commit stringlengths 40 40 | subject stringlengths 4 1.73k | repos stringlengths 5 127k | old_file stringlengths 2 751 | new_file stringlengths 2 751 | new_contents stringlengths 1 8.98k | old_contents stringlengths 0 6.59k | license stringclasses 13
values | lang stringclasses 23
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|---|---|---|---|---|---|---|---|---|
2d8d173b39f796a67c336e9af395415413005269 | Fix syntax errors | berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,ryanlovett/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub | deployments/publichealth/image/r-packages/ph-252.r | deployments/publichealth/image/r-packages/ph-252.r | #!/usr/bin/env Rscript
# For https://github.com/berkeley-dsep-infra/datahub/issues/2556
# For https://github.com/berkeley-dsep-infra/datahub/issues/2524
# For https://github.com/berkeley-dsep-infra/datahub/issues/2748
# For https://github.com/berkeley-dsep-infra/datahub/issues/2788
# Fall 2021
print("Installing package... | #!/usr/bin/env Rscript
# For https://github.com/berkeley-dsep-infra/datahub/issues/2556
# For https://github.com/berkeley-dsep-infra/datahub/issues/2524
# For https://github.com/berkeley-dsep-infra/datahub/issues/2748
# For https://github.com/berkeley-dsep-infra/datahub/issues/2788
# Fall 2021
print("Installing package... | bsd-3-clause | R |
a1b0268eb1e189ae23e04ae5d9238b7066dc5ca1 | Update source.r | svobodam/Deep-Learning-Text-Summariser,svobodam/Deep-Learning-Text-Summariser,svobodam/Deep-Learning-Text-Summariser | PreProcessingScript/source.r | PreProcessingScript/source.r | # Source control script for complete dataset processing
setwd('~/deep-Learning-Text-Summariser')
# LIBRARIES
library(RSQLite)
library(tm)
library(reshape2)
library(gsubfn)
# FUNCTIONS
# Connection to DB
connDB = function(z) {
# Initiate Connection to DB
conn = dbConnect(dbDriver("SQLite"), z)
return(conn)
}
... | # Source control script for complete dataset processing
setwd('~/summCode')
# LIBRARIES
library(RSQLite)
library(tm)
library(reshape2)
library(gsubfn)
# FUNCTIONS
# Connection to DB
connDB = function(z) {
# Initiate Connection to DB
conn = dbConnect(dbDriver("SQLite"), z)
return(conn)
}
# Disconnect from DB
... | mit | R |
6b917eeedc841d97c3231532eb1958f0f8ec9a6b | Document semantics of sys module better | klmr/codons,klmr/codons | scripts/sys.r | scripts/sys.r | # Command line tools don’t want to clutter their output with unnecessary noise.
library = function (...)
suppressMessages(base::library(...))
#' The command line arguments
args = commandArgs(trailingOnly = TRUE)
#' The name of the script
#'
#' @note If the script was invoked interactively, this is the empty strin... | # Command line tools don’t want to clutter their output with unnecessary noise.
library = function (...)
suppressMessages(base::library(...))
#' The command line arguments
args = commandArgs(trailingOnly = TRUE)
#' The name of the script
script_name = local({
file = grep('^--file=', commandArgs(trailingOnly =... | apache-2.0 | R |
059be9bd0bab6fc84d3f4425649050ce5239994d | return data | lukejharmon/traitathon | rAnalysis/RImportData.r | rAnalysis/RImportData.r | ## dummy code to be filled in with methods to draw trees and data from online
get_traits<-function(trait_file_path){
## this is to be replaced with a way of calling traits
## given species names
trait_mat<-read.csv(trait_file_path)
return(trait_mat)
}
get_tree<-function(tree_file_path){
require(ape)
## this is... | get_traits<-function(trait_file_path){
## this is to be replaced with a way of calling traits
## given species names
trait_mat<-read.csv(trait_file_path)
}
get_tree<-function(tree_file_path){
require(ape)
## this is to be replaced with a way of calling trees
## from Open Tree given species names
tree<-read.tree... | mit | R |
c1ac2640e53eb32ea720b0e9025e918369444b85 | Update mtcars.r | bgweber/RServer,bgweber/RServer,bgweber/RServer,bgweber/RServer | tasks/userDemo/mtcars.r | tasks/userDemo/mtcars.r | # Copyright (C) 2016 Electronic Arts Inc. All rights reserved.
str(mtcars)
print("Sleeping for 15 seconds")
Sys.sleep(15)
print("Saving RData file")
dir.create("/var/www/html/RServer/reports/mtcars")
save(mtcars, file = "/var/www/html/RServer/reports/mtcars/mtcars.RData")
fit <- lm(mpg~am + wt + hp, data = mtcars... | str(mtcars)
print("Sleeping for 15 seconds")
Sys.sleep(15)
print("Saving RData file")
dir.create("/var/www/html/RServer/reports/mtcars")
save(mtcars, file = "/var/www/html/RServer/reports/mtcars/mtcars.RData")
fit <- lm(mpg~am + wt + hp, data = mtcars)
summary(fit)
print("Saving Model")
Sys.sleep(10)
save(fit, ... | bsd-3-clause | R |
32595c2326c75f029bd1418b1f757dcab5e3f2fd | revert pskill warn supp, no effect | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | R/qsys_multicore.r | R/qsys_multicore.r | #' Process on multiple cores on one machine
#'
#' This makes use of rzmq messaging and sends requests via TCP/IP
MULTICORE = R6::R6Class("MULTICORE",
inherit = QSys,
public = list(
initialize = function(...) {
super$initialize(..., node="localhost")
},
submit_jobs = functio... | #' Process on multiple cores on one machine
#'
#' This makes use of rzmq messaging and sends requests via TCP/IP
MULTICORE = R6::R6Class("MULTICORE",
inherit = QSys,
public = list(
initialize = function(...) {
super$initialize(..., node="localhost")
},
submit_jobs = functio... | apache-2.0 | R |
fcd8d0a41cb3a1c1fd749dd02e65d2113fa0f745 | Update utci_class.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/utci_class.r | R/utci_class.r | #' utci_class
#'
#' Calculate ten (10) thermal class of Universal Thermal Climate Index ( UTCI) index.
#'
#' @param numeric t Air temperature in Celsius degrees.
#' @param numeric rh Air Relative humidity in percentage.
#' @param numeric wind Wind speed in meter per second.
#' @param numeric tmrt Mean radiant temperat... | #' utci_class
#'
#' Calculate ten (10) thermal class of Universal Thermal Climate Index ( UTCI) index.
#'
#' @param numeric t Air temperature in Celsius degrees.
#' @param numeric rh Air Relative humidity in percentage.
#' @param numeric wind Wind speed in meter per second.
#' @param numeric tmrt Mean radiant temperat... | mit | R |
4a056e731f2f6f9500dba98de8699f8e83356e6a | Update slavicreview.r | YaleDHLab/lab-workshops,YaleDHLab/lab-workshops,YaleDHLab/lab-workshops,YaleDHLab/lab-workshops,YaleDHLab/lab-workshops | rstudio_dfrtopics/slavicreview.r | rstudio_dfrtopics/slavicreview.r | #Create a new project in the folder that has the JSTOR data.
install.packages("devtools")
install_github("agoldst/dfrtopics")
install.packages("dplyr")
install.packages("ggplot2")
install.packages("lubridate")
install.packages("stringr")
install.packages("rJava")
install.packages("mallet")
library(devtools)
options... | Create a new project in the folder that has the JSTOR data.
install.packages("devtools")
install_github("agoldst/dfrtopics")
install.packages("dplyr")
install.packages("ggplot2")
install.packages("lubridate")
install.packages("stringr")
install.packages("rJava")
install.packages("mallet")
library(devtools)
options(... | mit | R |
eb68d7f64d1944ab4974589143f405def1d99d2e | use base rep if vector | mschubert/narray,mschubert/narray | R/rep.r | R/rep.r | #' Repeats an array along an arbitrary axis
#'
#' @param x An array object
#' @param n Integer, how often to repeat
#' @param along Along which axis to repeat (default: 1)
#' @return An array that is repeated `n` times on axis `along`
#' @export
rep = function(x, n, along=1) {
if (is.null(dim(x))) ... | #' Repeats an array along an arbitrary axis
#'
#' @param x An array object
#' @param n Integer, how often to repeat
#' @param along Along which axis to repeat (default: 1)
#' @return An array that is repeated `n` times on axis `along`
#' @export
rep = function(x, n, along=1) {
xl = base::rep(list(x... | apache-2.0 | R |
69a9ef23dcd06f517e70054507c24381a3f9f810 | Update R pipe operator to magrittr | klmr/.files,klmr/.files,klmr/.files | .R/pipe.r | .R/pipe.r | `%>%` <- magrittr::`%>%`
| # Pipe operator modified after Robert Sugar, e.g. at
# <http://markmail.org/thread/uygwsdulfvxlydlh>
`%|%` <- function (x, y) {
thecall <- match.call()
if (is.name(thecall$y) || is.function(thecall$y))
y(x)
else
eval(thecall$y, list(value = eval(thecall$x)))
}
| apache-2.0 | R |
2f38a43ed5d39149dd90a05f986cfda7963c1ede | add shift and addChr option | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/Annotation/getGeneLocus.r | lib/Annotation/getGeneLocus.r | require(biomaRt)
require(stringr)
if(!exists("host")){
host="grch37.ensembl.org"
}
if(!exists("dataset")){
dataset = "hsapiens_gene_ensembl"
}
if(!exists("symbolKey")){
symbolKey = "hgnc_symbol"
}
if(!exists('genesStr')){
genesStr<-"LDLR APOB PCSK9 LDLRAP1 STAP1 LIPA ABCG5 ABCGB APOE LPA PNPLA5 CH25H INSIG2... | require(biomaRt)
require(stringr)
if(!exists("host")){
host="grch37.ensembl.org"
}
if(!exists("dataset")){
dataset = "hsapiens_gene_ensembl"
}
if(!exists("symbolKey")){
symbolKey = "hgnc_symbol"
}
if(!exists('genesStr')){
genesStr<-"LDLR APOB PCSK9 LDLRAP1 STAP1 LIPA ABCG5 ABCGB APOE LPA PNPLA5 CH25H INSIG2... | apache-2.0 | R |
402e6595977fe555d0adc7d1d611b826c887e00e | Fix caching error | klmr/codons,klmr/codons | scripts/cache.r | scripts/cache.r | decorate = modules::import('decorate', attach = TRUE)
modules::import('ebits/base', attach = c('closure', 'match_call_defaults'))
cache = decorator %@% function (f) {
cache = new.env()
g = function (...) {
call = match_call_defaults()
args = call[-1]
# Use a helper to evaluate all argum... | decorate = modules::import('decorate', attach = TRUE)
modules::import('ebits/base', attach = c('closure', 'match_call_defaults'))
# FIXME: Doesn’t work with recursive functions
# Reproduce: fib = .cache %@% function (n) if (n < 2) 1 else fib(n - 1) + fib(n - 2)
# Suspicion: somehow, the state of the function is shared... | apache-2.0 | R |
26f0dff99fc7188f770ace435cfe819713f6caea | update code to data.table | DrewWham/Genetic-Structure-Tools | plotSTR.r | plotSTR.r | library(stringr)
library(ggplot2)
library(data.table)
