id stringlengths 40 40 | repo_name stringlengths 5 110 | path stringlengths 2 233 | content stringlengths 0 1.03M ⌀ | size int32 0 60M ⌀ | license stringclasses 15
values |
|---|---|---|---|---|---|
2b8fd89b4749253525141e2bd149d1a3082f1af5 | cran/siatclust | tests/ewkm01.R | library(siatclust)
csv <- "ewkm01.csv"
ds <- read.csv("ewkm01.csv")
set.seed(42)
km <- ewkm(ds, 10)
print(km)
cat(km$iterations, km$restarts, km$total.iterations, "\n")
set.seed(42)
km <- ewkm(ds, 10, maxrestart=50)
print(km)
cat(km$iterations, km$restarts, km$total.iterations, "\n")
set.seed(42)
km <- ewkm(ds, 10... | 536 | gpl-3.0 |
66daaa8e245e478ca922288c3afa522e72f65730 | lujiec/shiny_group_simulator | run_shiny.R | library(shiny)
library(ggplot2)
library(gridExtra)
setwd('..')
runApp('shiny_app') | 88 | mit |
ff7ab7d6a11ce5a607eb8ef31355ef7a2ccf628a | rho-devel/rho | src/extra/testr/filtered-test-suite/strsplit/tc_strsplit_10.R | expected <- eval(parse(text="list(c(\"A\", \"shell\", \"of\", \"class\", \"documentation\", \"has\", \"been\", \"written\", \"to\", \"the\", \"file\", \"'./myTst2/man/DocLink-class.Rd'.\"))"));
test(id=0, code={
argv <- eval(parse(text="list(\"A shell of class documentation has been written to the file './myTst... | 496 | gpl-2.0 |
ff7ab7d6a11ce5a607eb8ef31355ef7a2ccf628a | kmillar/cxxr | src/extra/testr/filtered-test-suite/strsplit/tc_strsplit_10.R | expected <- eval(parse(text="list(c(\"A\", \"shell\", \"of\", \"class\", \"documentation\", \"has\", \"been\", \"written\", \"to\", \"the\", \"file\", \"'./myTst2/man/DocLink-class.Rd'.\"))"));
test(id=0, code={
argv <- eval(parse(text="list(\"A shell of class documentation has been written to the file './myTst... | 496 | gpl-2.0 |
ff7ab7d6a11ce5a607eb8ef31355ef7a2ccf628a | ArunChauhan/cxxr | src/extra/testr/filtered-test-suite/strsplit/tc_strsplit_10.R | expected <- eval(parse(text="list(c(\"A\", \"shell\", \"of\", \"class\", \"documentation\", \"has\", \"been\", \"written\", \"to\", \"the\", \"file\", \"'./myTst2/man/DocLink-class.Rd'.\"))"));
test(id=0, code={
argv <- eval(parse(text="list(\"A shell of class documentation has been written to the file './myTst... | 496 | gpl-2.0 |
ff7ab7d6a11ce5a607eb8ef31355ef7a2ccf628a | cxxr-devel/cxxr | src/extra/testr/filtered-test-suite/strsplit/tc_strsplit_10.R | expected <- eval(parse(text="list(c(\"A\", \"shell\", \"of\", \"class\", \"documentation\", \"has\", \"been\", \"written\", \"to\", \"the\", \"file\", \"'./myTst2/man/DocLink-class.Rd'.\"))"));
test(id=0, code={
argv <- eval(parse(text="list(\"A shell of class documentation has been written to the file './myTst... | 496 | gpl-2.0 |
ff7ab7d6a11ce5a607eb8ef31355ef7a2ccf628a | kmillar/rho | src/extra/testr/filtered-test-suite/strsplit/tc_strsplit_10.R | expected <- eval(parse(text="list(c(\"A\", \"shell\", \"of\", \"class\", \"documentation\", \"has\", \"been\", \"written\", \"to\", \"the\", \"file\", \"'./myTst2/man/DocLink-class.Rd'.\"))"));
test(id=0, code={
argv <- eval(parse(text="list(\"A shell of class documentation has been written to the file './myTst... | 496 | gpl-2.0 |
0c514ad64a488918937febea02b70f9b4f559e2b | StanfordPsych254/replication_project | subsidiary_analysis/compute_sofer_es.R | rm(list=ls())
library(readr)
library(dplyr)
library(tidyr)
library(lsr)
sofer <- read_csv("../subsidiary_analysis/Experiment_1_Rps.csv")
d <- sofer %>%
mutate(subid = 1:n()) %>%
gather(datapoint, rating, starts_with("dft")) %>%
separate(datapoint, into = c("foo","DFT","trial_num"), sep = "_") %>%
mutate(condit... | 2,052 | mit |
ff7ab7d6a11ce5a607eb8ef31355ef7a2ccf628a | krlmlr/cxxr | src/extra/testr/filtered-test-suite/strsplit/tc_strsplit_10.R | expected <- eval(parse(text="list(c(\"A\", \"shell\", \"of\", \"class\", \"documentation\", \"has\", \"been\", \"written\", \"to\", \"the\", \"file\", \"'./myTst2/man/DocLink-class.Rd'.\"))"));
test(id=0, code={
argv <- eval(parse(text="list(\"A shell of class documentation has been written to the file './myTst... | 496 | gpl-2.0 |
5f04d4c75bdc6afb327e122769448325ab0f1f86 | sorensje/R_helperfunctions | aggregate_into_DF.R | aggregate_into_DF <- function(dataDF, form, fun, newVarName, inNewDF = TRUE){
# if(!is.na(subsetExp) & ! is.na(subsetVar)){
#
# }
# print(c("\n",substitute(dataDF)," type: ", expression(substitute(dataDF)),"\n"))
# convenience function that returns original df w/ new aggregated variable (maintain... | 1,894 | gpl-2.0 |
1a9d5776fb6b50e88b91021bdefd815a2b099e55 | jannes-m/RQGIS | tests/testthat/test-qgis-prerun.R | context("prerun")
library("raster")
library("sf")
test_that("qgis_session_info yields a list as output", {
skip_on_cran()
info <- qgis_session_info()
# check if the output is a list of length 5 or 6
expect_gt(length(info), 4)
})
test_that("find_algorithms finds QGIS geoalgorithms", {
skip_on_cran()
... | 1,586 | lgpl-3.0 |
9eebeeca8816b2a51a202ec89e7254f3a1bd15ea | RCollins13/CNValue | plotting_code/AllExampleLoci/SMARCA2/SMARCA2_CNV_tracks.plot.R | #!/usr/bin/env R
#rCNV Map Project
#Spring 2017
#Talkowski Lab & Collaborators
#Copyright (c) 2017 Ryan Collins
#Distributed under terms of the MIT License
#Code to plot various tracks for SMARCA2 figure
####################################
#####Set parameters & load libraries
####################################
W... | 10,020 | mit |
9eebeeca8816b2a51a202ec89e7254f3a1bd15ea | RCollins13/rCNVmap | plotting_code/AllExampleLoci/SMARCA2/SMARCA2_CNV_tracks.plot.R | #!/usr/bin/env R
#rCNV Map Project
#Spring 2017
#Talkowski Lab & Collaborators
#Copyright (c) 2017 Ryan Collins
#Distributed under terms of the MIT License
#Code to plot various tracks for SMARCA2 figure
####################################
#####Set parameters & load libraries
####################################
W... | 10,020 | mit |
00d66c1bd89f15a3205d5ef2b028f22416c8819f | Forever-Peace/GroundControl | Chapters/ch6-surprisal/gamescore_calc_only.R | #THIS SCRIPT JUST CALCULATES GAME SCORE, WITHOUT ANY OF THE PLOTTING FUNCTIONS ETC FOUND IN THE CHAPTER.
