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
values |
|---|---|---|---|---|---|---|---|---|
c0f319a3f4d16741efe0f364dd7f439ae67c6013 | Update R3-GUI download URL used in LOAD-GUI | zsx/r3,Pointillistic/rebol-lang,Pointillistic/rebol-lang,Pointillistic/rebol-lang,zsx/r3,zsx/r3,Pointillistic/rebol-lang,zsx/r3 | src/mezz/rma-patches.r | src/mezz/rma-patches.r | REBOL [
Title: "REBOL Graphics - load-gui patch"
]
load-gui: func [
"Download current Spahirion's R3-GUI module from web."
/local data
][
print "Fetching GUI..."
either error? data: try [load http://development.saphirion.com/resources/r3-gui.r3] [
either data/id = 'protocol [print "C... | REBOL [
Title: "REBOL Graphics - load-gui patch"
]
load-gui: func [
"Download current Spahirion's R3-GUI module from web."
/local data
][
print "Fetching GUI..."
either error? data: try [load http://www.saphirion.com/development/downloads-2/files/r3-gui.r3] [
either data/id = 'protoc... | apache-2.0 | R |
f6445381994679eef6a3b378bfd8dd2e9ede57f0 | add url | AndySouth/coverage | inst/shiny/coverage1/server.r | inst/shiny/coverage1/server.r | #coverage/inst/shiny/coverage1/server.r
#andy south 12/5/16
#https://andysouth.shinyapps.io/coverage1/
library(shiny)
#library(devtools)
#install_github('AndySouth/coverage')
library(coverage)
library(png)
shinyServer(function(input, output, session) {
################################
output$plot_feed <- rende... | #coverage/inst/shiny/coverage1/server.r
#andy south 12/5/16
library(shiny)
#install_github('AndySouth/coverage')
library(coverage)
library(png)
shinyServer(function(input, output, session) {
################################
output$plot_feed <- renderPlot({
#add dependency on the button
#if ( input$aBut... | mit | R |
a854f591af8463f257a43a50e64bbfcade7a9d27 | Add VCF download | GreatEmerald/geoscripting,GreatEmerald/geoscripting,GreatEmerald/geoscripting,GreatEmerald/geoscripting | Lesson8/Main.r | Lesson8/Main.r | # Team Rython, Dainius Masiliunas and Tim Weerman
# Date: 11 January, 2016
# Apache License 2.0
# Needed packages
# Source
# Download/load information
download.file("https://github.com/GeoScripting-WUR/AdvancedRasterAnalysis/raw/gh-pages/data/GewataB1.rda", "data/GewataB1.rda", "wget")
download.file("https://githu... | # Team Rython, Dainius Masiliunas and Tim Weerman
# Date: 11 January, 2016
# Apache License 2.0
# Needed packages
# Source
# Download/load information
download.file("https://github.com/GeoScripting-WUR/AdvancedRasterAnalysis/raw/gh-pages/data/GewataB1.rda", "data/GewataB1.rda", "wget")
download.file("https://githu... | apache-2.0 | R |
b3efef66d0f3428b2739fb28a9fe4997f8327c6c | Replace (non macOS non-existent) `realpath` | klmr/modules,klmr/modules | tests/testthat/helper-paths.r | tests/testthat/helper-paths.r | #' Compute normalized logical paths
#'
#' \code{realpath(path)} will return the normalized logical path for
#' \code{path}, similar to \code{normalizePath} but working correctly for
#' nonexistent paths on Unix systems.
#' @param path a character vector of paths
#' @note This function doesn’t work with paths containing... | #' Compute normalized logical paths
#'
#' \code{realpath(path)} will return the normalized logical path for
#' \code{path}, similar to \code{normalizePath} but working correctly for
#' nonexistent paths on Unix systems.
#' @param path a character vector of paths
#' @note This function doesn’t work with paths containing... | apache-2.0 | R |
47cbe68c19036d096b01cb6e33673d1766f7862c | Update banner | draegtun/ren-c,kealist/ren-c,kealist/ren-c,rgchris/ren-c,rgchris/ren-c,codebybrett/ren-c,draegtun/ren-c,giuliolunati/ren-c,codebybrett/ren-c,kealist/ren-c,hostilefork/rebol,draegtun/ren-c,hostilefork/rebol,kealist/ren-c,codebybrett/ren-c,codebybrett/ren-c,rgchris/ren-c,kealist/ren-c,rgchris/ren-c,codebybrett/ren-c,host... | src/mezz/mezz-banner.r | src/mezz/mezz-banner.r | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: Startup Banner"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2.0
See: http://www.apache.org/licenses/LICENS... | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: Startup Banner"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2.0
See: http://www.apache.org/licenses/LICENS... | apache-2.0 | R |
baa383ef3c9c66002f6b9de31dd9ca74e6683c1f | Set paths apppropriately. | owainkenwayucl/stats-plus-plus,owainkenwayucl/stats-plus-plus,owainkenwayucl/stats-plus-plus,owainkenwayucl/stats-plus-plus | r/pyconfconv.r | r/pyconfconv.r | #!/usr/bin/env Rscript
# This is a wrapper for doing the less pleasant parts of calling the converter
# from R.
# To use it, source this script and then:
# eval(parse(text=pyconfconverts(filename, section)))
# or eval(parse(text=pyconfconvert(filename)))
# Owain Kenway
# Where this is distributed it is done so under t... | #!/usr/bin/env Rscript
# This is a wrapper for doing the less pleasant parts of calling the converter
# from R.
# To use it, source this script and then:
# eval(parse(text=pyconfconverts(filename, section)))
# or eval(parse(text=pyconfconvert(filename)))
# Owain Kenway
# Where this is distributed it is done so under t... | mit | R |
ae552479b6a9d7503d1bae0553bf34a2152bd5b7 | Correct LAUNCH for unset refinement args | hostilefork/rebol,rgchris/ren-c,kealist/ren-c,draegtun/ren-c,rgchris/ren-c,kealist/ren-c,draegtun/ren-c,codebybrett/ren-c,codebybrett/ren-c,hostilefork/rebol,codebybrett/ren-c,hostilefork/rebol,giuliolunati/ren-c,hostilefork/rebol,kealist/ren-c,draegtun/ren-c,giuliolunati/ren-c,giuliolunati/ren-c,draegtun/ren-c,codebyb... | src/mezz/mezz-control.r | src/mezz/mezz-control.r | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: Control"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2.0
See: http:... | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: Control"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2.0
See: http:... | apache-2.0 | R |
174f84177cc624937e5d77f965c7d4a5f2d96e56 | add repo source for init.r | OwnYourData/app-template,OwnYourData/app-template | init.r | init.r | #
# Example R code to install packages
# See http://cran.r-project.org/doc/manuals/R-admin.html#Installing-packages for details
#
###########################################################
# Update this line with the R packages to install:
my_packages = c('shiny',
'shinyBS',
'devtoo... | #
# Example R code to install packages
# See http://cran.r-project.org/doc/manuals/R-admin.html#Installing-packages for details
#
###########################################################
# Update this line with the R packages to install:
my_packages = c('shiny',
'shinyBS',
'devtoo... | mit | R |
508b6f862a1215550a6012173bd7c5f269972db5 | Add needed packages | drosofff/tools-artbio,drosofff/tools-artbio,ARTbio/tools-artbio,ARTbio/tools-artbio,chamaelj/tools-artbio,ARTbio/tools-artbio,chamaelj/tools-artbio,ARTbio/tools-artbio,chamaelj/tools-artbio,drosofff/tools-artbio,drosofff/tools-artbio | tools/small_rna_map/test.r | tools/small_rna_map/test.r | # Table is the data frame
library("ggplot2")
library("gridExtra")
library("RColorBrewer")
library("gtable")
library("grid")
theme_set(theme_bw())
#Table=read.delim(your_input, header=T, row.names=NULL)
Table <- within(Table[1:27,], Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
p1 <- ggplot(Table, aes(x=... | # Table is the data frame
library("ggplot2")
library("gridExtra")
library(ggplus)
theme_set(theme_bw())
#Table=read.delim(your_input, header=T, row.names=NULL)
Table <- within(Table[1:27,], Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
p1 <- ggplot(Table, aes(x=Coordinate, y=Nbr_reads, colour=Polarity)) ... | mit | R |
144ca31db071d402ce2ddb6cff0532a25df3c9ff | Add GetAddresses | Nektar-io/LvWS | R/api-methods.r | R/api-methods.r | library(XML)
library(httr)
# General methods
get_xml <- function(path, query) {
url <- modify_url(url = .url,
path = file.path(.path, path),
query = query
)
x <- paste(readLines(url, warn = FALSE), collapse="")
xmlParse(x)
}
# API methods
GetAddresses <- fu... | library(XML)
library(httr)
# General methods
fetch_data <- function(path, query, nodes) {
url <- modify_url(url = .url,
path = file.path(.path, path),
query = query
)
get_xml(url, nodes)
}
get_xml <- function(url, nodes) {
x <- paste(readLines(url, warn = FA... | agpl-3.0 | R |
168706c14639f14c559f2c8b5fd988c90aba4c91 | Update 2016_report_config.r | PSC-CoTC/PSC-FRAM-Admin,PSC-CoTC/PSC-FRAM-Admin | config/2016_report_config.r | config/2016_report_config.r |
run.year <- 2016
post.season.fram.db <- "./fram db/Final pre and post databases/2018PFMC_NOF_ForPSC-Coho-Backwards-thru2016_compact.mdb"
post.season.run.name <- "bc-Coho1637 Final + BP27"
post.season.tamm <- "./fram db/TAMM_Files_Postseason/coho BK 2015 Final Feb 15th.xlsm"
pre.season.fram.db <- "./fram db/Fi... |
run.year <- 2016
post.season.fram.db <- "./fram db/Final pre and post databases/2018PFMC_NOF_ForPSC-Coho-Backwards-thru2016_compact.mdb"
post.season.run.name <- "bc-Coho1637 Final + BP27"
post.season.tamm <- "./fram db/TAMM_Files_Postseason/coho BK 2015 Final Feb 15th.xlsm"
pre.season.fram.db <- "./fram db/Fi... | mit | R |
425e02535c0fb5c70eaf70408b01c0f0f77f342e | fix paste | mynameisvinn/rstae | R/util.r | R/util.r | #' @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
}
| #' @export
test <- function(woof){
print(woof)
}
#' @export
fetch_trips <-function(municipalId){
uri = paste("https://municipal.systems/v1/municipalities/", municipalId, "/trips")
r <- GET(uri)
e = content(r)$results
f = as.data.frame(do.call(rbind, e))
f
}
| mit | R |
1c6aad7c786c73fd451800f994e5c6804616f134 | Document cache module | klmr/codons,klmr/codons | scripts/cache.r | scripts/cache.r | decorate = modules::import('decorate', attach = TRUE)
modules::import('ebits/base', attach = c('closure', 'match_call_defaults'))
#' Make function cached
#'
#' Cache a function call’s result so that subsequent calls of the function with
#' the same arguments do not re-evaluate the function: the cached result is
#' ret... | decorate = modules::import('decorate', attach = TRUE)
modules::import('ebits/base', attach = c('closure', 'match_call_defaults'))
cache = decorator %@% function (f) {
cache = new.env()
g = function (...) {
call = match_call_defaults()
args = call[-1]
# Use a helper to evaluate all argum... | apache-2.0 | R |
c91534b1be3c890e64fe2f45615a3cd7b9ad1170 | Fix font imports | klmr/ggplots | __init__.r | __init__.r | #' Pretty plotting module
export = import('./export', attach = 'export_from')
gg = import_package('ggplot2')
export_from(gg)
