlson} and {M.} and {Carvalho} and B. S. and {Bravo} and H. C. and {Davis} and {S.} and {Gatto} and {L.} and {Girke} and {T.} and {Gottardo} and {R.} and {Hahne} and {F.} and {Hansen} and K. D. and {Irizarry} and R. A. and {Lawrence} and {M.} and {Love} and M. I. and {MacDonald} and {J.} and {Obenchain} and {V.} and {{Ole's}} and A. K. and {{Pag`es}} and {H.} and {Reyes} and {A.} and {Shannon} and {P.} and {Smyth} and G. K. and {Tenenbaum} and {D.} and {Waldron} and {L.} and {Morgan} and {M.}},
  title = {{O}rchestrating high-throughput genomic analysis with {B}ioconductor},
  journal = {Nature Methods},
  year = {2015},
  volume = {12},
  number = {2},
  pages = {115--121},
  url = {http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html},
}

@Book{bookdown2016,
  title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2016},
  note = {ISBN 978-1138700109},
  url = {https://github.com/rstudio/bookdown},
}

@Article{GenomicRanges2013,
  title = {Software for Computing and Annotating Genomic Ranges},
  author = {Michael Lawrence and Wolfgang Huber and Herv\'e Pag\`es and Patrick Aboyoun and Marc Carlson and Robert Gentleman and Martin Morgan and Vincent Carey},
  year = {2013},
  journal = {{PLoS} Computational Biology},
  volume = {9},
  issue = {8},
  doi = {10.1371/journal.pcbi.1003118},
  url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118},
}

@Book{ggplot22016,
  author = {Hadley Wickham},
  title = {ggplot2: Elegant Graphics for Data Analysis},
  publisher = {Springer-Verlag New York},
  year = {2016},
  isbn = {978-3-319-24277-4},
  url = {https://ggplot2.tidyverse.org},
}

@Article{IRanges2013,
  title = {Software for Computing and Annotating Genomic Ranges},
  author = {Michael Lawrence and Wolfgang Huber and Herv\'e Pag\`es and Patrick Aboyoun and Marc Carlson and Robert Gentleman and Martin Morgan and Vincent Carey},
  year = {2013},
  journal = {{PLoS} Computational Biology},
  volume = {9},
  issue = {8},
  doi = {10.1371/journal.pcbi.1003118},
  url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118},
}

@Book{knitr2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {https://yihui.org/knitr/},
}

@InCollection{knitr2014,
  booktitle = {Implementing Reproducible Computational Research},
  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2014},
  note = {ISBN 978-1466561595},
  url = {http://www.crcpress.com/product/isbn/9781466561595},
}

@Book{rmarkdown2018,
  title = {R Markdown: The Definitive Guide},
  author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2018},
  note = {ISBN 9781138359338},
  url = {https://bookdown.org/yihui/rmarkdown},
}

@Book{survival-book,
  title = {Modeling Survival Data: Extending the {C}ox Model},
  author = {{Terry M. Therneau} and {Patricia M. Grambsch}},
  year = {2000},
  publisher = {Springer},
  address = {New York},
  isbn = {0-387-98784-3},
}

@Article{tidyverse2019,
  title = {Welcome to the {tidyverse}},
  author = {Hadley Wickham and Mara Averick and Jennifer Bryan and Winston Chang and Lucy D'Agostino McGowan and Romain François and Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},
  year = {2019},
  journal = {Journal of Open Source Software},
  volume = {4},
  number = {43},
  pages = {1686},
  doi = {10.21105/joss.01686},
}

gha_language: TeX

extension: bib