#Simply change the filepath here to load the csv (found in the Ground Control github page), the run the entire script. It will take a while.
df = read.csv("rushing_data_stack.csv") #point this to the location of th... | 5,412 | gpl-2.0 |
aced0b8bbf6b6d882c308d230c495cb74cf104cd | YvesBas/Tadarida-C | tadaridaC_src/xenocanto/XCwav_mix.R | library(tuneR)
DirW="C:/Users/yvesb/Documents/Tadarida/pollinisateurs/doc_voix_humaine/voix_humaine_database"
ListWrecent=list.files(DirW,pattern=".wav$",full.names=T)
WNrates=c(10,24,50,99)
CoeffSR=1
for (i in 1:length(WNrates))
{
DestMix=gsub("split202",paste0("wn",WNrates[i],"_202"),DirW)
dir.create(DestMix)
... | 966 | gpl-3.0 |
76f1318f1226a8e6a61085d948cbafd165883b96 | setempler/miscset | R/scale0.R | #' @name scale0
#' @keywords scale
#' @aliases scaler
#' @author Sven E. Templer
#' @title Scale Numeric Values to Defined Ranges
#' @description
#' Scale numeric values to a range from 0 to 1 with the function
#' \code{scale0} or to a chosen range with \code{scaler}.
#' @param x Numeric vector to transform.
#' @param... | 1,201 | gpl-3.0 |
7fc9be4ce25cd064720c8f7fa9b4a4c0ceb597aa | SANBI-SA/tools-iuc | tools/limma_voom/limma_voom.R | # This tool takes in a matrix of feature counts as well as gene annotations and
# outputs a table of top expressions as well as various plots for differential
# expression analysis
#
# ARGS: 1.countPath -Path to RData input containing counts
# 2.annoPath -Path to input containing gene annotations
# ... | 23,219 | mit |
e80d8b85766c2a2bef500f8de3a1cc4987a3f9c5 | sgagnon/runQuestionnaires | scripts/tools/analysis.R | working_dir = "~/Experiments/AssocMem/data/"
setwd(working_dir)
d0=read.csv("Source_HitRate_n=9.csv")
summary(d0)
with(d0, interaction.plot(ShockCond, TrialType, Source_HitRate))
fit <- aov(Source_HitRate~(ShockCond*TrialType)+Error(Subid/(ShockCond*TrialType)),
data=d0)
summary(fit)
library(ggplot2)
p... | 6,618 | bsd-3-clause |
af75da5ecc7411ff80c4402698c6ac4d6d5d4963 | gavinsimpson/analogue | R/crossval.wa.R | ## crossval method for wa()
`crossval.wa` <- function(obj, method = c("LOO","kfold","bootstrap"),
nboot = 100, nfold = 10, folds = 5,
verbose = getOption("verbose"), ...) {
method <- match.arg(method)
X <- obj$orig.x
ENV <- obj$orig.env
N <- NROW(X)
... | 5,200 | gpl-2.0 |
700f8bffc889de7467003d8554e1dd3c47c1de3e | mjharrigan/flux | src/etoh.R | #!/usr/bin/env Rscript
################################################################################
# etoh.R
#
# USAGE: Rscript etoh.R --args cfg = file.cfg
#
################################################################################
# Estimation procedure for heavy alcohol user (ETOH) initiation, remittance,... | 18,969 | mit |
2262140e6ed2cae58984943da628cb1cfab45906 | kmillar/cxxr | src/extra/testr/filtered-test-suite/attr/tc_attr_35.R | expected <- eval(parse(text="NULL"));
test(id=0, code={
argv <- eval(parse(text="list(structure(c(8.85169533448293e-238, 2.77884205079773e-237, 8.5330427463164e-242, 7.89244209468013e-215, 6.74732964729372e-231, 1.30818670504849e-217, 1.39113376416096e-208, 1.35683278955814e-215, 7... | 635 | gpl-2.0 |
2262140e6ed2cae58984943da628cb1cfab45906 | kmillar/rho | src/extra/testr/filtered-test-suite/attr/tc_attr_35.R | expected <- eval(parse(text="NULL"));
test(id=0, code={
argv <- eval(parse(text="list(structure(c(8.85169533448293e-238, 2.77884205079773e-237, 8.5330427463164e-242, 7.89244209468013e-215, 6.74732964729372e-231, 1.30818670504849e-217, 1.39113376416096e-208, 1.35683278955814e-215, 7... | 635 | gpl-2.0 |
2262140e6ed2cae58984943da628cb1cfab45906 | rho-devel/rho | src/extra/testr/filtered-test-suite/attr/tc_attr_35.R | expected <- eval(parse(text="NULL"));
test(id=0, code={
argv <- eval(parse(text="list(structure(c(8.85169533448293e-238, 2.77884205079773e-237, 8.5330427463164e-242, 7.89244209468013e-215, 6.74732964729372e-231, 1.30818670504849e-217, 1.39113376416096e-208, 1.35683278955814e-215, 7... | 635 | gpl-2.0 |
2262140e6ed2cae58984943da628cb1cfab45906 | ArunChauhan/cxxr | src/extra/testr/filtered-test-suite/attr/tc_attr_35.R | expected <- eval(parse(text="NULL"));