#
# Set a very minimal theme. Avoid chartjunk.
#
fonts = import('./fonts')
fonts$register_font('Roboto')
fonts$register_font('Roboto Condensed', 'RobotoCondensed')
theme_set(theme_minimal() ... | #' Pretty plotting module
export = import('./export', attach = 'export_from')
gg = import_package('ggplot2')
export_from(gg)
#
# Set a very minimal theme. Avoid chartjunk.
#
fonts = import('./fonts')
fonts$register_fonts(c('Roboto', 'Roboto Condensed'))
theme_set(theme_minimal() +
theme(panel.grid = elem... | apache-2.0 | R |
6b239c33903b44edb6dd11032201758201c83980 | change plot | sdwalsh/mst,sdwalsh/mst | plot.r | plot.r | library(car)
d <- read.csv("~/Documents/io/mirango/mst/max-edge-mst.txt")
ls <- loess(y ~ x, data=d)
pr.loess <- predict(ls)
m <-lm(y ~ x, data=d)
abline(coef(m), col="blue")
pr.abline <- predict(m)
plot(y ~ x, data=d, xlab="vertices", ylab="largest edge in mst", main="Largest Edge by Number of Vertices")
lines(pr.l... | library(car)
d <- read.csv("~/Documents/io/mirango/mst/max-edge-mst.txt")
scatterplot(y ~ x, data = d, xlab="number of vertices", ylab="largest edge in mst", main="Largest Edge by # of Vertices", labels=row.names(d), reg.line=TRUE)
fit <- lm(y ~ x, data=d)
summary(fit) | mit | R |
d57fdc3a4236fca54e47880bc010ae61179ea5fc | fix error in Butter-fly.r | foreverbell/parakeet | tests/Butter-fly/Butter-fly.r | tests/Butter-fly/Butter-fly.r | Gokigen na chou ni natte kirameku kaze ni notte
Ima sugu kimi ni ai ni yukou
Yokei na koto nante wasureta hou ga mashi sa
Kore ijou shareteru jikan wa nai
Nani ga wow wow～ kono sora ni todoku no darou
Dakedo wow wow～ ashita no yotei mo wakaranai
Mugendai na yume no ato no nanimo nai yo no naka ja
Sou sa itoshi... | Gokigen na chou ni natte kirameku kaze ni notte
Ima sugu kimi ni ai ni yukou
Yokei na koto nante wasureta hou ga mashi sa
Kore ijou shareteru jikan wa nai
Nani ga wow wow～ kono sora ni todoku no darou
Dakedo wow wow～ ashita no yotei mo wakaranai
Mugendai na yume no ato no nanimo nai yo no naka ja
Sou sa itoshi... | mit | R |
2c9e8998a37b4f393bf2b352aee48d9ca683bad1 | Install reticulate from github | ryanlovett/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub | deployments/r/image/extras.d/ph-w250fg.r | deployments/r/image/extras.d/ph-w250fg.r | #!/usr/bin/env Rscript
# From https://github.com/berkeley-dsep-infra/datahub/issues/881
print("Installing packages for PHW250F+G")
source("/tmp/class-libs.R")
# dplyr requires 0.2.1...cran only has 0.2.0
print("Installing assertthat...")
devtools::install_github('hadley/assertthat', ref='v0.2.1', upgrade_dependencies... | #!/usr/bin/env Rscript
# From https://github.com/berkeley-dsep-infra/datahub/issues/881
print("Installing packages for PHW250F+G")
source("/tmp/class-libs.R")
# dplyr requires 0.2.1...cran only has 0.2.0
print("Installing assertthat...")
devtools::install_github('hadley/assertthat', ref='v0.2.1', upgrade_dependencies... | bsd-3-clause | R |
c43efbc1356f02aa1231d3b3efe23b22b58047f9 | Fix grammar errors | FTAsr/wordvet,FTAsr/wordvet,FTAsr/wordvet,FTAsr/wordvet | trainGloveModel.r | trainGloveModel.r | args = commandArgs(trailingOnly=TRUE)
if (length(args) != 3) {
cat("trainGloveModel.R <size> <window> <iters>\n")
} else {
suppressMessages(library("text2vec"))
vectorSize <- as.numeric(args[1])
window <- as.numeric(args[2])
iters <- as.numeric(args[3])
print("started running trainGloveModel.r")
text... | print("started running trainGloveModel.r")
library("text2vec")
args = commandArgs(trailingOnly=TRUE)
if (length(args) != 3) {
cat("trainGloveModel.R <size> <window> <iters>\n")
} else {
vectorSize <- as.numeric(args[1])
window <- as.numeric(args[2])
iters <- as.numeric(args[3])
text8_file = "/data/... | apache-2.0 | R |
3bdbd9d07acda21e17e541c7b68e4b6837f407da | Add sample grouping. Refactoring. | thehyve/naa-SmartR,agapow/smartr,agapow/smartr,agapow/smartr,agapow/smartr,thehyve/heim-SmartR,thehyve/naa-SmartR,thehyve/heim-SmartR,thehyve/naa-SmartR,thehyve/heim-SmartR,thehyve/heim-SmartR | web-app/HeimScripts/heatmap/run.r | web-app/HeimScripts/heatmap/run.r | library(gplots)
dataset1color <- "coral3"
dataset2color <- "chartreuse3"
labelColumns <- c("Row.Label","Bio.marker")
#Input expected 1 or 2 dataframes ofwith columns: Row.Label, Bio.marker, ASSAY_0001 ASSAY_0002 ...
main <- function(){
datasets <- parseInput(loaded_variables) #this will just make sure we have eith... | library(gplots)
main <- function(){
dataset <- loaded_variables[[1]] #dataframe with columns: Row.Label, Bio.marker, ASSAY_0001 ASSAY_0002 ...
