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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|---|---|---|---|---|---|---|---|---|
008d85de05817cca1521c3f531f01eac721d3fe9 | fix merge conflicts | robertzk/s3mpi | R/s3store.r | R/s3store.r | #' Store an R object in S3 by key
#'
#' Any type of object that can be serialized as an RDS file
#' is capable of being retrieved using this interface.
#'
#' @export
#' @param obj ANY. An R object to save to S3.
#' @param name character. The S3 key to save to.
#' @param .path character. The S3 prefix, e.g., "s3://yourb... | #' Store an R object in S3 by key
#'
#' Any type of object that can be serialized as an RDS file
#' is capable of being retrieved using this interface.
#'
#' @export
#' @param obj ANY. An R object to save to S3.
#' @param name character. The S3 key to save to.
#' @param .path character. The S3 prefix, e.g., "s3://yourb... | mit | R |
e2a5052e85e07a2122269630b2f6e616d0c7bdc9 | 更新：第七章fig7-11 | shuaimeng/r | thesis/chap7/fig7-11.r | thesis/chap7/fig7-11.r | dyn.load('/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/server/libjvm.dylib')
library(rJava)
setwd("/Users/mengmengjiang/all datas/print")
library(xlsx)
# reading ux and sy
k1<-read.xlsx("doty.xlsx",sheetName="600",header=TRUE)
k2<-read.xlsx("doty.xlsx",sheetName="1khz",header=TRUE)
k3<-r... | mit | R | |
c699267ee17e76f60e71c35b20a22ee06f5b3fa8 | Update runShinyApp.r | xiaodaigh/shinydistro | windows/runShinyApp.r | windows/runShinyApp.r | .libPaths("./R-Portable/App/R-Portable/library")
# you need the full path to portable chrome
browser.path <- file.path(getwd(),"GoogleChromePortable/GoogleChromePortable.exe")
options(browser = "./GoogleChromePortable/GoogleChromePortable.exe")
shiny::runApp("./yourApp/Shiny/",port=8888,launch.browser=TRUE)
| options(browser = "./GoogleChromePortable/GoogleChromePortable.exe")
.libPaths("./R-Portable/App/R-Portable/library")
shiny::runApp("./yourApp/Shiny/",port=8888,launch.browser=TRUE)
| mit | R |
0cbb6269af8d44c96c4fd8157a582100483db9cd | Add test in global environment | klmr/modules,klmr/modules | inst/tests/test-path.r | inst/tests/test-path.r | context('Find module path relative files')
test_that('module_file works in global namespace', {
expect_that(module_file(), equals(getwd()))
expect_true(nchar(module_file('run-all.r')) > 0)
throws_error(module_file('XXX-does-not-exist', mustWork = TRUE),
'no file found')
})
test_that('modu... | context('Find module path relative files')
test_that('module_file works in global namespace', {
expect_that(module_file(), equals(getwd()))
expect_true(nchar(module_file('run-all.r')) > 0)
throws_error(module_file('XXX-does-not-exist', mustWork = TRUE),
'no file found')
})
test_that('modu... | apache-2.0 | R |
4fc64e95a9c0d9415b11315ccb03c2d45ca6a727 | Change git repository list's URL | koji-to/effort_calculator,koji-to/effort_calculator,koji-to/effort_calculator | generate_git_clone_sh.r | generate_git_clone_sh.r | ####### generate .sh script for "git clone"
##### Set git directory structure file path
gitweb<-"http://git.chromium.org/gitweb/?a=project_index"
#####
shell.df<-read.csv(gitweb,header=F)
### save git repository tree in local
write.table(shell.df,"chromium_git_repo_tree.txt",col.names=F,row.names=F,quote=F,append=F)
... | ####### generate .sh script for "git clone"
##### Set git directory structure file path
gitweb<-"https://git.chromium.org/gitweb/?a=project_index"
#####
shell.df<-read.csv(gitweb,header=F)
### save git repository tree in local
write.table(shell.df,"chromium_git_repo_tree.txt",col.names=F,row.names=F,quote=F,append=F)
... | mit | R |
5fbcc54a369737b9ebbd60f9ec5fc12e840bcdf3 | add pre and post season model runs | PSC-CoTC/PSC-FRAM-Admin,PSC-CoTC/PSC-FRAM-Admin | config/create_import_config.r | config/create_import_config.r |
#fram.db.name <- "./fram db/CohoFRAMVB2015Pre&PostNew.mdb"
#fram.run.name <- "bkCoho2015Post"
########### 2015 Post Season Catch #################
#fram.db.name <- "./fram db/Final pre and post databases/FramVS2-PSC-Coho-PostSeason.mdb"
#fram.run.name <- "bc-bkCoho2015 Final"
#run.year <- 2015
########### 2014 P... |