test(id=0, code={
argv <- eval(parse(text="list(structure(c(8.85169533448293e-238, 2.77884205079773e-237, 8.5330427463164e-242, 7.89244209468013e-215, 6.74732964729372e-231, 1.30818670504849e-217, 1.39113376416096e-208, 1.35683278955814e-215, 7... | 635 | gpl-2.0 |
2262140e6ed2cae58984943da628cb1cfab45906 | cxxr-devel/cxxr | src/extra/testr/filtered-test-suite/attr/tc_attr_35.R | expected <- eval(parse(text="NULL"));
test(id=0, code={
argv <- eval(parse(text="list(structure(c(8.85169533448293e-238, 2.77884205079773e-237, 8.5330427463164e-242, 7.89244209468013e-215, 6.74732964729372e-231, 1.30818670504849e-217, 1.39113376416096e-208, 1.35683278955814e-215, 7... | 635 | gpl-2.0 |
2262140e6ed2cae58984943da628cb1cfab45906 | krlmlr/cxxr | src/extra/testr/filtered-test-suite/attr/tc_attr_35.R | expected <- eval(parse(text="NULL"));
test(id=0, code={
argv <- eval(parse(text="list(structure(c(8.85169533448293e-238, 2.77884205079773e-237, 8.5330427463164e-242, 7.89244209468013e-215, 6.74732964729372e-231, 1.30818670504849e-217, 1.39113376416096e-208, 1.35683278955814e-215, 7... | 635 | gpl-2.0 |
092d23c63fb20c7f36370fc045f4669c017cb7a4 | dvera/gyro | R/bedtoolsCoverage.R | #' Calculate coverage of a set of bed files over intervals in a single bed file.
#'
#' \code{bedtoolsCoverage} is a wrapper for \code{bedtools intersect -c}.
#'
#' @param bedFiles A character vector of paths to bed files.
#' @param windowfile A string specifying the path to the bed file within which to calculate covera... | 2,127 | mit |
e0474f41cf57d4032a9c3c989108c2a059351d79 | mariodeng/FirebrowseR | R/Metadata.ClinicalNames.R | #' Retrieve names of all TCGA clinical data elements (CDEs).
#'
#' Retrieve names of all patient-level clinical data elements (CDES) available in TCGA, unioned across all disease cohorts. A CDE will be listed here only when it has a value other than NA for at least 1 patient case in any disease cohort. For more inform... | 962 | mit |
1488db29eb764dc221de9057684e7cc8c47a0ff9 | apache/arrow | r/R/feather.R | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | 9,702 | apache-2.0 |
1488db29eb764dc221de9057684e7cc8c47a0ff9 | kou/arrow | r/R/feather.R | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | 9,702 | apache-2.0 |
572a7be744e216f1346e00a5c6addf8a435f79c0 | jukiewiczm/renjin | packages/grid/src/main/R/renjinStubs.R |
validUnits <- function(units) {
answer <- NULL
n <- length(units)
integer(n)
}
| 87 | gpl-3.0 |
572a7be744e216f1346e00a5c6addf8a435f79c0 | hlin09/renjin | packages/grid/src/main/R/renjinStubs.R |
validUnits <- function(units) {
answer <- NULL
n <- length(units)
integer(n)
}
| 87 | gpl-3.0 |
7223aea80129539b0e0a5784023a29875517fc71 | nathanlazar/BaTFLED3D | R/im_2_mat.R | #' Plot heatmaps of two matrices in red and blue
#'
#' Displays two heatmaps of matrices using red and blue colors. Options to scale
#' and sort as well as any other graphical parameters with ... Sorting attempts to match
#' columns between the two matrices using their correlation over rows. If \code{sort==TRUE}
#' th... | 5,158 | mit |
696b261bcf6c6a2a78bfa8525f8bde85c69fa721 | CodeGit/SequenceImp | dependencies-bin/macosx/bin/R/lib/R/library/ShortRead/unitTests/test_SRList.R | test_SRList_construction <- function() {
srl <- SRList()
checkTrue(validObject(srl))
checkEquals(0, length(srl))
srl <- SRList(list())
checkTrue(validObject(srl))
checkEquals(0, length(srl))
srl <- SRList(list(1))
checkTrue(validObject(srl))
checkEquals(1, length(srl))
srl <- ... | 568 | gpl-3.0 |
a0e6bac81cf7f18e0f0ba0c5dc8858371b6a15e9 | cchacua/m2-migrations | scripts/rsql/queries.R | # To see secure folder:
# SHOW VARIABLES LIKE "secure_file_priv";
# mysql -h "localhost" -u "root" -p
# PATSTAT
dbListTables(patstat)
dbListFields(patstat, "TLS201_APPLN")
dbListFields(patstat, "TLS211_PAT_PUBLN")
dbListFields(patstat, "TLS211_SAMPLE")
# rs<-dbGetQuery(patstat, "SELECT APPLN_ID FROM TLS201_APPLN L... | 3,462 | gpl-3.0 |
a7034d95277f8c7f29fc568a060c5edaf5538df9 | aegorenkov/science_hackday_conservation | cvtest.R | library(boot)
setwd("~/DCHackday")