measurements <- extractMeasurements(dataset)
measurements <- assignNames(measurements,dataset)
measurements <- transform(measurements)
makeHeatmap(measurements)
}
... | apache-2.0 | R |
46c37c02e10eb42065a8e45c75697c2bc4363422 | 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 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]])),... | # 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 |
c549d6c79042c3ffe07b3a72ba72e0c8fd46f2ad | Add fix address lookup | aserlich/VIP-LivedData,aserlich/VIP-LivedData | ErrorChecksViz.r | ErrorChecksViz.r | library(stringr)
library(plyr)
##Detect problems with ward lookup
#############################
workd <- "/Volumes/Optibay-1TB/RSA_RCT/QA/LiveData/VIP-LivedData/"
exports <- list.files(path=workd, pattern ="contact_2014_[0-9].*")
currentFile <- tail(exports,1)[1]
setwd(paste0(workd,currentFile))
cat("Now loading th... | library(stringr)
library(plyr)
##Detect problems with ward lookup
#############################
workd <- "/Volumes/Optibay-1TB/RSA_RCT/QA/LiveData/VIP-LivedData/"
exports <- list.files(path=workd, pattern ="contact_2014_[0-9].*")
currentFile <- tail(exports,1)[1]
setwd(paste0(workd,currentFile))
cat("Now loading th... | mit | R |
20cfd9ead109beb3a6e7eee0c98b02f54cdfd4f7 | use default umap and assay for visualization | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/Signac.r | lib/scRNA/Signac.r | library(SignacX)
library(Seurat)
finalList=readRDS(parFile1)
obj=finalList$obj
defaultAssay = DefaultAssay(obj)
if(defaultAssay == "integrated"){
if("SCT" %in% names(obj@assays)){
DefaultAssay(obj)="SCT"
}else{
DefaultAssay(obj)="RNA"
}
obj <- SCTransform(obj, verbose = FALSE)
obj <- RunPCA(obj, ver... | library(SignacX)
library(Seurat)
finalList=readRDS(parFile1)
obj=finalList$obj
if(DefaultAssay(obj) == "integrated"){
if("SCT" %in% names(obj@assays)){
DefaultAssay(obj)="SCT"
}else{
DefaultAssay(obj)="RNA"
}
obj <- SCTransform(obj, verbose = FALSE)
obj <- RunPCA(obj, verbose = FALSE)
obj <- RunUM... | apache-2.0 | R |
8b0009cfdebdcf20b709575f700aa971f7aa5213 | add color for zone | hansthompson/shiny-server,hansthompson/shiny-server,hansthompson/shiny-server | muniexplorer/app.r | muniexplorer/app.r | library(shiny)
library(leaflet)
library(dplyr)
load("data/all_the_data.rda")
precincts <- levels(factor(all_the_data$NAME))
#input <- list(select = "Spenard")
ui <- bootstrapPage(
tags$style(type = "text/css", "html, body {width:100%;height:100%}"),
leafletOutput("map", width = "100%", height = "100%"),
... | library(shiny)
library(leaflet)
library(dplyr)
load("data/all_the_data.rda")
precincts <- levels(factor(all_the_data$NAME))
#input <- list(select = "Spenard")
ui <- bootstrapPage(
tags$style(type = "text/css", "html, body {width:100%;height:100%}"),
leafletOutput("map", width = "100%", height = "100%"),
... | mit | R |
5c342a0f270bfb951b8525832813ce4cf71c9d57 | UPDATE onUnload method | RBigData/pbdADIOS,RBigData/pbdADIOS,go-ski/pbdADIOS,RBigData/pbdADIOS,YupingLu/pbdADIOS,YupingLu/pbdADIOS,go-ski/pbdADIOS,RBigData/pbdADIOS,go-ski/pbdADIOS,YupingLu/pbdADIOS | R/zzz.r | R/zzz.r | # Hooks for Name Space events
# triggered by library()
.onLoad <- function(libname, pkgname)
{
pbdMPI::init() # pbdMPI initilization
if(.Platform$OS.type == "windows") print("windows")
else print("others")
}
# triggered by detach(2, unload=TRUE)
.onUnload <- function(libpath)
{
pbdMPI::finalize()
... | # Hooks for Name Space events
# triggered by library()
.onLoad <- function(libname, pkgname)
{
pbdMPI::init() # pbdMPI initilization
if(.Platform$OS.type == "windows") print("windows")
else print("others")
}
# triggered by detach()
.onUnload <- function(libpath)
{
pbdADIOS::finalize()
print("B... | mpl-2.0 | R |
5f0040ff2c912d980711acead68ee7d11e2530d0 | Update zzz.r | syberia/syberia | R/zzz.r | R/zzz.r | .onAttach <- function(...) {
load_github_packages(.github_packages)
if (exists('run')) rm('run')
makeActiveBinding('run', function() build_model, .GlobalEnv)
}
| .onAttach <- function(...) {
load_github_packages(.github_packages)
if (!exists('run')) makeActiveBinding('run', function() build_model, .GlobalEnv)
}
| mit | R |
73327fd7589a45d8f0289a7ccf33e7dab76407ad | fix load_dependency | 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(file.path(current_directory(), dep)))
if (!file.exi... | #' 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 |
81893f9c19ee6fb74e187cdb9cf69257a27ce8d3 | Fix documentation of import.attach option | 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 |
feab8974e380134e8bd350b8462ae05aeba1a98a | Fix url generation code | hadley/sfhousing,hadley/sfhousing,hadley/sfhousing | house-sales.r | house-sales.r | # Human readable url
# http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2007/12/30/REHS_alameda.txt
# Machine readable url
# http://www.sfgate.com/c/a/2008/06/15/REHS.tb
# Get the data -----------------------
start <- as.Date("2003-04-27")
end <- as.Date("2008-10-05")
sundays <- as.POSIXlt(seq.Date(start, end, "week... | # Human readable url
# http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2007/12/30/REHS_alameda.txt
# Machine readable url
# http://www.sfgate.com/c/a/2008/06/15/REHS.tb
# Get the data -----------------------
start <- as.Date("2003-04-27")
end <- as.Date("2008-10-05")
sundays <- as.POSIXlt(seq.Date(start, end, "week... | mit | R |
1e58cbe49a834fc9528e73793e33fa4510c7dde0 | Unify documentation spelling | klmr/modules,klmr/modules | R/find_module.r | R/find_module.r | #' Find a module’s source code location
#'
#' @param module expression containing the fully qualified module name
#' @return the full path to the corresponding module source code location. If
#' multiple hits are found, return the one with the highest priority, that is
#' coming earlier in the search path, with the loc... | #' Find a module’s source code location
#'
#' @param module Expression containing the fully qualified module name
#' @return The full path to the corresponding module source code location. If
#' multiple hits are found, return the one with the highest priority, that is
#' coming earlier in the search path, with the loc... | apache-2.0 | R |
3d154f95e8a413c34a85d455d2cd4f422fd1c0d0 | modify relative paths | 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 |
fab2b19faab943f55ef6e188d4d10b1b5786ea9d | Fix the syntax error in printf.r | giuliolunati/ren-c,codebybrett/ren-c,giuliolunati/ren-c,codebybrett/ren-c,rgchris/ren-c,kealist/ren-c,draegtun/ren-c,codebybrett/ren-c,hostilefork/rebol,giuliolunati/ren-c,hostilefork/rebol,draegtun/ren-c,kealist/ren-c,hostilefork/rebol,kealist/ren-c,hostilefork/rebol,codebybrett/ren-c,kealist/ren-c,draegtun/ren-c,drae... | tests/misc/printf.r | tests/misc/printf.r | REBOL []
recycle/torture
libc: make library! %libc.so.6
x64?: 40 = fifth system/version
size_t: either x64? ['int64]['int32]
printf: make-routine libc "printf" compose/deep [
return: [int32]
f [pointer]
...
]
;(printf "hello^/" 0 [pointer])
(printf "hello %s^/" "world" [pointer])
(printf "hello^/")
(pr... | REBOL []
recycle/torture
libc: make library! %libc.so.6
x64?: 40 = fifth system/version
size_t: either x64? ['int64]['int32]
printf: make-routine compose/deep [
[
f [pointer]
...
]
(libc) "printf"
]
printf ["hello"]
print "hi"
| apache-2.0 | R |
c8fb75fd80ccfabcf17cb468e9af1a847d03d32c | change theme to spacelab | hansthompson/shiny-server,hansthompson/shiny-server,hansthompson/shiny-server | CannabisZoning/App.r | CannabisZoning/App.r | library(shinythemes)
library(rgeos)
library(rgdal)
library(leaflet)
library(geojsonio)
load("map.rda")
ui <- bootstrapPage(theme = shinytheme("spacelab"),
title = "Cannabis Business Zoning",
tags$head(includeScript("google-analytics.js")),
tags$style(type = ... | library(shinythemes)
library(rgeos)
library(rgdal)
library(leaflet)
library(geojsonio)
load("map.rda")
ui <- bootstrapPage(theme = shinytheme("Spacelab"),
title = "Cannabis Business Zoning",
tags$head(includeScript("google-analytics.js")),
tags$style(type = ... | mit | R |
20622176265342ccbc81106d0f381b10bd0ac456 | 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 |
b48e99f5ee6f5262fc6cb7c52ecd423bf70942fa | Test that `module_name` keeps working globally | klmr/modules,klmr/modules | inst/tests/test-name.r | inst/tests/test-name.r | context('Module names')
test_that('the global namespace has no module name', {
expect_null(module_name())
})
test_that('modules have a name', {
a = import('a')
expect_equal(module_name(a), 'a')
expect_equal(a$get_modname(), 'a')
})
test_that('module names can be read inside functions', {
a = impo... | context('Module names')
test_that('the global namespace has no module name', {
expect_null(module_name())
})
test_that('modules have a name', {
a = import('a')
expect_equal(module_name(a), 'a')
expect_equal(a$get_modname(), 'a')
})
test_that('module names can be read inside functions', {
a = impo... | apache-2.0 | R |
15d4330c13ab557296eac2ebd16082944a9f7637 | Update CalcAlleleDiffs.r | wbooker/PloidyPal | R/CalcAlleleDiffs.r | R/CalcAlleleDiffs.r | #' @export
CalcAlleleDiffs <- function(f){
infoTable <- as.matrix(read.csv(f, header=TRUE))
BEG1 <- as.numeric(infoTable[1,2])
END1 <- as.numeric(infoTable[2,2])
str1 <- toString(infoTable[4,2])
for(j in BEG1:END1){
filePath <- paste(c(str1,"/I",j,"/I",j,"_allelesFromPost_4.txt"), collapse = ""... | #' @export
CalcAlleleDiffs <- function(f){
infoTable <- as.matrix(read.csv(f, header=TRUE))
BEG1 <- as.numeric(infoTable[1,2])
END1 <- as.numeric(infoTable[2,2])
str1 <- toString(infoTable[4,2])
for(j in BEG1:END1){
filePath <- paste(c(str1,"/I",j,"/I",j,"_allelesFromPost_4.txt"), collapse = ""... | mit | R |
cb6478a9de2e41af22879407cba801747250d2ad | Add write_submit_script SlurmBashScript method | 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 = "*") {
private$write_slurm_script(container$dir)
}
... | mit | R |
5f5a73923fc51756de9be9f7e1af8e144d695d1f | Update PACo.r | efcaguab/paco | R/PACo.r | R/PACo.r | #' Performs PACo/procustes analysis
#' @param D a list with the data
#' @param nperm Number of permutations
#' @param seed Seed if results need to be reproduced
#' @param margin The margin to sample (1 to sample rows, 2 to sample columns)
#' @export
#' @examples
#' data(gopherlice)
#' library(ape)
#' gdist <- cophenet... | #' Performs PACo/procustes analysis
#' @param D a list with the data
#' @param nperm Number of permutations
#' @param seed Seed if results need to be reproduced
#' @param margin The margin to sample (1 to sample rows, 2 to sample columns)
#' @export
#' @examples
#' data(gopherlice)
#' library(ape)
#' gdist <- cophenet... | mpl-2.0 | R |
a816ccf01b36645cac58140ad1f4c0eebfe855b9 | use absolute path | robertzk/syberiaStructure | R/traversal.r | R/traversal.r | # All functions related to traversal of file system for grabbing Syberia related files
#
# By convention, the structure from a syberia root project will look like this:
#
# - data # Data preparation for data sources coming from an external API
# - sources
# - data_source1
# - data_source1.r
# - h... | # All functions related to traversal of file system for grabbing Syberia related files
#
# By convention, the structure from a syberia root project will look like this:
#
# - data # Data preparation for data sources coming from an external API
# - sources
# - data_source1
# - data_source1.r
# - h... | mit | R |
473f2fa1af1237554962caad1f826c83c6bd252c | Create auth_public.r | GalDrnovsek/Fuzbal | auth_public.r | auth_public.r | db = 'sem2017_janp'
host = 'baza.fmf.uni-lj.si'
user = 'javnost'
password = 'javnogeslo'
| db = 'sem2017_janp'
host = 'baza.fmf.uni-lj.si'
user = 'javnost'
password = 'javnogeslo'
db = 'sem2017_gald'
host = 'baza.fmf.uni-lj.si'
user = 'javnost'
password = 'javnogeslo'
db = 'sem2017_zant'
host = 'baza.fmf.uni-lj.si'
user = 'javnost'
password = 'javnogeslo'
| mit | R |
ac044be8730ef29274b7afe783169ecea129e10b | Update ggplot2_formatter.r | fdryan/R,jezdata/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 |
0590b263117aca8548b283971d4acf6d416257bd | Add co-owner. | IndyActuaries/epic-fhir,IndyActuaries/epic-fhir | r/models.r | r/models.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 |
cb2a02f2327a546eaf4331110e50f680605609ee | use is instead of is.trigger | robertzk/syberiaStages,FeiYeYe/syberiaStages | R/data_stage.r | R/data_stage.r | #' Data stage for syberia models
#'
#' TODO: Document this more
#'
#' @param modelenv an environment. The persistent modeling environment.