#function for extracting the cluster Probs, requires STR infile because STRUCTURE likes to chop off the ends of your sample names so I have to use your original file to get your original names
read.STR<-function(STR.in,STR.out){
#read in data
str<-read.table(STR.in... | library(stringr)
library(ggplot2)
#function for extracting the cluster Probs, requires STR infile because STRUCTURE likes to chop off the ends of your sample names so I have to use your original file to get your original names
read.STR<-function(STR.in,STR.out){
#read in data
str<-read.table(STR.in,skip=1)
str.out<-r... | apache-2.0 | R |
5c196b4f5ecaf1322b306702e55ca3ca38199417 | use different line style | thomaskrause/graphANNIS,thomaskrause/graphANNIS,thomaskrause/graphANNIS,thomaskrause/graphANNIS,thomaskrause/graphANNIS,thomaskrause/graphANNIS,thomaskrause/graphANNIS | evaluation/evaluate-csv.r | evaluation/evaluate-csv.r | bench_getaql <- function(x, querydir) {
aqlFile <- ""
group <- x[1]
problemSpace = as.numeric(x[2])
if(problemSpace == 0) {
corpus <- sub("_[^_]+$", "", group)
fn <- substr(group, nchar(corpus)+2, nchar(group))
aqlFile <- paste(querydir, "/", corpus,"/", fn, ".aql", sep='')
} else {
aqlFi... | bench_getaql <- function(x, querydir) {
aqlFile <- ""
group <- x[1]
problemSpace = as.numeric(x[2])
if(problemSpace == 0) {
corpus <- sub("_[^_]+$", "", group)
fn <- substr(group, nchar(corpus)+2, nchar(group))
aqlFile <- paste(querydir, "/", corpus,"/", fn, ".aql", sep='')
} else {
aqlFi... | apache-2.0 | R |
f0c894353fe8b94a81e9c000f8c53ba1c44e10e0 | Update ggplot2_formatter.r | fdryan/R,1R151-1/R,jezdata/R | ggplot2_formatter.r | ggplot2_formatter.r |
require(scales)
# ---------------------------------------------------------------------------------------------
# Formatting functions for ggplot graph axis
# ---------------------------------------------------------------------------------------------
#' Human Numbers: Format numbers so they're legible for humans
... |
require(scales)
# ---------------------------------------------------------------------------------------------
# Formatting functions for ggplot graph axis
# ---------------------------------------------------------------------------------------------
#' Human Numbers: Format numbers so they're legible for humans
... | unlicense | R |
2d1e45ebf4e28526334bfce6cff8b151cabcab91 | Move all data to one dataframe | elephantum/r-basis | basis.r | basis.r | library('rjson')
library('RCurl')
getBasisData <- function(report_date='2013-09-14') {
user_id <- readLines('user_id.txt')
# '&start_offset=-10800',
# '&end_offset=10800',
basis.url <- sprintf(
paste0('https://app.mybasis.com/api/v1/chart/%s.json',
'?summary=true',
... | library('rjson')
library('RCurl')
getBasisData <- function(report_date='2013-09-14') {
user_id <- readLines('user_id.txt')
# '&start_offset=-10800',
# '&end_offset=10800',
basis.url <- sprintf(
paste0('https://app.mybasis.com/api/v1/chart/%s.json',
'?summary=true',
... | mit | R |
ce6d11cbad1f9ea64b6e029a209cfda2983edc81 | Update 1.r | glor/R,glor/R | aufgaben/blatt04/1.r | aufgaben/blatt04/1.r | #Blatt 4
#1.1 Runterladen
#1.2
hefe = read.table(file="[017]yeast.txt", sep="t", dec=".", header=TRUE)
#1.3
boxplot(hefe$content ~ hefe$type, data = hefe, main = "hefe" )
#Keine Normalverteilung, da es in jedem Typ einen Ausreisser gibt
#Varianzhomogenitaet, da die Unterschiede zwischen den beiden Boxen no... | #4.2
t.test(formula = hair$length_difference ~ hair$type, var.eqaul = TRUE, alternative = "two.sided", conf.level = 0.95, paired = TRUE)
| bsd-2-clause | R |
686d108aa977e31c74b8e74f6df73c2d98aab48a | Use relative path to find db | hadley/crantastic,tenforwardconsulting/crantastic,tenforwardconsulting/crantastic,tenforwardconsulting/crantastic,tenforwardconsulting/crantastic,hadley/crantastic,hadley/crantastic | lib/r/db.r | lib/r/db.r | suppressMessages(require(RSQLite, quiet=TRUE))
FILE <- (function() {
attr(body(sys.function()), "srcfile")
})()$filename
PATH <- normalizePath(dirname(FILE))
dbpath <- normalizePath(file.path(PATH, "/../../db/development.sqlite3"))
if (exists("db")) dbDisconnect(db)
db <- dbConnect(dbDriver("SQLite"), dbname = dbp... | suppressMessages(require(RSQLite, quiet=TRUE))
if (exists("db")) dbDisconnect(db)
db <- dbConnect(dbDriver("SQLite"), dbname = "/Users/hadley/Documents/crantastic/db/development.sqlite3")
add_version_to_db <- function(pkg) {
package.download(pkg)
pkg <- package.data(pkg)
insert_version(pkg)
}
insert_version <-... | mit | R |
023b83e38a6af5313e5bad44c717380c16093952 | Update simds.r | r-glennie/SimDs,r-glennie/SimDs,r-glennie/SimDs | src/simds.r | src/simds.r | # Author: Richard Glennie
# 2016
#
# Running a distance sampling simulation where animals move
library(Rcpp)
library(RcppArmadillo)
sourceCpp("simds.cc")
# set simulation parameters
population.size <- 100
region.size <- c(1000, 1000)
# simulation assumes all lines are randomly placed
# and have same length/width
... | # Author: Richard Glennie
# 2016
#
# Running a distance sampling simulation where animals move
library(Rcpp)
library(RcppArmadillo)
sourceCpp("simds.cc")
# set simulation parameters
population.size <- 100
region.size <- c(1000, 1000)
# simulation assumes all lines are randomly placed
# and have same length/width
... | mit | R |
e50561d1fcd9ad6fc5cfbd601520aa155291a900 | Bump version to prep for 3.1 alpha | rgchris/ren-c,codebybrett/ren-c,kealist/ren-c,draegtun/ren-c,codebybrett/ren-c,giuliolunati/ren-c,codebybrett/ren-c,mbk/ren-c,kealist/ren-c,hostilefork/rebol,rgchris/ren-c,giuliolunati/ren-c,codebybrett/ren-c,giuliolunati/ren-c,hostilefork/rebol,draegtun/ren-c,rgchris/ren-c,codebybrett/ren-c,mbk/ren-c,hostilefork/rebol... | src/boot/version.r | src/boot/version.r | 3.0.90.3.1
| 3.0.0.3.1
| apache-2.0 | R |
218977e6499a2a8d9df2fc66a94149c7583988fd | Add co-owner. | IndyActuaries/epic-fhir,IndyActuaries/epic-fhir | r/plots.r | r/plots.r | #' ## Code Owners: Kyle Baird, Shea Parkes
#' ### OWNERS ATTEST TO THE FOLLOWING:
#' * The `master` branch will meet Milliman QRM standards at all times.
#' * Deliveries will only be made from code in the `master` branch.
#' * Review/Collaboration notes will be captured in Pull Requests (prior to merging).
#'
#'... | #' ## Code Owners: Kyle Baird
#' ### OWNERS ATTEST TO THE FOLLOWING:
#' * The `master` branch will meet Milliman QRM standards at all times.
#' * Deliveries will only be made from code in the `master` branch.
#' * Review/Collaboration notes will be captured in Pull Requests (prior to merging).
#'
#'
#' ### Obje... | mit | R |
1833f64ab1a53bde390bd45dd5a276aaa83d8a05 | adjust figure width | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/seurat_group_umap.r | lib/scRNA/seurat_group_umap.r | rm(list=ls())
outFile='AK6383'
parSampleFile1='fileList1.txt'
parSampleFile2=''
parSampleFile3=''
parFile1='C:/projects/nobackup/kirabo_lab/shengq2/20220506_6383_scRNA_human/seurat_merge_03_choose_res/result/AK6383.final.rds'
parFile2=''
parFile3=''
setwd('C:/projects/nobackup/kirabo_lab/shengq2/20220506_6383_scRNA_... | rm(list=ls())
outFile='AK6383'
parSampleFile1='fileList1.txt'
parSampleFile2=''
parSampleFile3=''
parFile1='C:/projects/nobackup/kirabo_lab/shengq2/20220506_6383_scRNA_human/seurat_merge_03_choose_res/result/AK6383.final.rds'
parFile2=''
parFile3=''
setwd('C:/projects/nobackup/kirabo_lab/shengq2/20220506_6383_scRNA_... | apache-2.0 | R |
a62faf609a1af3fd9bc0ee4c39f8109b3136e6e4 | convert some more functions to arity 1s | syberia/syberia | R/construct_stage_runner.r | R/construct_stage_runner.r | #' Return a stageRunner object that parametrizes a list of stages.
#'
#' Each stage is first fed through a function that converts it to a stageRunner
#' or a function. For example, list(import = X, ...) gets converted by,
#' amongst other things, looking for a variable import_stage and passing
#' in X.
#'
#' This kind... | #' Return a stageRunner object that parametrizes a list of stages.
#'
#' Each stage is first fed through a function that converts it to a stageRunner
#' or a function. For example, list(import = X, ...) gets converted by,
#' amongst other things, looking for a variable import_stage and passing
#' in X.
#'
#' This kind... | mit | R |
d4d355e564685f81a081f8d449e4fd2d213763c6 | Update document. | snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3 | q3/docs/FormatDateFunction.rd | q3/docs/FormatDateFunction.rd | =begin
=@FormatDate
String @FormatDate(Time date, String format, Number timezone?)
==
dateŎw肳ꂽԂformatŎw肳ꂽŃtH[}bg܂B
ɂ͔Cӂ̕wł܂A%ɑԂ̈ꕔɒu܂B
:%Y2
̔Ni:06j
:%Y4
l̔Ni:2006j
:%M0
̌i:05j
:%M1
3̖̌Oi:Marj
:%M2
̖Oi:Januaryj
:%D
̓i:29j
:%W
3̗ji:Monji̎w͌Â`łB%W1gpĂj
:%W0
Zji:M, Tuj... | =begin
=@FormatDate
String @FormatDate(Time date, String format, Number timezone?)
==
dateŎw肳ꂽԂformatŎw肳ꂽŃtH[}bg܂B
ɂ͔Cӂ̕wł܂A%ɑԂ̈ꕔɒu܂B
:%Y2
̔Ni:06j
:%Y4
l̔Ni:2006j
:%M0
̌i:05j
:%M1
3̖̌Oi:Marj
:%D
̓i:29j
:%W
3̗ji:Monj
:%h
24Ԑł̓̎i:19j
:%m
̕i:34j
:%s
̕bi:02j... | mit | R |
cc5377d5609aa7243affeb026f4fdab80060ae47 | Check other condition in this test. | davluangu/stagerunner,robertzk/stagerunner,kirillseva/stagerunner,robertzk/stagerunner,syberia/stagerunner,syberia/stagerunner,davluangu/stagerunner | tests/testthat/test-compare_stage_keys.r | tests/testthat/test-compare_stage_keys.r | context('compare_stage_keys')
test_that("it gives FALSE when keys are incomparable", {
expect_false(compare_stage_keys("1/1", FALSE))
expect_false(compare_stage_keys(FALSE, "1/1"))
})
test_that("it gives TRUE when keys are identical", {
expect_true(compare_stage_keys(c(FALSE, TRUE), c(FALSE, TRUE)))
})
test_th... | context('compare_stage_keys')
test_that("it gives FALSE when keys are incomparable", {
expect_false(compare_stage_keys("1/1", FALSE))
expect_false(compare_stage_keys(FALSE, "1/1"))
})
test_that("it gives TRUE when keys are identical", {
expect_true(compare_stage_keys(c(FALSE, TRUE), c(FALSE, TRUE)))
})
test_th... | mit | R |
13966aa1efccad524c2934885f34eae52e2b5ba7 | use is.null instead | robertzk/s3mpi | R/s3read.r | R/s3read.r | #' Read an R object in S3 by key
#'
#' Any type of object that can be serialized as an RDS file
#' is capable of being stored using this interface.