data.model <- read.csv("datafinal.csv")
odds <- function(x) {
exp(x)/(exp(x)+1)
}
form = formula(protected~ Percent_of_HUC_Rare + MeanPrecip)
fold = 10
x <- na.omit(data.model)
n <- nrow(x)
prop <- n%/%fold
newseq <- rank(runif(n))
k <- as.factor((newseq - 1) %/% prop + 1)
y... | 885 | mit |
696b261bcf6c6a2a78bfa8525f8bde85c69fa721 | CodeGit/SequenceImp | dependencies-bin/linux/bin/R/lib64/R/library/ShortRead/unitTests/test_SRList.R | test_SRList_construction <- function() {
srl <- SRList()
checkTrue(validObject(srl))
checkEquals(0, length(srl))
srl <- SRList(list())
checkTrue(validObject(srl))
checkEquals(0, length(srl))
srl <- SRList(list(1))
checkTrue(validObject(srl))
checkEquals(1, length(srl))
srl <- ... | 568 | gpl-3.0 |
696b261bcf6c6a2a78bfa8525f8bde85c69fa721 | CodeGit/SequenceImp | dependencies-bin/windows/bin/R/library/ShortRead/unitTests/test_SRList.R | test_SRList_construction <- function() {
srl <- SRList()
checkTrue(validObject(srl))
checkEquals(0, length(srl))
srl <- SRList(list())
checkTrue(validObject(srl))
checkEquals(0, length(srl))
srl <- SRList(list(1))
checkTrue(validObject(srl))
checkEquals(1, length(srl))
srl <- ... | 568 | gpl-3.0 |
c29b0a495d8eac83cc473b84df69cd985109f1c2 | nsmader/acs-constructicon | pickacs/R/measure.R | measure <- function(obj) {
UseMethod("measure")
}
measure.default <- function(obj) {
warning("Unknown class: ", class(x))
}
| 132 | agpl-3.0 |
f4048b383d0ec5fcb68e8cb697e726fcbfbe676f | SergeyMirvoda/da2016 | classwork2/vectors.R | #Векторы числовой и строковый
num_vector <- c(1, 10, 49)
char_vector <- c("a", "b", "c")
# Заполните булевый вектор
bool_vector <-
# Выберите из числового вектора значения при помощи булевого вектора
num_vector[bool_vector]
# Повторите то же самое для строкововго вектора
#Составте булевый вектор из ч... | 902 | unlicense |
f4048b383d0ec5fcb68e8cb697e726fcbfbe676f | SergeyMirvoda/MD-DA-2017 | classwork2/vectors.R | #Векторы числовой и строковый
num_vector <- c(1, 10, 49)
char_vector <- c("a", "b", "c")
# Заполните булевый вектор
bool_vector <-
# Выберите из числового вектора значения при помощи булевого вектора
num_vector[bool_vector]
# Повторите то же самое для строкововго вектора
#Составте булевый вектор из ч... | 902 | mit |
06601c1037b821479f2af97648a4f1d6849afc32 | tudob/wfg | R/wfgTrafos.R | # Transformations
# the function-names are those in the wfg-paper plus prefix wfg
# in the spec the user uses only the part after the "_" (no b/s/r-kind)
# conventions used:
# a parameter-default of =NA shows that there is a default (which will be calculated on demand) as opposed to a required value
# function naming ... | 9,321 | mit |
f357c84594fc4f05c29b8384951fa2ac705e8947 | mjsmith037/mjsmith037.github.io | talks/ESA_08.2019/Code/NO-histogram.R | library(magrittr)
library(tidygraph)
library(ggraph)
library(tidyverse)
library(broom)
library(kableExtra)
tidy_p_value <- function(pvals) {
ifelse(pvals < 0.001, "< 0.001", format(pvals, digits=0, nsmall=3))
}
tidy_t_test_long <- function(dat, grouping, variable) {
factor_levels <- unique(dat[[grouping]])
t.te... | 4,325 | mit |
6b2e0643f064c2e59773b18f22c273d86bc7a3c9 | cfwstem/faculty-numbers | read-data.R | utkfacultydata<- read.csv('https://docs.google.com/spreadsheets/d/1--oEDQy-DIircR-xfdwLRQ0E_9MuFCF1We423l4YrYM/pub?output=csv')
| 128 | gpl-3.0 |
619790f457cbb6e7bfa5731bd3b692bca4b37451 | BenjiHu/CSCI2963-Labs | lab7/months.R | months
remove("months")
for(mon in month.name){
print(mon)
} | 62 | mit |
40b8521a1bca6eb2bed2863347666a02930e61da | mumtahena/bild_signatures | code/Archive/example_assign_corr.R | ## running ASSIGN for raf sing
trainingLabelr<-list(control=list(raf=1:12),raf=13:18)
sub_dir<-paste(basedir,"raf_25_gene_list",sep='/')
dir.create( sub_dir)
assign_easy_multi(trainingData = cbind(c_gfp,c_raf),test=c_test,trainingLabel1 = trainingLabelr,g=25,out_dir_base = sub_dir,single = 1)
sub_dir<-paste(basedir,"... | 2,274 | mit |
7e6d4e7146f6a12e90065ecead5115b94d21122b | cran/RSAGA | R/RSAGA-core.R | #' Internal functions that determine OS-specific path in which modules might be located.