#' @param munge_procedure a list. A list of mungepiece arguments,
#' first preprocessed then passed to munge.
#' @export
data_stage <- function(modelenv, munge_procedure) {
# ... | #' Data stage for syberia models
#'
#' TODO: Document this more
#'
#' @param modelenv an environment. The persistent modeling environment.
#' @param munge_procedure a list. A list of mungepiece arguments,
#' first preprocessed then passed to munge.
#' @export
data_stage <- function(modelenv, munge_procedure) {
# ... | mit | R |
ed88feead73a2c6154050ecda6c09c014ddc8c79 | Update processingDF.r | svobodam/Deep-Learning-Text-Summariser,svobodam/Deep-Learning-Text-Summariser,svobodam/Deep-Learning-Text-Summariser | PreProcessingScript/processingDF.r | PreProcessingScript/processingDF.r | # Data Frame processing
# Dataset used as .db file to allow managing DF from Python and R.
# This process process dataset to remove html tags.
# ***FUNCTIONS***
# Function which transorm DS to Corpus and preprocess it.
dfCorpusFN = function(data_frame) {
c = Corpus(VectorSource(data_frame))
removeText = funct... | # Author: Matej Svoboda
# Data Frame processing
# Dataset used as .db file to allow managing DF from Python and R.
# This process process dataset to remove html tags.
# ***FUNCTIONS***
# Function which transorm DS to Corpus and preprocess it.
dfCorpusFN = function(data_frame) {
c = Corpus(VectorSource(data_frame))... | mit | R |
bbbed89be9fb0e04500bf1bbcf22b6fe9b79f6de | Fix typo in R modules path | klmr/.files,klmr/.files,klmr/.files | .R/config.r | .R/config.r | options(pager = file.path(Sys.getenv('HOME'), '.R/pager.sh'),
# Imperial College London
repos = c(CRAN = 'http://cran.ma.imperial.ac.uk/'),
menu.graphics = FALSE, # Seriously, WHAT THE FUCK, R!?
import.path = '~/.R/modules',
devtools.name = 'Konrad Rudolph',
devtools.desc... | options(pager = file.path(Sys.getenv('HOME'), '.R/pager.sh'),
# Imperial College London
repos = c(CRAN = 'http://cran.ma.imperial.ac.uk/'),
menu.graphics = FALSE, # Seriously, WHAT THE FUCK, R!?
import.path = '~/R/modules',
devtools.name = 'Konrad Rudolph',
devtools.desc.... | apache-2.0 | R |
d56442105aabe4b36919165aacab2858c1b9e804 | rename group_id to job_group | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | template_LSF.r | template_LSF.r | infuser = import_package('infuser')
#' A template string used to submit jobs
template = "#BSUB-J {{ job_name }} # name of the job / array jobs
#BSUB-g {{ job_group | /rzmq }} # group the job belongs to
#BSUB-o {{ log_file | /dev/null }} # output is sent to logfile, stdout + stderr by default
#B... | infuser = import_package('infuser')
#' A template string used to submit jobs
template = "#BSUB-J {{ job_name }} # name of the job / array jobs
#BSUB-g {{ job_group | /rzmq }} # group the job belongs to
#BSUB-o {{ log_file | /dev/null }} # output is sent to logfile, stdout + stderr by default
#B... | apache-2.0 | R |
05e763150d108cddb29346ff5bc25c7e49a3aad3 | Add note about how find_globals only runs on main | jmousseau/Stain | R/globals.r | R/globals.r | #' Find unassigned global variables.
#'
#' This funciton sources files and loads objects into an environment
#' and then runs \code{codetools::findGlobals} on the environment.
#'
#' NOTE: Globals are determined for the \code{main()} function only!
#'
#' @param source_files R files containing globals to exclude such as
... | #' Find unassigned global variables.
#'
#' This funciton sources files and loads objects into an environment
#' and then runs \code{codetools::findGlobals} on the environment.
#'
#' @param source_files R files containing globals to exclude such as
#' function declarations.
#'
#' @param object_files Rdata files that con... | mit | R |
3fbdd6f24b814205aabf4ce33001758e803c8ae3 | update very outdated README | doudou/modelkit-component,doudou/modelkit-component | README.rd | README.rd | = Orogen: easy component building for Orocos/RTT
http://rock-robotics.org/stable/documentation/orogen
== What is oroGen ?
oroGen is a specification language and code generator for the Orocos Realtime
Toolkit (RTT). The Orocos/Real Time Toolkit is a C++ library allowing to build
component-based systems (http://www.... | = Orogen: easy component building for Orocos/RTT
* http://doudou.github.com/orogen
* http://github.com/doudou/orogen
* git://github.com/doudou/orogen.git
== What is oroGen ?