#'
#' @param name character. The key to grab from S3.
#' @param .path. The location of your S3 bucket.
#' @param cache logical. If true, use the local s3cache if available... | #' Read an R object in S3 by key
#'
#' Any type of object that can be serialized as an RDS file
#' is capable of being stored using this interface.
#'
#' @param name character. The key to grab from S3.
#' @param .path. The location of your S3 bucket.
#' @param cache logical. If true, use the local s3cache if available... | mit | R |
19da5b4ac0e39412055dae24e68f7dfb1d9cef71 | change call for catalog | david-beauchesne/Predict_interactions | Script/1-Similarity_matrix.r | Script/1-Similarity_matrix.r | # -----------------------------------------------------------------------------
# PROJECT:
# Evaluating the structure of the communities of the estuary
# and gulf of St.Lawrence
# -----------------------------------------------------------------------------
# -----------------------------------------------------... | # -----------------------------------------------------------------------------
# PROJECT:
# Evaluating the structure of the communities of the estuary
# and gulf of St.Lawrence
# -----------------------------------------------------------------------------
# -----------------------------------------------------... | mit | R |
bfdb1de09607687998ca05393c5d4cf0c017a718 | Add an option to embed script without compression | zsx/r3,Pointillistic/rebol-lang,Pointillistic/rebol-lang,Pointillistic/rebol-lang,zsx/r3,zsx/r3,zsx/r3,Pointillistic/rebol-lang | make/encap.r | make/encap.r | REBOL[]
args: parse system/script/args ""
exe: none
payload: none
output: none
as-is: false ;don't compress, in case people try to avoid decompression to speed up bootup
windows?: 3 = fourth system/version
while [not tail? args] [
arg: first args
case [
any [arg = "/rebol"
arg = "/r"] [
exe: second ar... | REBOL[]
args: parse system/script/args ""
exe: none
payload: none
output: none
windows?: 3 = fourth system/version
while [not tail? args] [
arg: first args
case [
any [arg = "/rebol"
arg = "/r"] [
exe: second args
args: next args
]
any [arg = "/payload"
arg = "/p"] [
payload: seco... | apache-2.0 | R |
5a779789d5184b9230ced7131be3ea7b678242d8 | Add link to all functions | klmr/modules,klmr/modules | R/modules-package.r | R/modules-package.r | #' An alternative module system for R
#'
#' Use \code{module = import('module')} to import a module for usage.
#' Fully qualified names are supported for nested modules, reminiscent of
#' Python’s module mechanism.
#' @section Package options:
#'
#' \itemize{
#' \item \code{import.path}:
#' A vector of paths whic... | #' An alternative module system for R
#'
#' Use \code{module = import('module')} to import a module for usage.
#' Fully qualified names are supported for nested modules, reminiscent of
#' Python’s module mechanism.
#' @section Package options:
#'
#' \itemize{
#' \item \code{import.path}:
#' A vector of paths whic... | apache-2.0 | R |
29c6c150adfabb737b6d7e0d43257f683f1bf823 | 更新：第六章fig6-9 | shuaimeng/r | thesis/chap6/fig6-9.r | thesis/chap6/fig6-9.r | dyn.load('/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/server/libjvm.dylib')
setwd("/Users/mengmengjiang/all datas/voltage")
##raeding datas of flow rates
eq<-read.xlsx("voltage.xls",sheetName="ethanol_q",header=TRUE)
aq<-read.xlsx("voltage.xls",sheetName="acetone_q",header=TRUE)
iq<-read... | dyn.load('/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/server/libjvm.dylib')
setwd("/Users/mengmengjiang/all datas/voltage")
##raeding datas of flow rates
eq<-read.xlsx("voltage.xls",sheetName="ethanol_q",header=TRUE)
aq<-read.xlsx("voltage.xls",sheetName="acetone_q",header=TRUE)
iq<-read... | mit | R |
b69f8520c8bc8d09ddb003c74ae8e24570d832ad | refactor syberia_models tests to use testthatsomemore | robertzk/syberiaStructure | inst/tests/test-syberia_models.r | inst/tests/test-syberia_models.r | require(testthatsomemore)
context('syberia_models')
test_that('it can discriminate between directoried and non-directoried models', {
within_file_structure(list('syberia.config', models = list(dev = list(
model_one = list(model_one.r = 'foo', helper.r = 'bar'),
model_two.r = 'blah'))), {
models <- c(... | require(testthatsomemore)
context('syberia_models')
local({
syberia_objects <- force(syberia_objects)
stub(syberia_objects, is.syberia_project) <- function(...) TRUE
stub(syberia_objects, file.exists) <- function(...) TRUE
stub(syberia_objects, syberia_root) <- function(...) ''
stub(syberia_models, syberia_o... | mit | R |
b8e9bd4aeb673881f5bbf02b4306960f8093b094 | check duplidated name | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/Annotation/findNearestGene.r | lib/Annotation/findNearestGene.r |
options(bitmapType='cairo')
library(testit)
library(ChIPpeakAnno)
genes <- read.table(parFile1, sep="\t", header=F)
dup<-genes[duplicated(genes$V4),]
dup$V4<-paste0(dup$V4,":",dup$V2)
genes[rownames(dup), "V4"] = dup$V4
assert(length(duplicated(genes$V4)) == 0)
colnames(genes)<-c("seqnames", "start", "... | options(bitmapType='cairo')
library(ChIPpeakAnno)
genes <- toGRanges(parFile1, format="BED", skip=1)
files<-read.table(parSampleFile1, sep="\t", header=F)
res=NULL
for (i in c(1:nrow(files))){
file = files[i,1]
name = files[i,2]
macsOutput <- toGRanges(file, format="BED", skip=1)
annotated <- ann... | apache-2.0 | R |
1f58f30ad28d7e85b8cd9ebbf01c60ae235d13c4 | Update complexity.r | lpfgarcia/m2n | measures/complexity.r | measures/complexity.r | # R Code
# DCoL Library
# Ho and Basu 2002; Ho et al. 2006; and Orriols-Puig et al. 2010
# A set of measures designed to characterize the apparent complexity of data sets
require(foreign);
cx.name = function(data) {
name = paste(".", paste(sample(letters, 20, replace=TRUE), collapse=""), sep="");
write.arff(data, ... | # R Code
# DCoL Library
# Ho and Basu 2002; Ho et al. 2006; and Orriols-Puig et al. 2010
# A set of measures designed to characterize the apparent complexity of data sets
require(foreign);
cx.name = function(data) {
name = paste(".", paste(sample(letters, 20, replace=TRUE), collapse=""), sep="");
write.arff(data, ... | mit | R |
b49c57050f3bf584c05b699da6e78e42e5f99cbd | fix export() | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | tests/testthat/test-worker.r | tests/testthat/test-worker.r | context("worker")
context = rzmq::init.context()
socket = rzmq::init.socket(context, "ZMQ_REP")
rzmq::bind.socket(socket, "tcp://*:55443")
Sys.sleep(0.5)
start_worker = function(id="1", url="tcp://localhost:55443") {
if (Sys.info()[['sysname']] == "Windows")
skip("Forking not available on Windows")
p... | context("worker")
context = rzmq::init.context()
socket = rzmq::init.socket(context, "ZMQ_REP")
rzmq::bind.socket(socket, "tcp://*:55443")
Sys.sleep(0.5)
start_worker = function(id="1", url="tcp://localhost:55443") {
if (Sys.info()[['sysname']] == "Windows")
skip("Forking not available on Windows")
p... | apache-2.0 | R |
d93ceaa99659f058cba495956ed04cb1b6514cb6 | Add some explanation in comments to the script. | thehyve/heim-SmartR,agapow/smartr,thehyve/naa-SmartR,agapow/smartr,thehyve/naa-SmartR,thehyve/naa-SmartR,thehyve/heim-SmartR,thehyve/heim-SmartR,agapow/smartr,agapow/smartr,thehyve/heim-SmartR | web-app/HeimScripts/heatmap/run.r | web-app/HeimScripts/heatmap/run.r | library(jsonlite)
library(reshape2)
main <- function(){
df <- loaded_variables[[1]] # SmartR does not support multiple HDD nodes yet
fields <- buildFields(df)
geneSymbols <- unique(fields["GENESYMBOL"])[,1] #[,1] in order to get a vector, otherwise we get a dataframe
patientIDs <-unique(fields["PATIENTID"]... | library(jsonlite)
library(reshape2)
main <- function(){
df <- loaded_variables[[1]]
fields <- buildFields(df)
geneSymbols <- unique(fields["GENESYMBOL"])[,1]
patientIDs <-unique(fields["PATIENTID"])[,1]
probes <- unique(fields["PROBE"])[,1]
significanceValues <- unique(fields["SIGNIFICANCE"])[,1]
... | apache-2.0 | R |
c05e57ea79e1a14db5a5fc083f0bf296fa25538f | fix var name lookup | jae0/bio.snowcrab,jae0/bio.snowcrab | R/lookup.datatransformation.r | R/lookup.datatransformation.r |
lookup.datatransformation = function( ) {
# determine data transformations based upon category of data and data source
log.transform = bio.snowcrab::variable.list.expand("log.transform")
scaled.centered = bio.snowcrab::variable.list.expand("scaled.centered")
sn = bio.snowcrab::variable.list.expand("... |
lookup.datatransformation = function( ) {
# determine data transformations based upon category of data and data source
log.transform = bio.snowcrab::variable.list.expand("log.transform")
scaled.centered = bio.snowcrab::variable.list.expand("scaled.centered")
sn = bio.snowcrab::variable.list.expand("... | mit | R |
2e2235b1ea2a4dfe8e441296447199dc5f239fdd | Update explorationDF.r | svobodam/Deep-Learning-Text-Summariser,svobodam/Deep-Learning-Text-Summariser,svobodam/Deep-Learning-Text-Summariser | PreProcessingScript/explorationDF.r | PreProcessingScript/explorationDF.r | # Data Frame exploration
# Dataset used as .db file to allow managing DF from Python and R.
# This script provides only basic exploration of the DF, including nrow(), ncol(), number of topics, number of documents and number summaries.
# FUNCTIONS
# Dataset preprocessing FUNCTION
dfExplore = function(data_frame) {
Nu... | # Author: Matej Svoboda
# Data Frame exploration
# Dataset used as .db file to allow managing DF from Python and R.
# This script provides only basic exploration of the DF, including nrow(), ncol(), number of topics, number of documents and number summaries.
# FUNCTIONS
# Dataset preprocessing FUNCTION
dfExplore = fun... | mit | R |
b470b5be1029f98b11f005e8acd9dfe6b4f01e2c | Fix main_file bash script path | jmousseau/Stain | R/slurm-bash-script.r | R/slurm-bash-script.r | #' SlurmBashScript R6 object.
#'
#' Generates the necessary bash script to submit through
#' the `sbatch` command.
SlurmBashScript <- R6::R6Class("SlurmBashScript",
public = list(
initialize = function(container, main_file, copy_back = c("*")) {
private$write_slurm_script(container$dir)
... | #' SlurmBashScript R6 object.