#'
#' @name rsaga.get.modules.path
#' @rdname rsaga.get.modules.path
#' @param sysname character: name of the operating system, determined by default by [base::Sys.info()]: e.g., `"Windows"`, `"Linux"`, `"Darwin"` (for Mac OSX)... | 65,948 | gpl-2.0 |
f381e4dcfd3cff5937cbe24efe7a3096ce7eaf4f | radfordneal/pqR | src/library/base/R/pmax.R | # File src/library/base/R/pmax.R
# Part of the R package, http://www.R-project.org
# Modifications for pqR Copyright (c) 2013, 2017, 2018 Radford M. Neal.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Soft... | 4,825 | gpl-2.0 |
a6c083ba7e1e85a3a93e9015fbcc23a97241de3a | wenjie2wang/splines2 | inst/examples/ex-ibs.R | library(splines2)
x <- seq.int(0, 1, 0.01)
knots <- c(0.2, 0.4, 0.7, 0.9)
ibsMat <- ibs(x, knots = knots, degree = 1, intercept = TRUE)
## get the corresponding B-splines by bSpline()
bsMat0 <- bSpline(x, knots = knots, degree = 1, intercept = TRUE)
## or by the deriv() method
bsMat <- deriv(ibsMat)
stopifnot(all.equ... | 704 | gpl-3.0 |
152ee95bde40e963d4d5df01029384e7ef986b11 | mkienzle/NSW-sea-garfish-stock-assessment | docs/docs/Script/CalculatePopulationTrendsWithUncertainties.R | # CREATED 13 Dec 2016
# MODIFIED 19 May 2019
# PURPOSE estimate abundance and recruitment point estimates and uncertainties
# METHOD according to S. Brandt, Data Analysis, 1999 Springer-Verlag
# The x% confidence region of the log-likelihood is contains with the minimum log-likelihood + chi-square (0.95, 4 df... | 3,560 | gpl-3.0 |
152ee95bde40e963d4d5df01029384e7ef986b11 | mkienzle/NSW-sea-garfish-stock-assessment | Script/CalculatePopulationTrendsWithUncertainties.R | # CREATED 13 Dec 2016
# MODIFIED 19 May 2019
# PURPOSE estimate abundance and recruitment point estimates and uncertainties
# METHOD according to S. Brandt, Data Analysis, 1999 Springer-Verlag
# The x% confidence region of the log-likelihood is contains with the minimum log-likelihood + chi-square (0.95, 4 df... | 3,560 | gpl-3.0 |
8ec6c23c15e6f034693b7b067e4d6472fd70ab58 | karmatarap/e107_Project_Test_Area | r/helper_functions/parse-binary_data.R | #' Parse binary data
#'
#' @description Parses the data with binary annotation¨
#'
#' @author AlexandeR Noll
#'
#' @return data frame
#'
#' @examples parse_binary_data()
#' @import dplyr, readr, stringr
parse_binary_data <- function(type) {
library(dplyr)
library(purrr)
library(readr)
library(stringr... | 987 | mit |
1f2815a8826cd0903c2abd9fa3963bd5af6dd9e1 | hcommenges/mapfitR | GarminFIT_script.R | ###########################################
######## Explore Garmin FIT tracks
######## Script
###########################################
# load packages ----
library(lubridate)
library(ISOweek)
library(ggplot2)
library(leaflet)
library(sf)
library(dplyr)
# load functions ----
source(file = "GarminFIT_fct.R")
# s... | 710 | agpl-3.0 |
a3e0e73a9ac966c61aba18d5a7a274cc48b95ad9 | WLOGSolutions/RSuite | packages/RSuite/R/28_repo_manager_dir.R | #----------------------------------------------------------------------------
# RSuite
# Copyright (c) 2017, WLOG Solutions
#
# Repo manager working on directory. Created by rsuite_repo_adapter_dir.
#----------------------------------------------------------------------------
#'
#' Create repo manager to manag... | 4,733 | apache-2.0 |
35fc9ff795ce73636b806120d134c8f3577eb56e | marchtaylor/fishdynr | R/growth_soVB2.R | #' @title seasonally oscillating von Bertalanffy growth function (using L0)
#' @description \code{growth_soVB2} describes the growth as a function of age (t)
#' using the seasonally oscillating von Bertalanffy growth function (Somers 1988).
#' The function differs slightly from \code{\link[fishdynr]{growth_soVB}}
#' b... | 1,173 | mit |
aeb543bf12b27c3fc955aea28540b05c95c5f8f3 | woobe/h2o | R/tests/testdir_jira/runit_v_11_datemanipulation.R | #
# date parsing and field extraction tests
#
setwd(normalizePath(dirname(R.utils::commandArgs(asValues=TRUE)$"f")))
source('../findNSourceUtils.R')
datetest <- function(conn){
Log.info('uploading date testing dataset')
hdf <- h2o.importFile(conn, normalizePath(locate('smalldata/jira/v-11.csv')))
# df shoul... | 2,436 | apache-2.0 |
858fc2ecec7cd26a172fca60b4c5c40661a1fe26 | sorensje/R_helperfunctions | zeropad.R | zeropad <- function(x){
if (x %/% 10 < 1){
padded_x <- paste('0',x,sep="")
}
else{
padded_x <- as.character(x)
}
return(padded_x)
} | 151 | gpl-2.0 |
035618c2b2c6e91a9571eb833f30563a40dd9d30 | h2oai/h2o-3 | h2o-r/demos/rdemo.supervised.large.R | library(h2o)
h2o.init()
runAll = function(data_path,split_ratio,response,predictors,flag,test_file_path){
#remove all keys from h2o prior to running the function
h2o.rm(as.character(grep(pattern = "", x = h2o.ls()$key,value=T)));
print(paste("Parse : ",data_path,sep=''));
time = system.time(data <- h2o.impor... | 6,561 | apache-2.0 |
9410009ce819a05cad8a6ff232c23186882d4472 | FTSRG/mondo-sam | reporting/shiny/filters/DataFilter.R | library("R.oo", , quietly = TRUE)
#' DataFilter class
setConstructorS3(name = "DataFilter", abstract = TRUE, function(selections = NULL){
extend(Object(), "DataFilter",
.selections = selections,
.container = NULL,
.selectedState = NULL,
.allCurrentStates = NULL,
.allState... | 3,190 | epl-1.0 |
adcded77e2798b3a199fb23e99075b1be188c015 | pik-piam/magclass | R/read.magpie.R | #' Read MAgPIE-object from file
#'
#' Reads a MAgPIE-file and converts it to a 3D array of the structure
#' (cells,years,datacolumn)
#'
#' This function reads from 13 different MAgPIE file\_types. "rds" is