oroGen is a specification language and code generator for the Orocos Realtime
Toolkit (RTT). The Orocos/Real Time Toolkit is a C++ library allo... | mit | R |
571870767ba9cdf7e5ad1c7ac9bace40d342de4e | Copy all but original files back to submit dir | 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) {
private$cat_main_file_magic(container$dir, main_file)
priv... | #' 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$cat_main_file_magic(container$dir, main_fi... | mit | R |
d5747d3670a765b0a88287967b9c9236b6d08da9 | Update classifier.r | suraj-deshmukh/myCodes,suraj-deshmukh/myCodes,suraj-deshmukh/myCodes | ml-ui/classifier.r | ml-ui/classifier.r | get_results<-function(input){
if(input$cv>1){
folds = createFolds(y,k=input$cv)
acc_matrix = NULL #confusion matrix variable
if(identical(input$class_algo,"c_svm")){
for(i in folds){
model = svm(x[-i,],y[-i],cost=input$cost,kernel=input$kernel,degree=input$degree,... | get_results<-function(){
if(input$cv>1){
if(identical(input$class_algo,"c_svm")){
folds = createFolds(y,k=input$cv)
c_matrix = NULL #confusion matrix variable
for(i in folds){
model = svm(x[-i,])
}
}
}
else{
}
} | mit | R |
2fa358d7c40426203aaed144a99c2c02820332c3 | Fix typo in test for deprecation | 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 |
e63ca1b16833e86817df9e3aea44dd02ae983619 | Add channel argument | jkarl/LandscapeToolbox,jkarl/LandscapeToolbox,jkarl/LandscapeToolbox | DIMA_Queries-Reports/DIMA_count_HAF_species.r | DIMA_Queries-Reports/DIMA_count_HAF_species.r | library(dplyr)
library(readr)
library(RODBC)
DIMA <- "filepath and filename to DIMA"
## This reduces it to forbs only in the process
haf.list <- read_csv("HAF_preferred_species_by_code.csv") %>% subset(GROWTH.HABIT == "FORB")
channel <- odbcConnectAccess(DIMA) ## Assumes 32-bit R and 32-bit Access. Use odbcConnectAc... | library(dplyr)
library(readr)
library(RODBC)
DIMA <- "filepath and filename to DIMA"
## This reduces it to forbs only in the process
haf.list <- read_csv("HAF_preferred_species_by_code.csv") %>% subset(GROWTH.HABIT == "FORB")
channel <- odbcConnectAccess(DIMA) ## Assumes 32-bit R and 32-bit Access. Use odbcConnectAc... | cc0-1.0 | R |
e78d39fb83fbb7ad55ebadfc42ac9afde25ea672 | Add patient_coef function. | pschulam-attic/sclero | R/mixed-effects.r | R/mixed-effects.r | fit_mixed_effects <- function(fixed, random, data) {
require(nlme)
fixed <- as.formula(fixed)
random <- as.formula(random)
lme.fit <- lme(fixed = fixed, random = random, data = data)
return(lme.fit)
}
patient_coef <- function(lme.fit) {
cf <- coef(lme.fit)
new.names <- if (length(cf) == 1) {
c("in... | fit_mixed_effects <- function(fixed, random, data) {
require(nlme)
fixed <- as.formula(fixed)
random <- as.formula(random)
lme.fit <- lme(fixed = fixed, random = random, data = data)
return(lme.fit)
}
| mit | R |
47fb440e2de181a409e0db2faae0c6fb479c7d82 | Add some more plot types - first draft only | tambora-org/tamboRapi | R/drawIndexBoxPlot.r | R/drawIndexBoxPlot.r | source("R/tmbImportPackages.R")
installDrawPackages <- function() {
# define needed packages
packages <- c("extrafont", "ggmap", "ggplot2")
tmbImportPackages(packages)
}
#' Draw summary of all tambora data to a map
#'
#' This function allows you to draw data inquired from tambora.org to a map
#' @param tamboraD... | source("R/tmbImportPackages.R")
installDrawPackages <- function() {
# define needed packages
packages <- c("extrafont", "ggmap", "ggplot2")
tmbImportPackages(packages)
}
#' Draw summary of all tambora data to a map
#'
#' This function allows you to draw data inquired from tambora.org to a map
#' @param tamboraD... | apache-2.0 | R |
9633b48a6b4f8527d51fc60532b0da3d5c74ee75 | Update a document. | snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3 | q3/docs/AddressAutoComplete.rd | q3/docs/AddressAutoComplete.rd | =begin
=AhX̎⊮
wb_GfBbgr[ŃAhX͂tB[hł́AAhX̎⊮s܂B
((<AhX̎⊮|"IMG:images/AddressAutoComplete.png">))
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AhXɓo^ĂȂ[AhXɃ[𑗐MƁÃAhXLA̎⊮ɌƂĎgp܂BftHgł͍ŐV10̃AhXL܂B... | =begin
=AhX̎⊮
wb_GfBbgr[ŃAhX͂tB[hł́AAhX̎⊮s܂B
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AhX̎⊮̑ΏۂɂȂ̂́AAhX̃GgAOAhX荞GgAŋߎgp[AhXłB͂ÃGg̖OAhXɊ܂܂((-ۂɂ́A[AhX̐擪hC̐擪AO̐擪ȂǂɂȂĂꍇ̂-))A⊮p̃hbv_EXg\܂BgpAhXIƓ͒̕ɒu܂B͂̂܂ܑƎIɌ₪i荞܂܂B
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AhXɓo^ĂȂ[AhXɃ[𑗐MƁÃAhXLA̎⊮ɌƂĎgp܂BftHgł͍ŐV10̃AhXL܂B... | mit | R |
15f2ff439dd8b9e379af72e73a896aba110742e7 | 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 |
bf2b7f9b675dfb5e7a17d347dfa38281a130f63c | Update uvoz_tabele5.r | ZavbiA/APPR-2017 | uvoz/uvoz_tabele5.r | uvoz/uvoz_tabele5.r | library(rvest)
library(gsubfn)
library(readr)
library(dplyr)
library(tibble)
library(reshape2)
library(gsubfn)
library(tidyr)
tabela5.tidy <- read_csv("podatki/stroski.csv",
locale = locale(encoding = "UTF-8"))
names(tabela5.tidy) <- c("mesto","leto","drzava","tip","st_dogodkov","st... | library(rvest)
library(gsubfn)
library(readr)
library(dplyr)
library(tibble)
library(reshape2)
library(gsubfn)
library(tidyr)
tabela5.tidy <- read_csv("podatki/stroski.csv",
locale = locale(encoding = "UTF-8"))
names(tabela5.tidy) <- c("mesto","leto","drzava","tip","st_dogodkov","st... | mit | R |
a3b52c36ba0b26bd04f11a81536d040a4db43840 | Load helper libraries by default | klmr/codons,klmr/codons | scripts/knit.r | scripts/knit.r | library = function (...) suppressMessages(base::library(...))
assign('library', library, globalenv())
library(knitr)
library(modules)
options(stringsAsFactors = FALSE,
import.path = c('scripts', file.path(Sys.getenv('HOME'), 'Projects/R')))
#opts_chunk$set(cache = TRUE)
# Pretty-print tables
library(pander... | library = function (...) suppressMessages(base::library(...))
assign('library', library, globalenv())
library(knitr)
library(modules)
options(stringsAsFactors = FALSE,
import.path = file.path(Sys.getenv('HOME'), 'Projects/R'))
#opts_chunk$set(cache = TRUE)
# Pretty-print tables
library(pander)
panderOptio... | apache-2.0 | R |
61e32291420aafd98d04b1275c4e39d93f3ca674 | Update shiny.r | aleksandrov2/APPR-2015-16 | shiny/shiny.r | shiny/shiny.r | library(shiny)
source("lib/libraries.r", encoding = "UTF-8")
source("uvoz/uvoz.r", encoding = "UTF-8")
runApp("shiny")
| library(shiny)
source("lib/uvozi.zemljevid.r", encoding = "UTF-8")
library(ggplot2)
library(dplyr)
pretvori.zemljevid <- function(zemljevid) {
fo <- fortify(zemljevid)
data <- zemljevid@data
data$id <- as.character(0:(nrow(data)-1))
return(inner_join(fo, data, by="id"))
}
# 1. Slovenske občine
obcine <- uvo... | mit | R |
8641813768265bfc7e15bb8df1752f9a4a6feada | correct tanimoto measurement formula | david-beauchesne/Predict_interactions | Script/tanimoto.r | Script/tanimoto.r | tanimoto <- function(resource_x, resource_y) {
# The Tanimoto similarity computes the sum of shared elements in vectors resource_x and resource_y and divides this by the length of the longest vector
# If either length of resource_x or resource_y == 0, similarity == 0
# The order of vectors consumer_x or consumer_... | tanimoto <- function(resource_x, resource_y) {
# The Tanimoto similarity computes the sum of shared elements in vectors resource_x and resource_y and divides this by the length of the longest vector
# If either length of resource_x or resource_y == 0, similarity == 0
# The order of vectors consumer_x or consumer_... | mit | R |
22c1d056392fa385f5e4bb7c9cdc02c6b833e727 | Update model_stage.r | syberia/syberia | R/model_stage.r | R/model_stage.r | #' Model stage for syberia models
#'
#' TODO: Document this more
#'
#' @param modelenv an environment. The persistent modeling environment.
#' @param model_parameters a list. Model-specific parameters, with the first
#' parameter always being the model keyword for the tundra container
#' (e.g., glm, gbm, etc.)
#... | #' Model stage for syberia models
#'
#' TODO: Document this more
#'
#' @param modelenv an environment. The persistent modeling environment.
#' @param model_parameters a list. Model-specific parameters, with the first
#' parameter always being the model keyword for the tundra container
#' (e.g., glm, gbm, etc.)
#... | mit | R |
1a4239bd56c88d49f47bd45a24b2c1b6a9500d79 | Fix bug in plot | ewels/NGI-ChIPseq,ewels/NGI-ChIPseq,ewels/NGI-ChIPseq,ewels/NGI-ChIPseq,ewels/NGI-ChIPseq | bin/plot_peak_intersect.r | bin/plot_peak_intersect.r | #!/usr/bin/env Rscript
################################################
################################################
## LOAD LIBRARIES ##
################################################
################################################
library(optparse)
library(UpSetR)
###############... | #!/usr/bin/env Rscript
################################################
################################################
## LOAD LIBRARIES ##
################################################
################################################
library(optparse)
library(UpSetR)
###############... | mit | R |
91abeb64ef7d8f7da4728addcbbbdfd8b8ce948b | Refactor loading of helpers at R startup | klmr/.files,klmr/.files,klmr/.files | .R/config.r | .R/config.r | options(pager = file.path(Sys.getenv('HOME'), '.R/pager.sh'),
# Imperial College London
repos = c(CRAN = 'http://cran.ma.imperial.ac.uk/'),
menu.graphics = FALSE, # Seriously, WHAT THE FUCK, R!?
import.path = '~/Projects/R',
devtools.name = 'Konrad Rudolph',
devtools.desc... | options(pager = file.path(Sys.getenv('HOME'), '.R/pager.sh'),
# Imperial College London
repos = c(CRAN = 'http://cran.ma.imperial.ac.uk/'),
menu.graphics = FALSE, # Seriously, WHAT THE FUCK, R!?