#'
#' Generates the necessary bash script to submit through
#' the `sbatch` command.
SlurmBashScript <- R6::R6Class("SlurmBashScript",
public = list(
initialize = function(container, main_file, copy_back = c("*")) {
private$write_slurm_script(container$dir)
... | mit | R |
0f3a9ef0b30f391a2910f900e00c7316bb9ba8b9 | Update FeatureSelection.r | phnmnl/workflow-demo,phnmnl/workflow-demo,phnmnl/workflow-demo,phnmnl/workflow-demo | FeatureSelection/FeatureSelection.r | FeatureSelection/FeatureSelection.r | args <- commandArgs(trailingOnly = TRUE)
input = args[1]
input2 = args[2]
output = args[3]
samples<-read.table(input,sep='\t',header=T)
cvs<-read.table(input2,sep='\t',header=F)
cv = apply(cvs,1,median,na.rm=T)
idx = which(cv < 0.3)
samples = samples[idx,]
write.table(samples,file=output,sep='\t',row.names=F)
| args <- commandArgs(trailingOnly = TRUE)
input = args[1]
path = args[2]
output = args[3]
setwd(path)
samples<-read.table(input,sep='\t',header=T)
filenames = list.files(pattern = "*.xls")
# remove mebendazole and controls
filenames = filenames[-grep("Contr", filenames)]
filenames = filenames[-grep("Meben", filenames... | apache-2.0 | R |
e9f67d79331c566deb585b9f202c87a92c062973 | handle contextPath of NA when creating url | RGLab/LabKeyModules,RGLab/LabKeyModules,RGLab/LabKeyModules,RGLab/LabKeyModules,RGLab/LabKeyModules,RGLab/LabKeyModules | HIPCMatrix/pipeline/tasks/create-matrix.r | HIPCMatrix/pipeline/tasks/create-matrix.r | library(data.table)
library(Rlabkey)
library(affy)
# NOTE: Affy will implicitly try to load bioc packages "hthgu133pluspmcdf" and "AnnotationDbi"
# but that won't work in an RServe enviornment if they haven't been installed yet.
# So we try to load the library early so they will fail if not installed.
library(hthgu133... | library(data.table)
library(Rlabkey)
library(affy)
# NOTE: also requires bioc packages: "hthgu133pluspmcdf" and "AnnotationDbi"
# read the job info
jobInfo <- read.table("${pipeline, taskInfo}",
col.names=c("name", "value", "type"),
header=FALSE, check.names=FALSE,
... | artistic-2.0 | R |
b1c6ffcdff975f141e15783e2bb4bf6f7ba7635d | Fix dataframe retrieval from loaded_variables | thehyve/naa-SmartR,thehyve/heim-SmartR,thehyve/heim-SmartR,agapow/smartr,thehyve/naa-SmartR,agapow/smartr,agapow/smartr,agapow/smartr,thehyve/heim-SmartR,thehyve/naa-SmartR,thehyve/heim-SmartR | web-app/HeimScripts/heatmap/run.r | web-app/HeimScripts/heatmap/run.r | library(gplots)
dataset <- loaded_variables[[1]] #dataframe with columns: Row.Label, Bio.marker, ASSAY_0001 ASSAY_0002 ...
measurements <- subset(dataset,select=-c(Row.Label,Bio.marker)) # this will select all columns other than Probe and Biomarker columns
measurements <- data.matrix(measurements)
measurements <- ... | #global_register <-list(rowNames = c("a","b"),
# columnNames = c("1","2"),
# origin = c(1,2),
# data = matrix(c(35,700),nrow=2,ncol=2)
# )
library(gplots)
# This script expects global_register to be populated before execution
# see... | apache-2.0 | R |
9df43421e8591f0240bd4f0ad3f510df0236a012 | Update rel_acclimatized.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/rel_acclimatized.r | R/rel_acclimatized.r | #' rel_acclimatized
#'
#' Calculate treshshold of risk realated to wbgt index for acclimatized people
#'
#' @param met numeric Metabolic rate in Watt following level of ISO FDIS 7243.#
#' @return REL
#'
#' @author Istituto per la Bioeconomia CNR Firenze Italy Alfonso Crisci \email{alfonso.crisci@@ibe.cnr.it}
#' @refer... | #' rel_acclimatized
#'
#' Calculate treshshold of risk realated to wbgt index for acclimatized people
#'
#' @param met numeric Metabolic rate in w/mq following level of ISO FDIS 7243.#
#' @return REL
#'
#' @author Istituto per la Bioeconomia CNR Firenze Italy Alfonso Crisci \email{alfonso.crisci@@ibe.cnr.it}
#' @refer... | mit | R |
9ae9e9a9d0f3f49a1c07279b85248d8269d2fd2c | Bump version for 3.1 beta | kealist/ren-c,hostilefork/rebol,hostilefork/rebol,giuliolunati/ren-c,mbk/ren-c,rgchris/ren-c,codebybrett/ren-c,rgchris/ren-c,hostilefork/rebol,giuliolunati/ren-c,giuliolunati/ren-c,mbk/ren-c,giuliolunati/ren-c,kealist/ren-c,codebybrett/ren-c,hostilefork/rebol,rgchris/ren-c,mbk/ren-c,kealist/ren-c,codebybrett/ren-c,drae... | src/boot/version.r | src/boot/version.r | 3.0.91.3.1
| 3.0.90.3.1
| apache-2.0 | R |
bb00c8156b6312f54fa75a8391ed4af609f6d8b7 | Rename variable | mattm/active-user-cohort-analysis | active-users.r | active-users.r | CSV_PATH = "data/test-data.csv"
CSV_SEPARATOR = "\t"
# TODO: Figure out how to prevent ggplot from rendering a thin line for
# cohorts that have zero active users in a month
PlotActiveUserCohorts <- function(data) {
# Convert the sign up month cohorts ("2015-01", etc) to
# dates so they can be used in in the ggplot... | CSV_PATH = "data/test-data.csv"
CSV_SEPARATOR = "\t"
# TODO: Figure out how to prevent ggplot from rendering a thin line for
# cohorts that have zero active users in a month
PlotActiveUserCohorts <- function(data) {
# Convert the sign up month cohorts ("2015-01", etc) to
# dates so they can be used in in the ggplot... | mit | R |
992727d0911d43f206e7a901b6e141e58d9467ad | Clean up sample patient code, add severity line. | pschulam-attic/sclero | demo/patient-sample.r | demo/patient-sample.r | require(sclero)
require(ggplot2)
require(plyr)
data(pft)
data(patient)
set.seed(1)
df <- add_date_since(pft, "date", "year", patient, "date.of.first.symptom")
n.train.visits <- ddply(subset(df, year >= 0 & year < 2), ~ patient.id + test.type, summarize, visits = length(na.omit(test.result)))
n.test.visits <- ddply(s... | require(sclero)
require(ggplot2)
require(plyr)
data(pft)
data(patient)
set.seed(2)
n.visits <- ddply(pft, ~ patient.id + test.type, summarize, visits = length(na.omit(test.result)))
n.fvc.visits <- subset(n.visits, test.type == "fvc")
patient.ids <- subset(n.fvc.visits, visits > 5)$patient.id
some.patients <- samp... | mit | R |
4849167cc21f4e7f59e209e7de3f225255aa7060 | Fix redundant unload in old test | klmr/modules,klmr/modules | inst/tests/test-operators.r | inst/tests/test-operators.r | context('Operator export test')
test_that('operators are attached by default', {
expect_false(exists('%or%'))
a = import('a')
on.exit(unload(a))
expect_true(exists('%or%'))
expect_that(1 %or% 2, equals(1))
expect_that(numeric(0) %or% 2, equals(2))
})
test_that('operator attachment can be disa... | context('Operator export test')
test_that('operators are attached by default', {
expect_false(exists('%or%'))
a = import('a')
on.exit(unload(a))
expect_true(exists('%or%'))
expect_that(1 %or% 2, equals(1))
expect_that(numeric(0) %or% 2, equals(2))
})
test_that('operator attachment can be disa... | apache-2.0 | R |
c11a42f00bf48aaace737eebc30f682dfe9af2a4 | Update server.r | aleksandrov2/APPR-2015-16 | shiny/server.r | shiny/server.r | library(shiny)
shinyServer(
server <- function(input, output) {
output$dolg <- renderPlot({
ggplot(podatki1 %>% filter(Cas == input$leto_1), aes(x = Drzava, y = Dolg, fill=Dolg)) +
scale_fill_continuous(low = "#69b8f6", high = "#142d45") +
geom_bar(stat ="identity") +
theme(axis.text.x = element_text(a... | library(shiny)
shinyServer(
server <- function(input, output) {
output$dolg <- renderPlot({
ggplot(podatki1 %>% filter(Cas == input$leto_1), aes(x = Drzava, y = Dolg, fill=Dolg)) +
scale_fill_continuous(low = "#69b8f6", high = "#142d45") +
geom_bar(stat ="identity") +
theme(axis.text.x = element_text(a... | mit | R |
6f87630171e840e44fd37509f5fb65089ad5ed98 | Update ggplot2_formatter.r | jezdata/R,fdryan/R,1R151-1/R | ggplot2_formatter.r | ggplot2_formatter.r |
require(scales)
# ---------------------------------------------------------------------------------------------
# Formatting functions for ggplot graph axis
# ---------------------------------------------------------------------------------------------
#' Human Numbers: Format numbers so they're legible for humans
... |
require(scales)
# ---------------------------------------------------------------------------------------------
# Formatting functions for ggplot graph axis
# ---------------------------------------------------------------------------------------------
#' Human Numbers: Format numbers so they're legible for humans
... | unlicense | R |
97197ec0b006b788e92ab4494c005346fa252af8 | Update ui.r | aleksandrov2/APPR-2015-16 | shiny/ui.r | shiny/ui.r | library(shiny)
shinyUI(
ui <- fluidPage(
titlePanel("Analiza dolga in primankljaja držav v Evropski uniji"),
sidebarLayout(
sidebarPanel(
sliderInput(inputId="leto_1",label="Leto",min=2006,max=2014,value=2007,step=1),
sliderInput(inputId="leto_2",label="Leto",min=2006,max=2014,value=2007,step=1),... | # This is the user-interface definition of a Shiny web application.
# You can find out more about building applications with Shiny here:
#
# http://www.rstudio.com/shiny/
#
library(shiny)
shinyUI(fluidPage(
plotOutput("prvi_graf"),
tableOutput("napoved.tabela"),
plotOutput("enajsti_graf")))
| mit | R |
fa70ca2923f3c1faf3e6e9166958e118f0e5dcf5 | Add missing rdname | klmr/modules,klmr/modules | R/export_submodule.r | R/export_submodule.r | #' Export a given submodule from the current module
#'
#' @param submodule character string of length 1 with the name of the submodule
#' @note Sometimes, a module may want to export all or some of its submodules in
#' bulk. Simply doing \code{import('submodule', attach = TRUE)} won’t work,
#' however, since \code{atta... | #' Export a given submodule from the current module
#'
#' @param submodule character string of length 1 with the name of the submodule
#' @note Sometimes, a module may want to export all or some of its submodules in
#' bulk. Simply doing \code{import('submodule', attach = TRUE)} won’t work,
#' however, since \code{atta... | apache-2.0 | R |
9b730e7ed447e170ca3c8523b23945905476240c | Remove , | raviqqe/tisp,raviqqe/tisp,tisp-lang/tisp,tisp-lang/tisp,raviqqe/tisp | examples/args.r | examples/args.r | ; . after ..args is not necessary. But it can be forced for readability.