#' a R-default format for storing R objects."cs2" or "cs2b" is the new standard
#' format for cellular data with o... | 10,761 | lgpl-3.0 |
73c10f480ead65a507ff46fb0ebecc6f359388cd | harmonlab/angio-pulse | R_scripts/polyploidy_analyses.R | require(geiger)
require(phylo)
## USING MLE tree
setwd("~/Documents/tank/angiosperms/angio-pulse") # change to match local directory
dat=get(load("spermatophyta_AToL_639_PL_MEDUSA_BATCH.effectsize.rda"))$summary
# only consider upshifts
dat=dat[which(dat$r>0),]
# get the tree
phy=get(load("spermatophyta_AToL_639_PL... | 9,554 | gpl-2.0 |
fe632709746c52681c0186fc369b085ca33c8669 | AlDanial/cloc | tests/inputs/utilities.R | # from https://github.com/lme4/lme4
if(getRversion() < "2.15")
paste0 <- function(...) paste(..., sep = '')
### Utilities for parsing and manipulating mixed-model formulas
##' From the result of \code{\link{findbars}} applied to a model formula and
##' and the evaluation frame, create the model matrix, etc. associa... | 33,475 | gpl-2.0 |
fe632709746c52681c0186fc369b085ca33c8669 | richarddavis/cloc | testcode/utilities.R | # from https://github.com/lme4/lme4
if(getRversion() < "2.15")
paste0 <- function(...) paste(..., sep = '')
### Utilities for parsing and manipulating mixed-model formulas
##' From the result of \code{\link{findbars}} applied to a model formula and
##' and the evaluation frame, create the model matrix, etc. associa... | 33,475 | gpl-2.0 |
fe632709746c52681c0186fc369b085ca33c8669 | garbear/cloc | testcode/utilities.R | # from https://github.com/lme4/lme4
if(getRversion() < "2.15")
paste0 <- function(...) paste(..., sep = '')
### Utilities for parsing and manipulating mixed-model formulas
##' From the result of \code{\link{findbars}} applied to a model formula and
##' and the evaluation frame, create the model matrix, etc. associa... | 33,475 | gpl-2.0 |
fe632709746c52681c0186fc369b085ca33c8669 | kindkaktus/cloc | testcode/utilities.R | # from https://github.com/lme4/lme4
if(getRversion() < "2.15")
paste0 <- function(...) paste(..., sep = '')
### Utilities for parsing and manipulating mixed-model formulas
##' From the result of \code{\link{findbars}} applied to a model formula and
##' and the evaluation frame, create the model matrix, etc. associa... | 33,475 | gpl-2.0 |
a92686491c2980bb92b6421720b4152e64670197 | dabrze/swirl_courses | Programowanie_w_R/vapply_i_tapply/initLesson.R | # Path to installed lesson
.lessonpath <- file.path(path.package("swirl.pl"), "Courses", "Programowanie_w_R",
"lapply_i_sapply")
# Path to dataset
.datapath <- file.path(.lessonpath, "flag.data.txt")
# Load dataset
flags <- read.csv(.datapath, header=FALSE)
# Set column names
colnames(f... | 1,067 | gpl-3.0 |
eba7fd47dce215000ec40ffc15aeb7bc692a18fe | nick-ulle/RCompilerExamples | tests/testthat/test_knn.R | # Description:
# Tests for the knn example.
test_that("compiled order function is correct", {
module = compile_knn()
.order = module[[".order"]]
x = c(1.3, -1.2, 2.1, 3.5, 7.1, -20, 4)
result = .llvm(.order, x, length(x))
target = order(x)
expect_equal(result, target)
x = c(-0.33, 2.02, -1.7, -1.01, ... | 2,426 | mit |
fde8b72a8959b0b477abaf7018d436e493491701 | benjjneb/dada2 | R/paired.R | ################################################################################
#' Merge denoised forward and reverse reads.
#'
#' This function attempts to merge each denoised pair of forward and reverse reads,
#' rejecting any pairs which do not sufficiently overlap or which contain too many
#' (>0 by default) mi... | 12,097 | lgpl-3.0 |
fe632709746c52681c0186fc369b085ca33c8669 | cosmicexplorer/cloc-code | testcode/utilities.R | # from https://github.com/lme4/lme4
if(getRversion() < "2.15")
paste0 <- function(...) paste(..., sep = '')
### Utilities for parsing and manipulating mixed-model formulas
##' From the result of \code{\link{findbars}} applied to a model formula and
##' and the evaluation frame, create the model matrix, etc. associa... | 33,475 | gpl-2.0 |
fe632709746c52681c0186fc369b085ca33c8669 | nexB/cloc-mirror | testcode/utilities.R | # from https://github.com/lme4/lme4
if(getRversion() < "2.15")
paste0 <- function(...) paste(..., sep = '')
### Utilities for parsing and manipulating mixed-model formulas
##' From the result of \code{\link{findbars}} applied to a model formula and
##' and the evaluation frame, create the model matrix, etc. associa... | 33,475 | gpl-2.0 |
ba8818e94cff901dd5fa651e2a9b6388c267492d | jackwasey/icd | R/who.R | # TODO: only download (and cache) WHO data as needed, rather than forcing user to wait minutes to download everything on first use.
#' Functions to get the WHO ICD-10 English 2016 and French 2008 data
#' @param resource Fragment of URL with specific ICD-10 resource requested
#' @param year Four-digit year as integer o... | 10,104 | gpl-3.0 |
d0e8a92d7271387a234583b2ef181bc631558a53 | kyoren/https-github.com-h2oai-h2o-3 | h2o-r/tests/testdir_algos/glm/runit_NOPASS_GLM_forloop_attack_medium.R | setwd(normalizePath(dirname(R.utils::commandArgs(asValues=TRUE)$"f")))
source('../../h2o-runit.R')
# Constants and setters
bools <- c(TRUE, FALSE)
set_x <- function(cols) {
if(sample(bools,1)) {
while (TRUE){
myX <- cols
for(i in 1:length(cols))
if (sample(bools, 1))
myX <- myX[-i]
... | 6,943 | apache-2.0 |
300efa20cd1230fd1e6f534413021473a44021c9 | caus-am/aci | R/utils/next_colex_comb.R | next_colex_comb<-function(x) {
#For a 0-1 vectors gives a next
#Can be used to quickly iterate over all subset of a given size.