import.path = '~/Projects/R',
devtools.name = 'Konrad Rudolph',
devtools.desc... | apache-2.0 | R |
da067e4a01a48f3870cc8e6fcac89a6a7765953b | Update TwitterSupport.r | xxu26/how-to-use | How-to/TwitterSupport.r | How-to/TwitterSupport.r | #connect Rstudio to Twitter
library(twitteR)
library(RJSONIO)
library(ROAuth)
library(RCurl)
library(bitops)
options(RCurlOptions = list(cainfo = system.file("CurlSSL", "cacert.pem", package = "RCurl")))
download.file(url="http://curl.haxx.se/ca/cacert.pem", destfile="cacert.pem")
api_key <- "yZ6xhaxgTrMT3vbGyJE3x... | rm(list=ls())
library(twitteR)
library(RJSONIO)
library(ROAuth)
library(RCurl)
library(bitops)
options(RCurlOptions = list(cainfo = system.file("CurlSSL", "cacert.pem", package = "RCurl")))
download.file(url="http://curl.haxx.se/ca/cacert.pem", destfile="cacert.pem")
api_key <- "yZ6xhaxgTrMT3vbGyJE3xwbAe"
api_secre... | isc | R |
be094aad97af1534a259cfa0527f0ccdafb308ed | add case of gov't having all bargaining power to DGH.r | kbuzard/SOP_repeated | DGH.r | DGH.r | #Solve for optimal lobby effort under DGH97-style model with obj fcn W + e
#reserve space for loop output
tau = seq(0.001,.166,0.001) #this will be counter variable in loop
PSx = matrix(NA,length(tau),1)
CSx = matrix(NA,length(tau),1)
TR = matrix(NA,length(tau),1)
PSy = matrix(NA,length(tau),1)
CSy = matrix(NA,length(... | #Solve for optimal lobby effort under DGH97-style model with obj fcn W + e
#reserve space for loop output
tau = seq(0.001,.166,0.001) #this will be counter variable in loop
PSx = matrix(NA,length(tau),1)
CSx = matrix(NA,length(tau),1)
TR = matrix(NA,length(tau),1)
PSy = matrix(NA,length(tau),1)
CSy = matrix(NA,length(... | mit | R |
3185c72cd590ff67859812d9d3a97b50f0f54006 | update main.r | wikimedia-research/Blockr | main.r | main.r | #Blockr - a project to accurately triage data on blocked Wikipedia users, identify
#the underlying rationales and test various hypotheses as to any outcome
#
# @Year = 2013
# @Copyright: Oliver Keyes
# @License = MIT (http://opensource.org/licenses/MIT)
#Load in query-dependent config variables
source(file = file.pat... | #Blockr - a project to accurately triage data on blocked Wikipedia users, identify
#the underlying rationales and test various hypotheses as to any outcome
#
# @Year = 2013
# @Copyright: Oliver Keyes
# @License = MIT (http://opensource.org/licenses/MIT)
#Load in query-dependent config variables
source(file = file.pat... | mit | R |
c569dd27d1fddc1229e2746eb2b181020942b44b | Rework reshape | vikjam/bcstatsR | R/bcstats.r | R/bcstats.r | #' Join two data frames together
#'
#' @param surveydata The survey data
#' @param bcdata The back check data
#' @param id the unique ID
#' @param t1vars The list of "type 1" variables
#' @param t2vars The list of "type 2" variables
#' @param t3vars The list of "type 3" variables
#' @return A data.frame with the erro... | #' Join two data frames together
#'
#' @param surveydata The survey data
#' @param bcdata The back check data
#' @param id the unique ID
#' @param t1vars The list of "type 1" variables
#' @param t2vars The list of "type 2" variables
#' @param t3vars The list of "type 3" variables
#' @return A data.frame with the erro... | mit | R |
fdd1b3117427740167cbaf2b29fca966c6185d74 | Update splitSupermatrices.r | NathanWhelan/Split_supermatrix_into_partitions,NathanWhelan/Split_supermatrix_into_partitions | splitSupermatrices.r | splitSupermatrices.r | #########################################################################################################################
#This script was written by Nathan Whelan.
# THIS SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY... | #########################################################################################################################
#This script was written by Nathan Whelan.
# THIS SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY... | mit | R |
b74222131cf7a164588469a1c0da6e9b1e05684f | add more debugging | snowch/biginsight-examples,snowch/biginsight-examples | examples/BigR/connect.r | examples/BigR/connect.r | ################################################################################
# environment variables
################################################################################
libdir <- Sys.getenv("libdir")
hostname <- Sys.getenv("hostname")
username <- Sys.getenv("username")
password <- Sys.getenv("passwor... | ################################################################################
# environment variables
################################################################################
libdir <- Sys.getenv("libdir")
hostname <- Sys.getenv("hostname")
username <- Sys.getenv("username")
password <- Sys.getenv("passwor... | apache-2.0 | R |
bea08f3cb846fbfdaf84b4cbed376cae02554413 | 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 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]])),... | # Author: Matej Svoboda
# Data Frame exploration.
# Extract data from Documents and summaries into rewsum1 to table in DB
# SUBSET CREATION
# Create Subset and merge all columns into one column called "Documents". Column "Summaries" = summary of document
dfData = with(df, paste0(Document1, Document2, Document3, Docu... | mit | R |
c8db3319b3eaec20a674751b59a7a3906c5d9b1b | fix ouput assigment error in small_rna_map.r | drosofff/tools-artbio,ARTbio/tools-artbio,ARTbio/tools-artbio,drosofff/tools-artbio,chamaelj/tools-artbio,chamaelj/tools-artbio,ARTbio/tools-artbio,drosofff/tools-artbio,chamaelj/tools-artbio,drosofff/tools-artbio,ARTbio/tools-artbio | tools/small_rna_map/small_rna_map.r | tools/small_rna_map/small_rna_map.r | library(optparse)
library(ggplot2)
library(gridExtra)
option_list <- list(
make_option(c("-r", "--output_tab"), type="character", help="path to tabular file"),
make_option("--output_pdf", type = "character", help="path to the pdf file with plot")
)
parser <- OptionParser(usage = "%prog [options] file", op... | library(optparse)
library(ggplot2)
library(gridExtra)
option_list <- list(
make_option(c("-r", "--output_tab"), type="character", help="path to tabular file"),
make_option("--output_pdf", type = "character", help="path to the pdf file with plot")
)
parser <- OptionParser(usage = "%prog [options] file", op... | mit | R |
d1c140dd675123696c1487f02444402690f7d90d | fix data aggregation bugs | wikimedia-research/Blockr | functions.r | functions.r | # functions.r centralises miscellaneous functions used throughout the Blockr project
#
# Copyright (c) 2013 Oliver Keyes
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restrict... | # functions.r centralises miscellaneous functions used throughout the Blockr project
#
# Copyright (c) 2013 Oliver Keyes
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restrict... | mit | R |
5648f4a3f290fd65433ba3c3446cab11e19bb68a | fix typos | johnrfleck/water-tools | flow_threshold.r | flow_threshold.r | # For drought analysis, determines the number of days in each year
# of the historic record in which flow at a USGS river gauge
# fell below an arbitrary threshold.
# Uses USGS's excellent dataRetrieval package
# tutorial here: https://owi.usgs.gov/R/dataRetrieval.html#1
# Albuquerque gauge to use as example: 08330000
... | # For drought analysis, determines the number of days in each year
# of the historic record in which flow at a USGS river gauge
# fell below an arbitrary threshold.
# Uses USGS's excelelent dataRetrieval package
# tutorial here: https://owi.usgs.gov/R/dataRetrieval.html#1
# Albuquerque gauge to use as example: 08330000... | mit | R |
a37766e380c6922c991315e3ec1f1da0c971689e | set filename | khufkens/phenor | tests/testthat/test_data_downloads.r | tests/testthat/test_data_downloads.r | # Phenor unit tests
# test all data downloads
test_that("test data downloads",{
# download npn data
npn_data = try(download_npn(species = 3,
path = paste0(tempdir(),"/npn_test.rds"),
internal = FALSE))
# download npn data internal
npn_data_internal ... | # Phenor unit tests
# test all data downloads
test_that("test data downloads",{
# download npn data
npn_data = try(download_npn(species = 3,
path = tempdir(),
internal = FALSE))
# download npn data internal
npn_data_internal = try(download_npn(speci... | agpl-3.0 | R |
3858af14754207a262d450f4156bee6820af23bd | Add support for email settings | jmousseau/Stain | R/slurm-settings.r | R/slurm-settings.r | #' SlurmSettings R6 object.
#'
#' An interface to SBATCH settings.
#'
#' @export
SlurmSettings <- R6::R6Class("SlurmSettings",
public = list(
nodes = NA,
cpus_per_task = NA,
time = NA,
memory = NA,
mail_to = NA,
mail_type = NA,
initialize = function(nodes = 1,... | #' SlurmSettings R6 object.
#'
#' An interface to SBATCH settings.