(def (func x1 x2 (x3 123) (x4 456) ..args . y1 (y2 123) y3 (y4 456) ..kwargs)
(+ x1 x2 x3 x4))
(func 1 2 3 ..[1 "foo" "bar"] . y1 123 y3 456 foo 2049 ..{"y4" 123 "y6" 456})
| ; . after ..args is not necessary. But, it can be forced for readability.
(def (func x1 x2 (x3 123) (x4 456) ..args . y1 (y2 123) y3 (y4 456) ..kwargs)
(+ x1 x2 x3 x4))
(func 1 2 3 ..[1 "foo" "bar"] . y1 123 y3 456 foo 2049 ..{"y4" 123 "y6" 456})
| mit | R |
7ae0d3fcad073998860602590ea678c4cfc9b245 | Update test.r | snowch/biginsight-examples,snowch/biginsight-examples | examples/BigR/test.r | examples/BigR/test.r |
if (!dir.exists('./lib')) {
# create directory to hold libraries
dir.create('./lib')
# install libraries
install.packages('rJava', repos='http://cran.us.r-project.org', lib='./lib', quiet=FALSE)
install.packages('base64enc', repos='http://cran.us.r-project.org', lib='./lib', quiet=FALSE)
inst... |
if (!dir.exists('./lib')) {
# create directory to hold libraries
dir.create('./lib')
# install libraries
install.packages('rJava', repos='http://cran.us.r-project.org', lib='./lib', quiet=FALSE)
install.packages('base64enc', repos='http://cran.us.r-project.org', lib='./lib', quiet=FALSE)
inst... | apache-2.0 | R |
e28e36c6b818b653a711ca8a96aabef0585c0239 | add hint to ignore error msg | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | tests/testthat/test-work_chunk.r | tests/testthat/test-work_chunk.r | context("work_chunk")
df = as.data.frame(tibble::data_frame(
a = 1:3,
b = as.list(letters[1:3]),
c = setNames(as.list(3:1), letters[1:3])
))
test_that("data types and arg names", {
fx = function(c, a, b) a + c
expect_equal(work_chunk(df, fx), as.list(rep(4,3)))
})
test_that("check call classes", ... | context("work_chunk")
df = as.data.frame(tibble::data_frame(
a = 1:3,
b = as.list(letters[1:3]),
c = setNames(as.list(3:1), letters[1:3])
))
test_that("data types and arg names", {
fx = function(c, a, b) a + c
expect_equal(work_chunk(df, fx), as.list(rep(4,3)))
})
test_that("check call classes", ... | apache-2.0 | R |
a8af0dbd6bce34fbefab649ae7587551b2cb7e50 | use 1 thread in tests | wrathematics/sylcount,wrathematics/sylcount,wrathematics/sylcount | Rpkg/tests/degenerate_cases.r | Rpkg/tests/degenerate_cases.r | library(sylcount)
test = readability("", nthreads=1)
truth =
data.frame(
chars = 0L,
wordchars = 0L,
words = 0L,
nonwords = 0L,
sents = 0L,
sylls = 0L,
polys = 0L,
re = NaN,
gl = NaN,
ari = NA_integer_,
smog = NaN,
cl = NaN
)
stopifnot(identical(test, truth))
test = doc_counts("", nthreads... | library(sylcount)
test = readability("")
truth =
data.frame(
chars = 0L,
wordchars = 0L,
words = 0L,
nonwords = 0L,
sents = 0L,
sylls = 0L,
polys = 0L,
re = NaN,
gl = NaN,
ari = NA_integer_,
smog = NaN,
cl = NaN
)
stopifnot(identical(test, truth))
test = doc_counts("")
truth = truth[, 1:7]... | bsd-2-clause | R |
0882d0e6212597be4d3d4476cf86202ab38f4d5c | Use GET-WORD on TRY wrapper for handler | kealist/ren-c,rgchris/ren-c,rgchris/ren-c,rgchris/ren-c,hostilefork/rebol,hostilefork/rebol,draegtun/ren-c,hostilefork/rebol,giuliolunati/ren-c,giuliolunati/ren-c,codebybrett/ren-c,kealist/ren-c,draegtun/ren-c,giuliolunati/ren-c,codebybrett/ren-c,hostilefork/rebol,kealist/ren-c,rgchris/ren-c,hostilefork/rebol,codebybre... | src/mezz/mezz-legacy.r | src/mezz/mezz-legacy.r | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: Legacy compatibility"
Rights: {
Copyright 1997-2015 REBOL Technologies
Copyright 2012-2015 Rebol Open Source Contributors
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache ... | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: Legacy compatibility"
Rights: {
Copyright 1997-2015 REBOL Technologies
Copyright 2012-2015 Rebol Open Source Contributors
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache ... | apache-2.0 | R |
d62e7e3b479781182c1a756697bc734e4a690b04 | Adjust test import paths | klmr/modules,klmr/modules | inst/tests/test-relative-import.r | inst/tests/test-relative-import.r | context('Relative imports test')
test_that('Imports are absolute by default', {
ra = import('./modules/nested/relative_a')
expect_that(ra$a_which(), equals('/a'))
})
test_that('Relative import are always local', {
ra = import('./modules/nested/relative_a')
expect_that(ra$local_a_which(), equals('neste... | context('Relative imports test')
test_that('Imports are absolute by default', {
ra = import('relative_a')
expect_that(ra$a_which(), equals('/a'))
})
test_that('Relative import are always local', {
ra = import('relative_a')
expect_that(ra$local_a_which(), equals('nested/a'))
})
| apache-2.0 | R |
2eb7f47c7adf7552d511455733dd70491b37eb71 | fix paste | mynameisvinn/rstae | R/util.r | R/util.r | #' @export
test1 <- function(woof){
print(woof)
}
#' @export
fetch_trips <-function(municipalId){
uri = paste("https://municipal.systems/v1/municipalities/", municipalId, "/trips", sep="")
r <- GET(uri)
e = content(r)$results
f = as.data.frame(do.call(rbind, e))
f
}
| #' @export
test <- function(woof){
print(woof)
}
#' @export
fetch_trips <-function(municipalId){
uri = paste("https://municipal.systems/v1/municipalities/", municipalId, "/trips", sep="")
r <- GET(uri)
e = content(r)$results
f = as.data.frame(do.call(rbind, e))
f
}
| mit | R |
5cf510c1f6b46c28ac8a744266de999831eaea85 | Update 1.r | glor/R,glor/R | aufgaben/blatt03/1.r | aufgaben/blatt03/1.r | #Blatt 3
#1.1 Datei lokal speichern
#1.2
maeuse = read.table(file="mice.txt", sep="t", dec=".", header=TRUE)
#1.3
boxplot(maeuse$speed ~ maeuse$health, date = maeuse, main = "kranke Maeuse" )
# Beide Gruppen sind normalverteilt, es gibt keine Aussreisser. (diese wuerden als Punkte ausserhalb der Boxen darge... | #Blatt 3
#1.1 Datei lokal speichern
#1.2
maeuse = read.table(file="mice.txt", sep="t", dec=".", header=TRUE)
#1.3
boxplot(maeuse$speed ~ maeuse$health, date = maeuse, main = "kranke Maeuse" )
# Beide Gruppen sind normalverteilt, es gibt keine Aussreisser. (diese wuerden als Punkte ausserhalb der Boxen darge... | bsd-2-clause | R |
3e522d8e20094a1e08d4dd30554fffad32f858f9 | Update extracterDB.r | svobodam/Deep-Learning-Text-Summariser,svobodam/Deep-Learning-Text-Summariser,svobodam/Deep-Learning-Text-Summariser | PreProcessingScript/extracterDB.r | PreProcessingScript/extracterDB.r | # Data Frame extraction.
# Extract data from Documents and document summaries into new subset and prepare them for extarction to table in DB.
# Extract Documents from df > dfData
counter = 1
while(counter <= 25){
for (m in doc) {
if ((exists("dfData"))==TRUE) {
dfEdit=data.frame(with(df, paste0(df[[m]])), ... | # Data Frame exploration.
# Extract data from Documents and document summaries into new subset and prepare them for extarction to table in DB.
# Extract Documents from df > dfData
counter = 1
while(counter <= 25){
for (m in doc) {
if ((exists("dfData"))==TRUE) {
dfEdit=data.frame(with(df, paste0(df[[m]])),... | mit | R |
bb8fc1d4994cf01cafba1164c631f201c60fc1c9 | check plotting routines transtion dates | khufkens/phenocamr | tests/testthat/test_ancillary_functions.r | tests/testthat/test_ancillary_functions.r | # Phenocamr unit tests
# ancillary functions
test_that("check ancillary routines",{
# download initial data
df = try(download_phenocam(site = "harvard$",
vegetation = "DB",
roi_id = "1",
frequency = 3,
outlier_de... | # Phenocamr unit tests
# ancillary functions
test_that("check ancillary routines",{
# download initial data
df = try(download_phenocam(site = "harvard$",
vegetation = "DB",
roi_id = "1",
frequency = 3,
outlier_de... | agpl-3.0 | R |
5945b00302271b9fec7e12db1d69fd8af16a8007 | Fix bug in explore deciles | hadley/sfhousing,hadley/sfhousing,hadley/sfhousing | explore-deciles.r | explore-deciles.r | # Explore the difference between the cheapest and most expensive houses
library(ggplot2)
source("date.r")
source("explore-data.r")
# Calculate monthly deciles
midmonth <- function(date) {
mday(date) <- 15
date
}
deciles <- ddply(geo, .(date = midmonth(date)), summarise,
decile = seq_len(9),
value = quantile(... | # library(ggplot2)
# source("date.r")
# source("explore-data.r")
#
# Explore the difference between the cheapest and most expensive houses
# Calculate monthly deciles
midmonth <- function(date) {
mday(date) <- 15
date
}
deciles <- ddply(geo, .(date = midmonth(date)), function(df) {
data.frame(
decile = seq... | mit | R |
ead0230a9e704e4576f8069e49a31cc9639d0911 | Make TO-REFINEMENT an alias for TO-PATH | hostilefork/rebol,hostilefork/rebol,giuliolunati/ren-c,draegtun/ren-c,rgchris/ren-c,rgchris/ren-c,hostilefork/rebol,hostilefork/rebol,giuliolunati/ren-c,hostilefork/rebol,giuliolunati/ren-c,draegtun/ren-c,giuliolunati/ren-c,rgchris/ren-c,draegtun/ren-c,giuliolunati/ren-c,rgchris/ren-c,draegtun/ren-c,rgchris/ren-c,draeg... | src/mezz/mezz-types.r | src/mezz/mezz-types.r | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: To-Type Helpers"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2.0
Se... | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: To-Type Helpers"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2.0
Se... | apache-2.0 | R |
3580b5ef7930ea6e36d92fa6ad7472f41ed4728c | Update heat_risk_level.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/heat_risk_level.r | R/heat_risk_level.r | #' heat_risk_level
#'
#' Calculate the heat risk level for worker as four classes level.
#'
#' @param wbgt numeric Wetbulb globe temperature index in degC
#' @param cav numeric Clothing adjusted value due to worker clothing ensemble
#' @param tresh numeric treshshold for heat risk in degC ( RAL or REL)
#'
#' @return nu... | #' heat_risk_level
#'
#' Calculate the heat risk level for worker as four classes level.