#Just start with (1,1,1,….,1,0,…,0). In the end returns 0.
#The underlying mechanism to determine the successor is to determine the lowest block of ones
#and move its highest bit one positio... | 617 | bsd-2-clause |
329b1c1c8c86b8530af11a063810f68ee4841d66 | heggy231/R_Bootcamp_DataWeek_2015 | 8_-_Data_Manipulation.R |
# title: "8 - Data Manipulation"
author: "Joseph Rickert"
date: "September 28, 2015"
# In this script we will show some basic data wrangling.
## Fetch some data from Yahoo Finance
# Go to http://finance.yahoo.com/q/hp?s=IBM+Historical+Prices and copy the link to the table.
# Then read the data directly from the ... | 5,394 | mit |
329b1c1c8c86b8530af11a063810f68ee4841d66 | joseph-rickert/R_Bootcamp_DataWeek_2015 | 8_-_Data_Manipulation.R |
# title: "8 - Data Manipulation"
author: "Joseph Rickert"
date: "September 28, 2015"
# In this script we will show some basic data wrangling.
## Fetch some data from Yahoo Finance
# Go to http://finance.yahoo.com/q/hp?s=IBM+Historical+Prices and copy the link to the table.
# Then read the data directly from the ... | 5,394 | mit |
73ff14eebb0796f2b0551c5b691905cca074806c | illiHub/R | Misc/eventDetails.R | ###########################################
# SCRIPT START
###########################################
# set working directory
setwd(workdir1)
# import table
#j<-1
for (j in 1:length(subjects)){
file <- subjects[j]
mainmat_events <- read.table(file, header = T, sep = "\t", dec = ",",fill = FALSE, na.strings="NA", bla... | 2,425 | mit |
6180ac829ef92cf962600e5271eaff80d35b6562 | personlin/GMPEhaz | R/Crustal_Common_Form.R | #' GMPE function for Crustal Common form 001 (2017)
#'
#' \code{Cru.Com.001} returns the ground-motion prediction with it sigma of Crustal Common form 001 GMPE.
#'
#'Crustal Common form 001
#'
#' @param Mag Earthquake momnet magnitude, Numeric.
#' @param Rrup Rupture distance(km), Numeric.
#' @param Rjb Joyner and Boor... | 32,534 | gpl-3.0 |
4c313053b91967aa4b77b73a79afdac976b09a64 | poissonconsulting/tulip | R/directory.R | #' Delete directory
#'
#' Deletes directory specified by dir after possibly checking with user.
#'
#' @param dir a character scalar of the directory to delete
#' @param check a logical scalar indicating whether to check with user
#' @return an invisible logical scalar indicating whether successful.
#' @export
delete_... | 2,000 | mit |
8fd195072e11ab254775e00004b28e6e61639938 | sje30/eglen2015 | vignettes/w81s1_sims.R | ## ---- get-rgc-data
##rgc.of = read.table('~/mosaics/data/w81s1of.txt')
##rgc.on = read.table('~/mosaics/data/w81s1on.txt')
rgc.of.file = system.file("extdata/w81s1/w81s1of.txt", package="eglen2015")
rgc.on.file = system.file("extdata/w81s1/w81s1on.txt", package="eglen2015")
rgc.w.file = system.file("extdata/w81s1/w8... | 717 | mit |
2f9094fe4a55b43a6d315c9a0f11feebacb072a7 | bmatthie/diamonds | ui.R | # ===========================================================================
# File: ui.R
#
# Copyright 2015 Brian Robert Matthiesen
#
# 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
#
# h... | 1,486 | apache-2.0 |
f677e3288b3a86caf188aa02fa8c2f78e80d7339 | petertbryant/MidCoastTMDL | 05e_ParameterUncertaintyAnalysis.R | library(SSN)
library(plyr)
library(RODBC)
library(ggplot2)
library(reshape2)
library(MASS)
options(stringsAsFactors = FALSE)
#Get fit object from 06_scenarios.R
fit <- models[[7]]
#Generate confidence intervals using assumptions of indepent normality
df_ci <- confint.glmssn(fit, level = .9)
df_ci <- cbind(df_ci, fit$... | 1,739 | gpl-3.0 |
71f2f9e5271cabf7a4b433bac531e35f89fd6cc9 | wch/r-source | src/library/tools/R/userdir.R | # File src/library/tools/R/userdir.R
# Part of the R package, https://www.R-project.org
#
# Copyright (C) 2020 The R Core Team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either vers... | 2,861 | gpl-2.0 |
83de570ca3872b4a79f72dbfd9d6ac96e4101dca | XiaoruiZhu/AdpQMLE | AdaptQMLE/R/gen.lin.R | #' Generating function for single linear model y = a + b*x.
#'
#' @title Single linear model y = a + b*x.
#'
#' @param intercept The intercept of single linear model.
#' @param slope The parameter b, which is the slope of y = a + b*x.
#' @param noise.variance The variance of error series.
#' @param x The depedent varia... | 998 | mit |
fc70d93d079bfa82849db3d7e073b90fced998f7 | tomoakin/TCC | TCC/tests/DESDES1.R | library(TCC)
set.seed(12734)
tcc <- simulateReadCounts(Ngene = 100, PDEG = 0.2, DEG.assign = c(0.9, 0.1),replicate=c(1,1))
tcc <- calcNormFactors(tcc, norm.method = "deseq", test.method = "deseq",
FDR = 0.1, floorPDEG = 0.05)
cat("tcc$norm.factors: ")
cat(tcc$norm.factors)
cat("\n")
cat("tcc$s... | 382 | gpl-2.0 |
c5ae5684555d54c3833ef3bb143e00aec757ed6a | 52North/sensorweb4R | R/class-timeseries.R | #' @include generic-methods.R
#' @include class-phenomenon.R
#' @include class-service.R
#' @include class-feature.R
#' @include class-offering.R
#' @include class-procedure.R
#' @include class-category.R
#' @include class-station.R
#' @include class-tvp.R
NULL
#' Timeseries
#'
#' Represents a timeseries.