#'
#' @export
SlurmSettings <- R6::R6Class("SlurmSettings",
public = list(
nodes = NA,
cpus_per_task = NA,
time = NA,
memory = NA,
initialize = function(nodes = 1, cpus_per_task = 12,
... | mit | R |
e47dbeafbf0493cdc203bd81994a0be5026423b6 | revise comment | koji-to/effort_calculator,koji-to/effort_calculator,koji-to/effort_calculator | calculate_metrics.r | calculate_metrics.r | #extract commit log from each relase cycle
##### setting section #####
release_cycle<-42#days(= 6 weeks = 1.5month)
threshold<-2#commits/release_cycle
newest_relase_date<-as.Date("2014-06-20")#ver37
num_release<-8#: a number of past release to trace
##### processing section #####
# import merged git log file
git_log.... | #extract commit log from each relase cycle
##### setting section #####
release_cycle<-42#days(= 6 weeks = 1.5month)
threshold<-2#commits/release_cycle
newest_relase_date<-as.Date("2014-06-20")#ver37
num_release<-8#: a number of past release to trace
##### processing section #####
# import merged git log file
git_log.... | mit | R |
2000bd589775f286221a08a02026a5c0cd2a87e1 | Bump version to 3.0.99 | zsx/r3,zsx/r3,zsx/r3,zsx/r3 | src/boot/version.r | src/boot/version.r | 3.0.99.3.1
| 3.0.91.3.1
| apache-2.0 | R |
abb60f880284056e9cb4d4945fa469e53e18ceb0 | remove verboses and fix predict value | syberia/tundra,robertzk/tundra | inst/tests/test-tundra_ensemble.r | inst/tests/test-tundra_ensemble.r | context('tundra ensemble')
# A very simple model mock for testing tundra containers
assign('tundra_simple', function(mp = list(), defaults = list()) {
tundra_container$new('simple',
function(dataframe) output$val <<- dataframe[1, 1] + input$twiddle,
function(dataframe)
if (input$master) output$val + ap... | context('tundra ensemble')
# A very simple model mock for testing tundra containers
assign('tundra_simple', function(mp = list(), defaults = list()) {
tundra_container$new('simple',
function(dataframe) output$val <<- dataframe[1, 1] + input$twiddle,
function(dataframe)
if (input$master) apply(dataframe... | mit | R |
6c154c90e6db7a1b6e9289f7f5b4a4cecfd03e55 | read object | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/gene_localization_map.r | lib/scRNA/gene_localization_map.r |
library(Seurat)
library(ggplot2)
library(ggpubr)
obj<-read_object(parFile1)
groups_tbl<-read.table(parSampleFile2, sep="\t", stringsAsFactors = F)
groups=split(groups_tbl$V2, groups_tbl$V1)
obj$group = unlist(groups[obj$orig.ident])
ngroup=length(unique(groups_tbl$V2))
#using RNA assay for visualization
DefaultAss... | source("scRNA_func.r")
library(Seurat)
library(ggplot2)
library(ggpubr)
finalList<-readRDS(parFile1)
obj<-finalList$obj
groups_tbl<-read.table(parSampleFile2, sep="\t", stringsAsFactors = F)
groups=split(groups_tbl$V2, groups_tbl$V1)
obj$group = unlist(groups[obj$orig.ident])
ngroup=length(unique(groups_tbl$V2))
... | apache-2.0 | R |
ea1408cea3d3c4290fbfab6a042e78fe33a364b1 | Modify args example | tisp-lang/tisp,tisp-lang/tisp,raviqqe/tisp,raviqqe/tisp,raviqqe/tisp | examples/args.r | examples/args.r | (let kwargs {'y5 123 'y6 456})
((\ (x1 x2 (x3 123) (x4 456) args.. y1 (y2 123) y3 (y4 456) kwargs...) x)
1 2 3 4 list.. . y1 123 y3 456 kwargs...)
; We don't have to support neither `*[123 456]` nor `**{'y5 123 'y6 456}`
; because they can just be expanded into arguments directly.
; (e.g. `(func 123 456 * y5 123 y6 ... | (let kwargs {'y5 123 'y6 456})
((\ (x1 x2 (x3 123) (x4 456) *args y1 (y2 123) y3 (y4 456) **kwargs) x)
1 2 3 4 *list * y1 123 y3 456 **kwargs)
; We don't have to support neither `*[123 456]` nor `**{'y5 123 'y6 456}`
; because they can just be expanded into arguments directly.
; (e.g. `(func 123 456 * y5 123 y6 456)... | mit | R |
5d35f9524702a05ce5ae9583c9acae37b5934397 | clean up comments | mschubert/narray,mschubert/narray | R/construct.r | R/construct.r | #' A wrapper around reshape2::acast using a more intuitive formula syntax
#'
#' The construct() function can be called either with the data.frame as the
#' first argument or the formula and then specify `data=<data.frame>`
#'
#' @param data A data frame
#' @param formula A formula: value ~ axis1 [+ axi... | #' A wrapper around reshape2::acast using a more intuitive formula syntax
#'
#' The construct() function can be called either with the data.frame as the
#' first argument or the formula and then specify `data=<data.frame>`
#'
#' @param data A data frame
#' @param formula A formula: value ~ axis1 [+ axi... | apache-2.0 | R |
0276ead2f2fc3ef69f5c378880bfabbde89d3365 | use base::rep, not narray::rep (#27) | mschubert/narray,mschubert/narray | R/construct.r | R/construct.r | #' Transform a data.frame with axes and value into an array
#'
#' The construct() function can be called either with the data.frame as the
#' first argument or the formula and then specify `data=<data.frame>`
#'
#' @param data A data frame
#' @param formula A formula: value ~ axis1 [+ axis2 + axis n ..... | #' Transform a data.frame with axes and value into an array
#'
#' The construct() function can be called either with the data.frame as the
#' first argument or the formula and then specify `data=<data.frame>`
#'
#' @param data A data frame
#' @param formula A formula: value ~ axis1 [+ axis2 + axis n ..... | apache-2.0 | R |
16b1784b255f08e23ccd918c4970b80e9486e063 | 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(knitr)
library(ggplot2)
library(dplyr)
require(gsubfn)
require(rvest)
require(xml2)
require(ggplot2)
library(sp)
library(maptools)
library(dendextend)
# Uvozimo funkcije za pobiranje in uvoz zemljevida.
library(shiny)
if ("server.R" %in% dir()) {
setwd("..")
}
| mit | R |
229d0527c48722a0f6423570ecb75cd73e5174be | Add plot line | 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",
col = "blue",
main = "Google Analytics",
ylim = c(0, 200))
... | unlicense | R |
53780650785f05c64d8c1bcd324960d651fd7493 | Change input to folder where dtm is | HIIT/digivaalit-2015,HIIT/digivaalit-2015,HIIT/digivaalit-2015 | topics/create_topics.r | topics/create_topics.r | source('topics.r')
args <- commandArgs(trailingOnly = TRUE)
print( args[1] )
load( paste( args[1] , 'dtm.rdata', sep='' ) )
k <- as.integer( args[2] )
model <- create_model( dtm , k )
path <- paste( args[1] , '/topic-', args[2], '.rdata' , sep = '' )
save( model , file = path )
| source('topics.r')
args <- commandArgs(trailingOnly = TRUE)
load( args[1] )
k <- as.integer( args[2] )
model <- create_model( dtm , k )
path <- paste( args[1] , '-', args[2], '.rdata' , sep = '' )
save( model , file = path )
| mit | R |
2d3e369c9dffdbc22fc9fa7322fa0e4c0900ca97 | Update polyester.r | sains1/UTRonsProject,sains1/UTRonsProject | scripts/polyester.r | scripts/polyester.r | ###################################################################################################################
# R script to simulate rna-seq reads from hg38 transcriptome reference using polyester simulator #
########################################################################################... | library(Biostrings)
library(polyester)
#Set num of repeats
num_repeats = 4
the_seed = 1
# Path to cdna file
fastapath <- '../../refiles/transcripts.fa'
# Read DNA file into var transcripts
transcripts = readDNAStringSet(fastapath)
# splitting the fasta into chunks based on the number of trnascripts
chunks = 50
tra... | mit | R |
f31739924ff7c485c5a82be66184394335b1e21d | update calcor.r | isezen/sahra,isezen/sahra | code/calcor.r | code/calcor.r | # Saharan Dust Transport Research
# 2016-05-04 Ismail SEZEN
# sezenismail@gmail.com
source("code/correlation.r")
calcor <- function(files = stop("'file' must be specified")) {
pm <- read_pm10()
dir_out <- "data/cor"
dir.create(dir_out, showWarnings = F)
nof <- length(files)
i <- 1
for (f in files) {
f... | # Saharan Dust Transport Research
# 2016-05-04 Ismail SEZEN
# sezenismail@gmail.com
source("code/correlation.r")
calcor <- function(files = stop("'file' must be specified")) {
pm <- read_pm10()
dir_out <- "data/cor"
dir.create(dir_out, showWarnings = F)
nof <- length(files)
i <- 1
for (f in files) {
w... | mit | R |
b6f06e88db25aab98c3466b68130b0ef8743c632 | Remove some unecessary arguments | metagraf/rVega | R/geopath.r | R/geopath.r | #' Vega geopath
#'
#' Create a geopath visualization
#'
#' @export
geopath <- function(
fill.color = "pink",
hover.color = "lightblue",
border.color = "black",
url = "data/us-states.json",
projection = "albersUsa",
scale = 500,
translate = c(a$opt$width / 2, a$opt$height / 2), # as defa... | #' Vega geopath
#'
#' Create a geopath visualization
#'
#' @export
geopath <- function(
data,
labels = names(data),
width = 600,
height = 400,
font = "Helvetica Neue",
font.size = 14,
fill.color = "pink",
hover.color = "lightblue",
border.color = "black",
padding = c(0, 0... | agpl-3.0 | R |
2930def36522c9001082f2ff06c25f65797fb015 | Update uvoz_tabela1.r | ZavbiA/APPR-2017 | uvoz/uvoz_tabela1.r | uvoz/uvoz_tabela1.r | # 2. faza: Uvoz podatkov
library(rvest)
library(gsubfn)
library(readr)
library(dplyr)
# Funkcija, ki uvozi število medalj po državah iz Wikipedije
link <- "https://en.wikipedia.org/wiki/All-time_Olympic_Games_medal_table"
stran <- html_session(link) %>% read_html()
tabela <- stran %>% html_nodes(xpath="//table[@class... | # 2. faza: Uvoz podatkov
library(rvest)
library(gsubfn)
library(readr)
library(dplyr)
# Funkcija, ki uvozi število medalj po državah iz Wikipedije
link <- "https://en.wikipedia.org/wiki/All-time_Olympic_Games_medal_table"
stran <- html_session(link) %>% read_html()
tabela <- stran %>% html_nodes(xpath="//table[@class... | mit | R |
588db6c246764a43844ae65dbfdbbd8b7a378bb6 | Add even more bands! | GreatEmerald/geoscripting,GreatEmerald/geoscripting,GreatEmerald/geoscripting,GreatEmerald/geoscripting | Lesson8/Main.r | Lesson8/Main.r | # Team Rython, Dainius Masiliunas and Tim Weerman
# Date: 11 January, 2016
# Apache License 2.0
# Needed packages
# Source
# Download/load information
download.file("https://github.com/GeoScripting-WUR/AdvancedRasterAnalysis/raw/gh-pages/data/GewataB1.rda", "data/GewataB1.rda", "wget")
download.file("https://githu... | # Team Rython, Dainius Masiliunas and Tim Weerman
# Date: 11 January, 2016
# Apache License 2.0
# Needed packages
# Source
# Download/load information
download.file("https://github.com/GeoScripting-WUR/AdvancedRasterAnalysis/raw/gh-pages/data/GewataB1.rda", "data/GewataB1.rda", "wget")
download.file("https://githu... | apache-2.0 | R |
202f7748beb7b0450d19e40155acb69cfcceeeb3 | add pie exposure and stop feed indoors > feed man | AndySouth/coverage | inst/shiny/coverage1/server.r | inst/shiny/coverage1/server.r | #coverage/inst/shiny/coverage1/server.r
#andy south 12/5/16
library(shiny)
#install_github('AndySouth/coverage')
library(coverage)
library(png)
shinyServer(function(input, output, session) {
################################
output$plot_feed <- renderPlot({
#add dependency on the button
#if ( input$aBut... | #coverage/inst/shiny/coverage1/server.r
#andy south 12/5/16
library(shiny)
#install_github('AndySouth/coverage')
library(coverage)
library(png)
shinyServer(function(input, output, session) {
################################
output$plot_feed <- renderPlot({
#add dependency on the button
#if ( input$aBut... | mit | R |
91c0705d323cb1345f94cede302fb84e11e1a82f | fix a uninitialized word in run-all.r. | NikolayShubenkovProgSchool/red,red-eco/red,vehar/red,red-eco/red,rheber/red,NikolayShubenkovProgSchool/red,rheber/red,vehar/red | tests/run-all.r | tests/run-all.r | REBOL [
Title: "Builds and Runs the Red Tests"
File: %run-all.r
Author: "Peter W A Wood"
Version: 0.5.0
License: "BSD-3 - https://github.com/dockimbel/Red/blob/master/BSD-3-License.txt"
]
;; should we run non-interactively?