#'
#' @param wbgt numeric Wetbulb globe temperature index in degC
#' @param cav numeric Clothing adjusted value due to worker clothing ensemble
#' @param tresh numeric treshshold for heat risk in degC ( RAL or REL)
#'
#' @return nu... | mit | R |
077117f0b4215eb1e779a93e3fd6d214aebecd12 | Normalize angles from start angle | gadomski/rivlib-utils | scripts/chart-inclinations.r | scripts/chart-inclinations.r | library(ggplot2)
library(reshape2)
filenames <- c(
"Zuma/140117_160540_inclinations.txt",
"Zuma/140117_163141_inclinations.txt",
"Zuma/140123_202748_inclinations.txt",
"Zuma/140201_185848_inclinations.txt",
"Zuma/140226_163837_inclinations.txt"... | library(ggplot2)
library(reshape2)
filenames <- c("Zuma/140123_202748_inclinations.txt",
"Zuma/140201_185848_inclinations.txt",
"Zuma/140226_163837_inclinations.txt",
"EastWall/140123_180026_inclination.txt",
"EastWall/140201_205741_inclination.txt")
plotInc... | mit | R |
8c946cba3b17c600d4f9b1972082ad6ab0d0f096 | Update the document about ViewNextMessagePageAction. | snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3 | q3/docs/ViewNextMessagePageAction.rd | q3/docs/ViewNextMessagePageAction.rd | =begin
=ViewNextMessagePageANV
ݕ\Ă郁bZ[W̃y[WɃXN[܂BłɍŌ܂ŃXN[Ăꍇɂ́A((<ViewNextMessageANV|URL:ViewNextMessageAction.html>))ƓlɐU܂BA((<[IvV][̑]pl|URL:OptionMisc.html>))[Ō܂ŃXN[玟̖ǂ\]Ƀ`FbNĂꍇɂ́A((<ViewNextUnseenMessageANV|URL:ViewNextUnseenMessageAction.html>))ƓlɐU܂B
==
Ȃ
==LȃEBhEEr[
*Xgr[
*vr[
*bZ[WEBhE
=end
... | =begin
=ViewNextMessagePageANV
ݕ\Ă郁bZ[W̃y[WɃXN[܂BłɍŌ܂ŃXN[Ăꍇɂ́A((<ViewNextMessageANV|URL:ViewNextMessageAction.html>))ƓlɐU܂B
==
Ȃ
==LȃEBhEEr[
*Xgr[
*vr[
*bZ[WEBhE
=end
| mit | R |
a47135a5ee0e7ba79f9975f35b35488f11fcfa51 | Fix typos in print-test.r | NikolayShubenkovProgSchool/red,red-eco/red,rheber/red,rheber/red,vehar/red,vehar/red,NikolayShubenkovProgSchool/red,red-eco/red | tests/source/compiler/print-test.r | tests/source/compiler/print-test.r | REBOL [
Title: "Red print test script"
Author: "Peter W A Wood"
File: %print-test.r
Tabs: 4
Rights: "Copyright (C) 2011-2012 Peter W A Wood. All rights reserved."
License: "BSD-3 - https://github.com/dockimbel/Red/blob/origin/BSD-3-License.txt"
]
~~~start-file~~~ "Red print"
--test-- "Red print 1"
... | REBOL [
Title: "Red print test script"
Author: "Peter W A Wood"
File: %print-test.r
Tabs: 4
Rights: "Copyright (C) 2011-2012 Peter W A Wood. All rights reserved."
License: "BSD-3 - https://github.com/dockimbel/Red/blob/origin/BSD-3-License.txt"
]
~~~start-file~~~ "Red print"
--test-- "Red print 1"
... | bsd-3-clause | R |
568d54ff5f08bccbefc475cdcdb962b1fe356688 | remove argument name left in by mistake | markdunning/galaxy-fgsea | fgsea.r | fgsea.r | options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
suppressPackageStartupMessages({
library("fgsea")
library("optparse")
})
... | options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
suppressPackageStartupMessages({
library("fgsea")
library("optparse")
})
... | mit | R |
0358fd6f0def2dcaa7e9bbb94df1c85e349a1819 | Remove errant comma | jkarl/LandscapeToolbox,jkarl/LandscapeToolbox,jkarl/LandscapeToolbox | package_installation.r | package_installation.r | ###############################################
### COMMONLY USED PACKAGES IN AIM R SCRIPTS ###
###############################################
#### DATA WRANGLING ####
install.packages(
c(
"dplyr", ## Notably useful for data frame manipulation with group_by(), summarize(), and mutate() and the piping operator %... | ###############################################
### COMMONLY USED PACKAGES IN AIM R SCRIPTS ###
###############################################
#### DATA WRANGLING ####
install.packages(
c(
"dplyr", ## Notably useful for data frame manipulation with group_by(), summarize(), and mutate() and the piping operator %... | cc0-1.0 | R |
0610e9ce90da5d49327aebc2a2b77acadf760e9d | set repo earlier | rdatsci/travis-r-tools | update-packages.r | update-packages.r | # updates all outdated packages
# in contrast to 'update.packages()' this will also update
# packages in the system lib by 'overloading' these packages
# with an installation to the user lib
options(repos = "http://cran.rstudio.com")
tryCatch({
cat("Searching for outdated packages ...\n", file = stdout())
getPkgs ... | # updates all outdated packages
# in contrast to 'update.packages()' this will also update
# packages in the system lib by 'overloading' these packages
# with an installation to the user lib
tryCatch({
cat("Searching for outdated packages ...\n", file = stdout())
getPkgs = function(x) if (is.null(x)) character(0L) ... | bsd-2-clause | R |
48c2d71d911937975e7d62514b694c8aae6f78d6 | add useDynLib: | snoweye/pbdDEMO,wrathematics/pbdDEMO,wrathematics/pbdDEMO,RBigData/pbdDEMO,RBigData/pbdDEMO,snoweye/pbdDEMO,snoweye/pbdDEMO,RBigData/pbdDEMO,wrathematics/pbdDEMO | R/pbdDEMO-package.r | R/pbdDEMO-package.r | #' Demonstrations and Examples for the pbd Project
#'
#' Demos
#'
#' \tabular{ll}{ Package: \tab pbdDMAC\cr Type: \tab Package\cr License: \tab
#' GPL\cr LazyLoad: \tab yes\cr } This package requires an MPI library
#' (OpenMPI, MPICH2, or LAM/MPI).
#'
#' @import methods, pbdMPI, pbdBASE, pbdDMAT
#' @useDynLib pbdDEM... | #' Demonstrations and Examples for the pbd Project
#'
#' Demos
#'
#' \tabular{ll}{ Package: \tab pbdDMAC\cr Type: \tab Package\cr License: \tab
#' GPL\cr LazyLoad: \tab yes\cr } This package requires an MPI library
#' (OpenMPI, MPICH2, or LAM/MPI).
#'
#' @name pbdDEMO-package
#' @docType package
#' @author Drew Schm... | mpl-2.0 | R |
7146d57b72ae542b2ac69e3a39a249438fea89a3 | Add codacy badge | Exsul/endpoint,Exsul/endpoint,Exsul/endpoint,Exsul/endpoint | README.rd | README.rd | [](https://www.codacy.com/app/enelar/bootstrap)
Self-documented preconfigured enviroment, created to achieve best possible framework first experiense.
You could see live example at https://phoxy-bootstrap.appspot.com/ | Self-documented preconfigured enviroment, created to achieve best possible framework first experiense.
You could see live example at https://phoxy-bootstrap.appspot.com/ | apache-2.0 | R |
f7f4dd83b5ecfe300c4725533d60c446b5c8de3f | Add notes | Upward-Spiral-Science/the-fat-boys,Upward-Spiral-Science/the-fat-boys | code/covarianceMatrix.r | code/covarianceMatrix.r | #Displays the covariance matrix
covarianceMatrix <- function(data){
require(reshape)
require(ggplot2)
require(naturalsort)
temp <- cov(data,data)
temp <- melt(temp)
levels(temp[,1]) <- naturalsort(levels(temp[,1]))
levels(temp[,2]) <- naturalsort(levels(temp[,2]))
temp = temp[naturalorder(temp[,1]),]
for... | #Displays the covariance matrix
covarianceMatrix <- function(data){
require(reshape)
require(ggplot2)
require(naturalsort)
temp <- cov(data,data)
temp <- melt(temp)
levels(temp[,1]) <- naturalsort(levels(temp[,1]))
levels(temp[,2]) <- naturalsort(levels(temp[,2]))
temp = temp[naturalorder(temp[,1]),]
for... | apache-2.0 | R |
71fe06dc44774d83f8a5746c4d9142232a2d4fc2 | check file existance | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/eQTL/MatrixEQTL.r | lib/eQTL/MatrixEQTL.r | library("MatrixEQTL")
args = commandArgs(trailingOnly=TRUE)
snp_genotype_file=args[1]
snp_location_file=args[2]
gene_expression_file=args[3]
gene_location_file=args[4]
output_cis_file=args[5]
output_trans_file=args[6]
cat("snp_genotype_file=", snp_genotype_file, "\n")
cat("snp_location_file=", snp_location_file, "\n... | library("MatrixEQTL")
args = commandArgs(trailingOnly=TRUE)
snp_genotype_file=args[1]
snp_location_file=args[2]
gene_expression_file=args[3]
gene_location_file=args[4]
output_cis_file=args[5]
output_trans_file=args[6]
cat("snp_genotype_file=", snp_genotype_file, "\n")
cat("snp_location_file=", snp_location_file, "\n... | apache-2.0 | R |
c5b498b005e6fc3964942f19f07a46372272c011 | Add cachlines accessed to qwords plot. | danluu/BitFunnel,danluu/BitFunnel,BitFunnel/BitFunnel,danluu/BitFunnel,BitFunnel/BitFunnel,danluu/BitFunnel,danluu/BitFunnel,danluu/BitFunnel,BitFunnel/BitFunnel,BitFunnel/BitFunnel,BitFunnel/BitFunnel,BitFunnel/BitFunnel | src/Scripts/plot-qwords.r | src/Scripts/plot-qwords.r | library("ggplot2")
library("reshape")
setwd("~/dev/BitFunnel/src/Scripts")
queries <- read.csv(header=TRUE, file="/tmp/QueryPipelineStatistics.csv")
pos = seq(1, length(queries$quadwords))
df_temp <- data.frame(pos, queries$quadwords, queries$cachelines)
df <- melt(df_temp, id=c("pos"))
png(filename="qwords.png",wid... | library("ggplot2")
setwd("~/dev/BitFunnel/src/Scripts")
png(filename="qwords.png",width=1600,height=1200)
queries <- read.csv(header=TRUE, file="/tmp/QueryPipelineStatistics.csv")
pos = seq(1, length(queries$quadwords))
df <- data.frame(pos, queries$quadwords)
ggplot(df, aes(x=pos,y=queries.quadwords)) +
theme_bw() +... | mit | R |
b6ad031b8b16ab7ffeb897bbfbb25aa9bc83422b | use a global fetch here to allow other packages to intercept loading from source | robertzk/Ramd | R/load_dependency.r | R/load_dependency.r | #' Load a bunch of dependencies by filename
#'
#' @param dep Name of dependency, e.g., relative filename (without .r)
#' \dontrun{
#' helper <- load_dependency('path/to/helper')
#' }
load_dependency <- function(dep) {
path <- suppressWarnings(base::normalizePath(
paste(current_directory(), "/", dep, sep ... | #' Load a bunch of dependencies by filename
#'
#' @param dep Name of dependency, e.g., relative filename (without .r)
#' \dontrun{
#' helper <- load_dependency('path/to/helper')
#' }
load_dependency <- function(dep) {
path <- suppressWarnings(base::normalizePath(
paste(current_directory(), "/", dep, sep ... | mit | R |
5949f53956f66ba861d4fa929be594893e8d2643 | Add some plot parameters | thoolihan/GoogleAnalyticsRExample | explore.r | explore.r |
data <- read.csv("~/workspace/data/ga2-hoolihan.csv", sep=",")
with(data, {
Day.Index <- as.Date(Day.Index, format="%m/%d/%Y")
plot(Day.Index,
Pageviews,
xlab = "Date",
type = "b",
col = "blue",
main = "Google Analytics",
ylim = c(0, 200))
... |
data <- read.csv("~/workspace/data/ga2-hoolihan.csv", sep=",")
with(data, {
Day.Index <- as.Date(Day.Index, format="%m/%d/%Y")
plot(Day.Index,
Pageviews,
xlab = "Date",
type = "b")
})
| unlicense | R |
4611c2c1aef28936718d34712557d1ad645f85a8 | Use application/json over text/json. | robertzk/microserver,robertzk/microserver | R/response.r | R/response.r | #' Simple S3 class to denote JSON responses for httupv.