#'
#' @famil... | 12,619 | apache-2.0 |
e95ff8bfbf65ee55e1ac57b3c30e182f521a227b | cxxr-devel/cxxr | src/extra/testr/filtered-test-suite/max/tc_max_27.R | expected <- 3
test(id=23, code={
argv <- structure(list(2, 3, NA, na.rm = TRUE), .Names = c("", "", "",
"na.rm"))
do.call('max', argv);
}, o = expected);
| 157 | gpl-2.0 |
e95ff8bfbf65ee55e1ac57b3c30e182f521a227b | kmillar/cxxr | src/extra/testr/filtered-test-suite/max/tc_max_27.R | expected <- 3
test(id=23, code={
argv <- structure(list(2, 3, NA, na.rm = TRUE), .Names = c("", "", "",
"na.rm"))
do.call('max', argv);
}, o = expected);
| 157 | gpl-2.0 |
e95ff8bfbf65ee55e1ac57b3c30e182f521a227b | ArunChauhan/cxxr | src/extra/testr/filtered-test-suite/max/tc_max_27.R | expected <- 3
test(id=23, code={
argv <- structure(list(2, 3, NA, na.rm = TRUE), .Names = c("", "", "",
"na.rm"))
do.call('max', argv);
}, o = expected);
| 157 | gpl-2.0 |
bbcd7b37a4df12cd9a36b1905aec0c4cddb1e205 | splaticvoid/datasciencecoursera | Assignment 1/complete.R | complete <- function(directory, id = 1:332) {
## 'directory' is a character vector of length 1 indicating
## the location of the CSV files
## 'id' is an integer vector indicating the monitor ID numbers
## to be used
## Return a data frame of the form:
## id nobs
## 1 117
## 2 1041
## ...
## ... | 1,541 | cc0-1.0 |
e95ff8bfbf65ee55e1ac57b3c30e182f521a227b | kmillar/rho | src/extra/testr/filtered-test-suite/max/tc_max_27.R | expected <- 3
test(id=23, code={
argv <- structure(list(2, 3, NA, na.rm = TRUE), .Names = c("", "", "",
"na.rm"))
do.call('max', argv);
}, o = expected);
| 157 | gpl-2.0 |
e95ff8bfbf65ee55e1ac57b3c30e182f521a227b | rho-devel/rho | src/extra/testr/filtered-test-suite/max/tc_max_27.R | expected <- 3
test(id=23, code={
argv <- structure(list(2, 3, NA, na.rm = TRUE), .Names = c("", "", "",
"na.rm"))
do.call('max', argv);
}, o = expected);
| 157 | gpl-2.0 |
e95ff8bfbf65ee55e1ac57b3c30e182f521a227b | krlmlr/cxxr | src/extra/testr/filtered-test-suite/max/tc_max_27.R | expected <- 3
test(id=23, code={
argv <- structure(list(2, 3, NA, na.rm = TRUE), .Names = c("", "", "",
"na.rm"))
do.call('max', argv);
}, o = expected);
| 157 | gpl-2.0 |
376eec2b46b7f8aca2756688676e56d0a1106212 | mexindian/TileMaker | tests/testthat.R | library(testthat)
library(TileMaker)
test_check("TileMaker")
| 62 | mit |
73b2aae2e90d43d90bf04a6128c96bf80a11fa16 | aappling-usgs/gsplot | R/lines.R | #' gsplot lines
#'
#' Creating a line by specifying specific plot points. See \code{\link[graphics]{lines}} for more details.
#'
#' @param object gsplot object
#' @param \dots Further graphical parameters may also be supplied as arguments. See 'Details'.
#'
#' @details Additional graphical parameter inputs:
#' \ite... | 1,958 | cc0-1.0 |
73b2aae2e90d43d90bf04a6128c96bf80a11fa16 | jiwalker-usgs/gsplot | R/lines.R | #' gsplot lines
#'
#' Creating a line by specifying specific plot points. See \code{\link[graphics]{lines}} for more details.
#'
#' @param object gsplot object
#' @param \dots Further graphical parameters may also be supplied as arguments. See 'Details'.
#'
#' @details Additional graphical parameter inputs:
#' \ite... | 1,958 | cc0-1.0 |
73017f0a824a912163a9f897515f8df287f4918a | ivanhigueram/deforestacion | modeling/reg_dis_het_effects.R | ##############################################################################################
##############################################################################################
### RUN REGRESSION DISCONTINUITY MODELS ###
### THIS CODE WILL READ THE DIS... | 23,029 | mit |
dcbfcb072cee134e44e035cf1bb2435dc3d1ec09 | B1aine/kaggle-allstate | doSubmission.R | library(cvTools)
library(gbm)
########################################
############## TRAINING ################
########################################
load('data/train_2014.04.05.RData')
nam = names(data)
omitClass <- c(which(nam=="targetA"),which(nam=="targetB"),which(nam=="targetC"),which(nam=="targetD"),
... | 4,343 | mit |
fa7b616742d8eddd1ece1f5a8e85373c81052129 | happynotes/PIHM.AnalysisR | R/datafilter.R | #' Find the cells/segments that match your filters.
#' Developed by Lele Shu( lele.shu at gmail.com lzs157 at psu.edu )
#' Created by Fri Apr 17 14:11:46 EDT 2015
#'
#' @param data in TS
#' @param filter. If filter<0, find the IDs where is smaller than filter. If filter>0, find the IDs where is larger than filter... | 5,597 | gpl-2.0 |
73017f0a824a912163a9f897515f8df287f4918a | banco-republica-research/deforestacion | modeling/reg_dis_het_effects.R | ##############################################################################################
##############################################################################################
### RUN REGRESSION DISCONTINUITY MODELS ###
### THIS CODE WILL READ THE DIS... | 23,029 | mit |
5fe0311ef0711532e4176209605ff6e1af56eb66 | thehyve/Rmodules_oncoprint | web-app/Rscripts/Heatmap/HeatmapLoader.R | ###########################################################################
# Copyright 2008-2012 Janssen Research & Development, LLC.
#
# 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
#
# ... | 12,166 | apache-2.0 |
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