each-mode: no
if args: any [system/script/args system/options/args][
batch-mode: fi... | REBOL [
Title: "Builds and Runs the Red Tests"
File: %run-all.r
Author: "Peter W A Wood"
Version: 0.5.0
License: "BSD-3 - https://github.com/dockimbel/Red/blob/master/BSD-3-License.txt"
]
;; should we run non-interactively?
if args: any [system/script/args system/options/args][
batch-mode: find args "--batc... | bsd-3-clause | R |
b8edf972bd52c0f29c4d63c966801c486503f3d5 | 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$source(system.file("js/biometeo.js", package = pkgname))
}
| #' .onLoad
#'
#' @importFrom V8 new_context
ct <- NULL
.onLoad <- function(libname, pkgname){
ct <<- V8::new_context()
ct$source(system.file("js/biometeo.js", package = pkgname))
}
| mit | R |
8e2a3ef5c3d9c1815378783eac153b2e510b1f40 | Modify plotting script to handle drop stats. | draios/falco,draios/falco,draios/falco,draios/falco,draios/falco,draios/falco,draios/falco,draios/falco | test/plot-live.r | test/plot-live.r | require(jsonlite)
library(ggplot2)
library(GetoptLong)
initial.options <- commandArgs(trailingOnly = FALSE)
file.arg.name <- "--file="
script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
script.basename <- dirname(script.name)
if (substr(script.basename, 1, 1) != '/') {
sc... | require(jsonlite)
library(ggplot2)
library(GetoptLong)
initial.options <- commandArgs(trailingOnly = FALSE)
file.arg.name <- "--file="
script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
script.basename <- dirname(script.name)
if (substr(script.basename, 1, 1) != '/') {
sc... | apache-2.0 | R |
16860a944166415c86905e7b50f36fb422e50419 | Update test.r | snowch/biginsight-examples,snowch/biginsight-examples | examples/BigR/test.r | examples/BigR/test.r | .libPaths('lib')
# create directory to hold libraries
dir.create('./lib')
# install libraries
install.packages('rJava', repos='http://cran.us.r-project.org', lib='./lib', quiet=TRUE)
install.packages('base64enc', repos='http://cran.us.r-project.org', lib='./lib', quiet=TRUE)
install.packages('data.table', repos... |
# check if lib dir exists
if("lib" %in% dir() == FALSE) {
# 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'... | apache-2.0 | R |
d5d0a5e9c8b76ac36b2722a6140d0cdf0b005b78 | Add test cases for detach on unload | klmr/modules,klmr/modules | inst/tests/test-z-attach.r | inst/tests/test-z-attach.r | context('Test attach')
# File name starts with `z` so that the test is executed last.
test_that('attach works locally', {
c = import('c')
# c attaches `a`. So check that `a` is *not* attached here.
expect_that(length(grep('^module:a$', search())), equals(0))
})
test_that('module can be attached to global... | context('Test attach')
# File name starts with `z` so that the test is executed last.
test_that('attach works locally', {
c = import('c')
# c attaches `a`. So check that `a` is *not* attached here.
expect_that(length(grep('^module:a$', search())), equals(0))
})
test_that('module can be attached to global... | apache-2.0 | R |
d58677404c20a0d3a52513713598c398bef4cbbd | fix object name | sestaton/sesbio,sestaton/sesbio,sestaton/sesbio,sestaton/sesbio | transposon_annotation/r_scripts/hann_lines_analysis.r | transposon_annotation/r_scripts/hann_lines_analysis.r | library(plyr)
library(ggplot2)
setwd("Desktop/Hannuus_lines_repeat_analysis")
lines <- read.table("all_lines_family_stats_6-30.tsv",header=T,sep="\t",comment.char="")
lines.filtered <- lines[lines$GenomeFrac >= 0.01,]
ggplot(lines.filtered, aes(x=reorder(Identifier, GenomeFrac), y=GenomeFrac)) + geom_bar(aes(fill=Fa... | library(plyr)
library(ggplot2)
setwd("Desktop/Hannuus_lines_repeat_analysis")
lines <- read.table("all_lines_family_stats_6-30.tsv",header=T,sep="\t",comment.char="")
lines.filtered <- lines[lines$GenomeFrac >= 0.01,]
ggplot(alllines.filt, aes(x=reorder(Identifier, GenomeFrac), y=GenomeFrac)) + geom_bar(aes(fill=Family... | mit | R |
6efc0ad8150f3f5ae83c726ababb3e8183c5bc13 | Make GSA less verbose | klmr/codons,klmr/codons | scripts/gsa.r | scripts/gsa.r | deseq = modules::import_package('DESeq2')
piano = modules::import_package('piano')
modules::import_package('dplyr', attach = TRUE)
#' @export
prepare_gene_set = function (gene_set)
piano$loadGSC(gene_set, 'data.frame')
#' @export
gsa_de = function (data, col_data, contrast, go_genes) {
stopifnot(inherits(go_g... | deseq = modules::import_package('DESeq2')
piano = modules::import_package('piano')
modules::import_package('dplyr', attach = TRUE)
#' @export
prepare_gene_set = function (gene_set)
piano$loadGSC(gene_set, 'data.frame')
#' @export
gsa_de = function (data, col_data, contrast, go_genes) {
stopifnot(inherits(go_g... | apache-2.0 | R |
e17d6ddf169ee2f99d30d63e8d70aaddf074e99f | add package | ryanlovett/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub | deployments/datahub/images/default/r-packages/stat-20.r | deployments/datahub/images/default/r-packages/stat-20.r | #!/usr/bin/env Rscript
print("Installing packages for stat-20")
source("/tmp/class-libs.R")
class_name = "stat-20"
class_libs = c(
"tidycensus", "1.0",
"openintro", "2.2.0",
"infer", "1.0.0",
"patchwork", "1.1.1",
"tigris", "1.0",
"googlesheets4", "0.2.0",
"xaringanthemer", "0.4.0",
"... | #!/usr/bin/env Rscript
print("Installing packages for stat-20")
source("/tmp/class-libs.R")
class_name = "stat-20"
class_libs = c(
"tidycensus", "1.0",
"openintro", "2.2.0",
"infer", "1.0.0",
"patchwork", "1.1.1",
"tigris", "1.0",
"googlesheets4", "0.2.0",
"xaringanthemer", "0.4.0",
"... | bsd-3-clause | R |
9cbf47373edfb84520efc335983662b69d4c8fe4 | Fix typo | jmousseau/Stain | R/slurm-container.r | R/slurm-container.r | #' SlurmContainer R6 object.
#'
#' A slurm container is simply a directory with a specific
#' structure, particulary it has a submit.slurm script at the
#' top level.
SlurmContainer <- R6::R6Class("SlurmContainer",
public = list(
dir = NULL,
initialize = function(dir = ".") {
name <- pas... | #' SlurmContainer R6 object.
#'
#' A slurm container is simply a directory with a specific
#' structure, particulary it has a submit.slurm script at the
#' top level.
SlurmContainer <- R6::R6Class("SlurmContainer",
public = list(
dir = NULL,
initialize = function(dir = ".") {
name <- pas... | mit | R |
c81ff404384fa3a21dab221748c9c559b8fead11 | Update clomax_7730.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/clomax_7730.r | R/clomax_7730.r | #' clomax_7730
#'
#' Calculate maximal clothing insulation value needed for thermal comfort in moderate thermal environments based on PMV ISO 7730.
#'
#' @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.
... | #' clomax_7730
#'
#' Calculate maximal clothing insulation value needed for thermal comfort in moderate thermal environments based on PMV ISO 7730.
#'
#' @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.
... | mit | R |
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