#'
#' @param response ANY. The R object to send as a response parameter.
#' If the header is set to application/json it will be converted into a JSON string.
#'
#' @param status integer. HTTP status (default is \code{200}).
#' @param headers list. A list of HTTP h... | #' Simple S3 class to denote JSON responses for httupv.
#'
#' @param response ANY. The R object to send as a response parameter.
#' If the header is set to text/json it will be converted into a JSON string.
#'
#' @param status integer. HTTP status (default is \code{200}).
#' @param headers list. A list of HTTP headers ... | mit | R |
f4957db1d456dfdc64b91e07b227586b227828a1 | Update onLoad.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/onLoad.r | R/onLoad.r | #' .onLoad
#'
#' @importFrom V8 new_context
ct <- NULL
.onLoad <- function(libname, pkgname){
ct <<- V8::new_context()
ct$source(system.file("js/biometeo.js", package = pkgname))
}
| #' .onLoad
#'
#' @importFrom V8 new_context
ct <- NULL
.onLoad <- function(libname, pkgname){
ct <<- V8::v8()
ct$source(system.file("inst/js/biometeo.js", package = pkgname))
}
| mit | R |
bb69a13f5f7c7aeae8958f2ec0e49df2ac7733d7 | Update test file name to account for new test data path | mattm/active-user-cohort-analysis | analysis.r | analysis.r | PlotActiveUserCohorts <- function(data) {
#cohortData <- read.csv("2010-cohorts.csv")
# Convert the sign up month cohorts ("2015-01", etc) to
# dates so they can be used in in the ggplot below
data$signed.up <- as.Date(paste(data$signed.up, "-01", sep = ""))
graph <- ggplot(data,
aes(x = signed.up, y = active.u... | PlotActiveUserCohorts <- function(data) {
#cohortData <- read.csv("2010-cohorts.csv")
# Convert the sign up month cohorts ("2015-01", etc) to
# dates so they can be used in in the ggplot below
data$signed.up <- as.Date(paste(data$signed.up, "-01", sep = ""))
graph <- ggplot(data,
aes(x = signed.up, y = active.u... | mit | R |
33f497d488df9917ee8d992f6ee0ed93badd917c | Implement calculation of Ws | klmr/codons,klmr/codons | scripts/tai.r | scripts/tai.r | # Based on the paper by Dos Reis & al, 2004
s = list(naive = c(0, 0, 0, 0, 0.5, 0.5, 0.75, 0.5, 0.5, 0.5),
ecoli = c(0, 0, 0, 0, 0.41, 0.28, 0.9999, 0.68, 0.89))
get_s = function (species)
if (species %in% names(s)) s[[species]] else s$naive
# Reverse complement of the anticodons, in the order of antico... | # Based on the paper by Dos Reis & al, 2004
s = list(naive = c(0, 0, 0, 0, 0.5, 0.5, 0.75, 0.5, 0.5, 0.5),
ecoli = c(0, 0, 0, 0, 0.41, 0.28, 0.9999, 0.68, 0.89))
get_s = function (species)
if (species %in% names(s)) s[[species]] else s$naive
# Reverse complement of the anticodons, in the order of antico... | apache-2.0 | R |
3a9b2b4027f7310959f94a6b607ad5c24457159f | Update analiza.r | Anchiqua/APPR-2015-16 | analiza/analiza.r | analiza/analiza.r | # 4. faza: Analiza podatkov
#naredimo skupine za države glede na število igralcev in točk
tabela5 <- inner_join(tabela3, tabela2)
rownames(tabela5) <- tabela5$drzava
tabela5.norm <- tabela5 %>% select(-drzava) %>% scale()
k1 <- kmeans(tabela5.norm, 3)
#head(k$cluster, n = 15, nstart=1000)
table(k$cluster)
k1 <- km... | # 4. faza: Analiza podatkov
#naredimo skupine za države glede na število igralcev in točk
tabela4 <- inner_join(tabela3, tabela2)
rownames(tabela4) <- tabela4$drzava
tabela4.norm <- tabela4 %>% select(-drzava) %>% scale()
k1 <- kmeans(tabela4.norm, 5)
#head(k$cluster, n = 15, nstart=1000)
table(k$cluster)
k1 <- km... | mit | R |
389ffa875709f49836da59f73b1879bafe802e1f | Add square root to calculation | GreatEmerald/geoscripting,GreatEmerald/geoscripting,GreatEmerald/geoscripting,GreatEmerald/geoscripting | Lesson8/src/RMSE.r | Lesson8/src/RMSE.r | # Team Rython, Dainius Masiliunas and Tim Weerman
# Date: 11 January, 2016
# Apache License 2.0
# Calculate the Root Mean Squared Error
RMSE = function(truth, prediction)
{
return(sqrt(mean((truth-prediction)^2, na.rm=TRUE)))
}
# Calculate partial RMSE for different zones by generating squared difference rasters.... | # Team Rython, Dainius Masiliunas and Tim Weerman
# Date: 11 January, 2016
# Apache License 2.0
# Calculate the Root Mean Squared Error
RMSE = function(truth, prediction)
{
return(sqrt(mean((truth-prediction)^2, na.rm=TRUE)))
}
# Calculate partial RMSE for different zones by generating squared difference rasters.... | apache-2.0 | R |
c8cf3c12758d45a31a23a7ae4cbe91b3939a6504 | Add missing mouse contrasts | klmr/codons,klmr/codons | config_mouse.r | config_mouse.r | species = 'mouse'
trna_counts = './data/trna-counts-mm10.tsv'
mrna_counts = './data/rnaseq-counts-mm10.tsv'
trna_annotation = './data/tRNA_Scan_Mus_musculus.GRCm38.69_301014.filtered.out'
mrna_annotation = './data/Mus_musculus.GRCm38.75.gene_annot.tsv'
cds = './data/Mus_musculus.GRCm38.cds.all.fa.gz'
trna_design = './d... | species = 'mouse'
trna_counts = './data/trna-counts-mm10.tsv'
mrna_counts = './data/rnaseq-counts-mm10.tsv'
trna_annotation = './data/tRNA_Scan_Mus_musculus.GRCm38.69_301014.filtered.out'
mrna_annotation = './data/Mus_musculus.GRCm38.75.gene_annot.tsv'
cds = './data/Mus_musculus.GRCm38.cds.all.fa.gz'
trna_design = './d... | apache-2.0 | R |
d412b2418c89f41c5fc1d3fae4f925bc8160c179 | Update es.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/es.r | R/es.r | #' es
#'
#'Given a temperature Celsius value give Vapor Pressure in hPa. Hardy, R.; ITS-90 Formulations for Vapor Pressure, Frostpoint
#' Temperature, Dewpoint Temperature and Enhancement Factors in the Range -100 to 100 degC;
#'
#'
#' @param numeric t Air temperature in Celsius degrees.
#' @return Saturation Vapor P... | #' es
#'
#'Given a temperature Celsius value give Vapor Pressure in hPa. Hardy, R.; ITS-90 Formulations for Vapor Pressure, Frostpoint
#' Temperature, Dewpoint Temperature and Enhancement Factors in the Range -100 to 100 degC;
#'
#'
#' @param numeric t Air temperature in Celsius degrees.
#' @return Saturation Vapor P... | mit | R |
11d1385f4dd5a5053eeda9b58bbdbdfc9367ed52 | Comment der | smehan/App-data-reqs,smehan/App-data-reqs | plot.r | plot.r | ###########################################################
Plot.r is a class that reads in a cleaned csv from source
data and performs some pre-processing. It then creates
some plots mainly slicing on Assignee, Calendar duration,
created year and month (which are calculated values)
###################... | ***********************************************************
Plot.r is a class that reads in a cleaned csv from source
data and performs some pre-processing. It then creates
some plots mainly slicing on Assignee, Calendar duration,
created year and month (which are calculated values)
*******************... | apache-2.0 | R |
e40eca95ca7894bc66c4b2e4cfadd2944f785697 | check clinical data for mafreport | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/Annotation/mafReport.r | lib/Annotation/mafReport.r | rm(list=ls())
outFile=''
parSampleFile1='fileList1.txt'
parSampleFile2=''
parSampleFile3=''
parFile1='/home/shengq2/program/projects/breast_cancer_spore/20220713_wgs/BRE15136_Summary_21Oct2021_correctedv5.csv'
parFile2=''
parFile3=''
clinicalFeatures='ARM,CBR_6,TNBCtype_4,TIL_call,PDL1_IHC_Agg,BMI_CLASS,diabetes';geno... | rm(list=ls())
outFile=''
parSampleFile1='fileList1.txt'
parSampleFile2=''
parSampleFile3=''
parFile1=''
parFile2=''
parFile3=''
genome='hg38'
setwd('/scratch/cqs/breast_cancer_spore/analysis/all/gatk4_13_report/result')
### Parameter setting end ###
library(mafreport)
#https://github.com/PoisonAlien/maftools/issue... | apache-2.0 | R |
a3bbe5668894a13d6ec8b076f3876f09cd41b901 | add a newline | syberia/syberia | inst/tests/test-data_stage.r | inst/tests/test-data_stage.r | context("data stage")
test_that("it turns a munge_procedure into a stagerunner", {
tmp <- new.env(); tmp$data <- iris
munge_procedure <- rep(list(list(column_transformation(function(x) 2 * x), 1)), 2)
data_stage(tmp, munge_procedure)$run()
expect_equal(tmp$data[[1]], 4 * iris[[1]])
})
# TODO: Test triggers!
... | context("data stage")
test_that("it turns a munge_procedure into a stagerunner", {
tmp <- new.env(); tmp$data <- iris
munge_procedure <- rep(list(list(column_transformation(function(x) 2 * x), 1)), 2)
data_stage(tmp, munge_procedure)$run()
expect_equal(tmp$data[[1]], 4 * iris[[1]])
})
# TODO: Test triggers!
| mit | R |
b1ff0b7b36a8bfba23c78cd0f6757aa9c85bebd4 | adjust pdf width and bugfix | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/scRNAMarkerGenes.r | lib/scRNA/scRNAMarkerGenes.r |
library(Seurat)
library(ggplot2)
finalList<-readRDS(parFile1)
geneFile<-parFile2
obj<-finalList$obj
celltypes<-read.table(geneFile, sep="\t", header=T, stringsAsFactors = F)
celltypes$Gene<-gsub("\\s.+", "", celltypes$Gene)
celltypes$Gene<-toupper(celltypes$Gene)
missGenes<-celltypes[!(celltypes$Gene %in% rownames... |
library(Seurat)
library(ggplot2)
finalList<-readRDS(parFile1)
geneFile<-parFile2
obj<-finalList$obj
celltypes<-read.table(geneFile, sep="\t", header=T, stringsAsFactors = F)
celltypes$Gene<-gsub("\\s.+", "", celltypes$Gene)
celltypes$Gene<-toupper(celltypes$Gene)
missGenes<-celltypes[!(celltypes$Gene %in% rownames... | apache-2.0 | R |
0c0eb601fd41b91a8c6b64b8d63282c7efc20e07 | add 3th OR example | mhermans/tabulr | examples.r | examples.r | source('table_export_openxlsx.r')
# BASIC EXAMPLES #
# ============== #
d <- as.data.frame(Titanic)
tab1 <- table(d$Class, d$Sex)
tab2 <- table(d$Class, d$Survived)
tab3 <- table(d$Sex, d$Survived)
# write single table
# ------------------
wb <- createWorkbook()
addWorksheet(wb = wb, sheetName = 'OR_tables')
wb ... | source('table_export_openxlsx.r')
# BASIC EXAMPLES #
# ============== #
d <- as.data.frame(Titanic)
tab1 <- table(d$Class, d$Sex)
tab2 <- table(d$Class, d$Survived)
tab3 <- table(d$Sex, d$Survived)
# write single table
# ------------------
wb <- createWorkbook()
addWorksheet(wb = wb, sheetName = 'OR_tables')
wb ... | agpl-3.0 | R |
c32b8bfea6f3130950f3650824fb07bcd8940f47 | Fix boundaries for dtm | HIIT/digivaalit-2015,HIIT/digivaalit-2015,HIIT/digivaalit-2015 | topics/topics.r | topics/topics.r | create_dtm <- function( path ) {
library(tm)
library(Matrix)
a <- Corpus( DirSource( path ) )
ndocs <- length(a)
minDocFreq <- ndocs * 0.1 ## not common words enough
maxDocFreq <- ndocs * 0.8 ## too commong words
a <- tm_map(a, removeNumbers)
a <- tm_map(a , stripWhitespace)
a <- tm_map(a, removeP... | create_dtm <- function( path ) {
library(tm)
library(Matrix)
a <- Corpus( DirSource( path ) )
a <- tm_map(a, removeNumbers)
a <- tm_map(a , stripWhitespace)
a <- tm_map(a, removePunctuation)
a <- tm_map(a, content_transformer(tolower) )
a <- tm_map(a, removeWords, stopwords("finnish") )
dtm <-Docum... | mit | R |
465618d4649221bb29339b233915639e48ec0dd2 | fix doc #2 | mschubert/narray,mschubert/narray | R/lambda.r | R/lambda.r | #' Lambda syntax for array iteration
#'
#' @param fml A call prefixed with a tilde
#' @param along A named vector which objects to subset (eg: c(x=1))
#' @param group Not implemented
#' @param simplify Return array instead of index+result if scalar
#' @param expand_grid Use all combinations of indices (... | #' Lambda syntax for array iteration
#'
#' @param fml A call prefixed with a tilde
#' @param along A named vector which objects to subset (eg: c(x=1))
#' @param group Not implemented
#' @param simplify Return array instead of index+result if scalar
#' @param envir Environment where variables can be f... | apache-2.0 | R |
53c801df4f076e434c8e14657942749789e80e63 | speed up execution of test_basic.r | cscheid/rgithub,s-u/rgithub,akhmed1/rgithub,aronlindberg/rgithub | inst/tests/test_basic.r | inst/tests/test_basic.r | context("Basic Tests")
test_that("A basic rgithub context can be acquired", {
create.github.context("https://api.github.com")
repos <- get.user.repositories("cscheid")
repos_overview <- do.call("rbind",
lapply(repos$content[1:5], function(x) {
data.frame(name = x$name,
... | context("Basic Tests")
test_that("A basic rgithub context can be acquired", {
create.github.context("https://api.github.com")
repos <- get.user.repositories("cscheid")
print(repos)
})
| mit | R |
1c460e4b384771bb82708607ff2e2c9a8b49408e | Improve calling sequence, namespaces, returned object | mconlon17/vivo-r,mconlon17/vivo-r | sparql/vivo.query.r | sparql/vivo.query.r | vivo.query <- function(query, endpoint= 'http://localhost:8080/vivo/api/sparqlQuery',
email= 'vivo_root@mydomain.edu', password= 'v;bisons',
ns = c(
"rdf","<http://www.w3.org/1999/02/22-rdf-syntax-ns#>",
"rdfs","<http://www.w3.org/2000/01/rdf-schema#>",
"xsd","<http://www.w3.org/2001/XMLSchema#>",
"... | vivo.query <- function(query, endpoint= 'http://localhost:8080/vivo/api/sparqlQuery',
email= 'vivo_root@school.edu', password= '*******', format="tsv",
ns = c(
"rdf","<http://www.w3.org/1999/02/22-rdf-syntax-ns#>",
"rdfs","<http://www.w3.org/2000/01/rdf-schema#>",
"xsd","<http://www.w3.org/2001/XMLSchem... | bsd-2-clause | R |
95edf9c277b7a50805c71bd93b6b7b77324f546d | Update vizualizacija.r | GalDrnovsek/APPR-2015-16 | vizualizacija/vizualizacija.r | vizualizacija/vizualizacija.r | # 3. faza: Izdelava zemljevida
# Uvozimo zemljevid.
#zemljevid <- uvozi.zemljevid("http://e-prostor.gov.si/fileadmin/BREZPLACNI_POD/RPE/OB.zip",
# "OB/OB", encoding = "Windows-1250")
# Preuredimo podatke, da jih bomo lahko izrisali na zemljevid.
#druzine <- preuredi(druzine, zemljevid, "OB... | # 3. faza: Izdelava zemljevida
# Uvozimo zemljevid.
zemljevid <- uvozi.zemljevid("http://e-prostor.gov.si/fileadmin/BREZPLACNI_POD/RPE/OB.zip",
"OB/OB", encoding = "Windows-1250")
# Preuredimo podatke, da jih bomo lahko izrisali na zemljevid.
druzine <- preuredi(druzine, zemljevid, "OB_UI... | mit | R |
6fe47b77a56aba476ddd162772996b365be9b5b6 | remove a stray browser | syberia/syberia | R/construct_stage_runner.r | R/construct_stage_runner.r | #' Return a stageRunner object that parametrizes a list of stages.
#'
#' Each stage is first fed through a function that converts it to a stageRunner
#' or a function. For example, list(import = X, ...) gets converted by,
#' amongst other things, looking for a variable import_stage and passing
#' in X.
#'
#' This kind... | #' Return a stageRunner object that parametrizes a list of stages.
#'
#' Each stage is first fed through a function that converts it to a stageRunner
#' or a function. For example, list(import = X, ...) gets converted by,
#' amongst other things, looking for a variable import_stage and passing
#' in X.
#'
#' This kind... | mit | R |
2869e9d4ec565b3c1fba48e1056d77b586f6d1eb | remove ; and " from log file | koji-to/effort_calculator,koji-to/effort_calculator,koji-to/effort_calculator | format_main_log_to_csv.r | format_main_log_to_csv.r | ####### preprocessing main logs and change to .csv
file_list.df<-read.table("git_log_main/git_log_main_list.txt",header=F)
dir.create("git_log_main_proc")
for(i in 1:nrow(file_list.df)){
open_file_name<-paste("git_log_main/",file_list.df[i,1],sep="")
if(file.access(open_file_name)==0){
proc_main_log.df<-data.f... | ####### preprocessing main logs and change to .csv
file_list.df<-read.table("git_log_main/git_log_main_list.txt",header=F)
dir.create("git_log_main_proc")
for(i in 1:nrow(file_list.df)){
open_file_name<-paste("git_log_main/",file_list.df[i,1],sep="")
if(file.access(open_file_name)==0){
proc_main_log.df<-data.f... | mit | R |
519cce60b627981c879b7741839f92f61bd7edf6 | Update 1.r | glor/R,glor/R | aufgaben/blatt03/1.r | aufgaben/blatt03/1.r | #Blatt 3
#1.1 Datei lokal speichern
#1.2
maeuse = read.table(file="mice.txt", sep="t", dec=".", header=TRUE)
#1.3
boxplot(maeuse$speed ~ maeuse$health, date = maeuse, main = "kranke Maeuse" )
# Beide Gruppen sind normalverteilt, es gibt keine Aussreisser. (diese wuerden als Punkte ausserhalb der Boxen darge... | #Blatt 3
#1.1 Datei lokal speichern
#1.2
maeuse = read.table(file="mice.txt", sep="t", dec=".", header=TRUE)
#1.3
boxplot(maeuse$speed ~ maeuse$health, date = maeuse, main = "kranke Maeuse" )
# Beide Gruppen sind normalverteilt, es gibt keine Aussreisser. (diese wuerden als Punkte ausserhalb der Boxen darge... | bsd-2-clause | R |
51b78700877a1c315aad7dff0008462459995ed6 | Use random number seed | eggplantbren/STATS331,eggplantbren/STATS331,eggplantbren/STATS331 | Code/use_jags.r | Code/use_jags.r | model = "model
{
theta ~ dunif(0, 1)
x ~ dbin(theta, N)
}
"
# The data (use NA for no data)
data = list(x=2, N=5)
# Variables to monitor
variable_names = c('theta')
# How many burn-in steps?
burn_in = 1000
# How many proper steps?
steps = 10000
# Thinning?
thin = 1
# Random number seed
seed = 42
# NO NEED T... | model = "model
{
theta ~ dunif(0, 1)
x ~ dbin(theta, N)
}
"
# The data (use NA for no data)
data = list(x=2, N=5)
# Variables to monitor
variable_names = c('theta')
# How many burn-in steps?
burn_in = 1000
# How many proper steps?
steps = 10000
# Thinning?
thin = 1
# NO NEED TO EDIT PAST HERE!!!
# Just run... | mit | R |
148e8136f84f23d79538f58ead4d5ebef9b140e9 | Update libraries.r | GalDrnovsek/APPR-2015-16 | lib/libraries.r | lib/libraries.r | library(knitr)
require(dplyr)
require(rvest)
require(gsubfn)
require(ggplot2)
# Uvozimo funkcije za delo z datotekami XML.
source("lib/xml.r", encoding = "UTF-8")
# Uvozimo funkcije za pobiranje in uvoz zemljevida.
source("lib/uvozi.zemljevid.r", encoding = "UTF-8")
| library(knitr)
require(dplyr)
require(rvest)
require(gsubfn)
# Uvozimo funkcije za delo z datotekami XML.
source("lib/xml.r", encoding = "UTF-8")
# Uvozimo funkcije za pobiranje in uvoz zemljevida.
source("lib/uvozi.zemljevid.r", encoding = "UTF-8") | mit | R |
1422e1266bb915dd27aa13af81dbec95e88b5631 | Update PMV_ISO7730.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/PMV_ISO7730.r | R/PMV_ISO7730.r | #' PMV_ISO7730
#'
#' Calculate Predicted Mean Vote (PMV) following ISO 7730.
#'
#' @param t numeric Air temperature in degC.
#' @param rh numeric Relative humidity in percentage.
#' @param wind numeric Windspeed in meter per second.
#' @param tr numeric Mean radiant temperature in degC.
#' @param M numeric Meta... | #' PMV_ISO7730
#'
#' Calculate Predicted Mean Vote (PMV) following ISO 7730.
#'
#' @param t numeric Air temperature in degC.
#' @param rh numeric Relative humidity in percentage.
#' @param wind numeric Windspeed in meter per second.
#' @param tr numeric Mean radiant temperature in degC.
#' @param M numeric Meta... | mit | R |
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