fram.db.name <- "./fram db/CohoFRAMVB2015Pre&PostNew.mdb"
fram.run.name <- "bkCoho2015Post"
| mit | R |
51f312a1667e76ae6387520e8f682b561ac001dc | Fix test check error | klmr/modules,klmr/modules | tests/testthat/test-basic.r | tests/testthat/test-basic.r | context('Basic import test')
test_that('module can be imported', {
a = import('a')
expect_true(is_module_loaded(module_path(a)))
expect_true('double' %in% ls(a))
})
test_that('import works in global namespace', {
local({
# Necessary since private names are not exported to global environment
... | context('Basic import test')
test_that('module can be imported', {
a = import('a')
expect_true(is_module_loaded(module_path(a)))
expect_true('double' %in% ls(a))
})
test_that('import works in global namespace', {
local({
a = import('a')
on.exit(unload(a)) # To get rid of attached opera... | apache-2.0 | R |
9aceeb52320921f95ef7d41114ac935ac6971c0f | Fix test that unloads the knitr package | klmr/modules,klmr/modules | tests/testthat/test-knitr.r | tests/testthat/test-knitr.r | context('Test that modules works with knitr')
check_knitr = function () skip_if_not_installed('knitr')
safe_unload_namespace = function (ns) {
users = getNamespaceUsers(ns)
for (user in users) safe_unload_namespace(user)
unloadNamespace(ns)
}
test_that('modules are found when knitr is not loaded', {
... | context('Test that modules works with knitr')
check_knitr = function () skip_if_not_installed('knitr')
test_that('modules are found when knitr is not loaded', {
check_knitr()
# Ensure knitr isn’t loaded
unloadNamespace('knitr')
expect_paths_equal(script_path(), getwd())
})
test_that('modules are foun... | apache-2.0 | R |
2ab36212046595a1268e2853d119b566136d90c0 | fix factor df subset + add test | mschubert/narray,mschubert/narray | subset.r | subset.r | #' Subsets an array using a list with indices or names
#'
#' @param X The array to subset
#' @param index A list of vectors to use for subsetting, or vector if along is given
#' @param along Along which dimension to subset if index is a vector; default is last dimension
#' @return The subset of the array
s... | #' Subsets an array using a list with indices or names
#'
#' @param X The array to subset
#' @param index A list of vectors to use for subsetting, or vector if along is given
#' @param along Along which dimension to subset if index is a vector; default is last dimension
#' @return The subset of the array
s... | apache-2.0 | R |
9af45ce5e0b45a94ce56c6dbdc07f51b07182d0b | Update 2014_PR_config.r | PSC-CoTC/PSC-FRAM-Admin,PSC-CoTC/PSC-FRAM-Admin | config/2014_PR_config.r | config/2014_PR_config.r | #note: here "pre.season" means "original BK post-season" for the Periodic Report comparison tables
run.year <- 2014
post.season.fram.db <- "./fram db/PeriodicReportdb/FramVS2-PSC-Coho-Backwards-redo 2010-2016 January 2019 products.mdb"
post.season.run.name <- "bc-bkCoho2014 step 3"
post.season.tamm <- "./fram db/Perio... |
run.year <- 2014
post.season.fram.db <- "./fram db/PeriodicReportdb/FramVS2-PSC-Coho-Backwards-redo 2010-2016 January 2019 products.mdb"
post.season.run.name <- "bc-bkCoho2014 step 3"
post.season.tamm <- "./fram db/PeriodicReportdb/updated2010-2016TAMMfiles/BK 2014 January 2019 redo step 3.xlsm"
post.season.tamm.fish... | mit | R |
40a6df1eded6bf3d2850bd789a1e5f3945584a96 | remove debugging statements | 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 read using this interface.
#'
#' If you wish to read non-vanilla R objects, such as those
#' containing external pointers to C structures, see
#' \code{\link{s3normalize}}.
#'
#' @seealso \code{\link{s... | #' Read an R object in S3 by key
#'
#' Any type of object that can be serialized as an RDS file
#' is capable of being read using this interface.
#'
#' If you wish to read non-vanilla R objects, such as those
#' containing external pointers to C structures, see
#' \code{\link{s3normalize}}.
#'
#' @seealso \code{\link{s... | mit | R |
b7a8dd7b4f272af9d34445dbeea21dbe60663334 | fix direction edge.data.frame problem | shiva1387/keggParser,etheleon/keggParser,etheleon/keggParser,shiva1387/keggParser | kegg.0500.igraphMetabolism.r | kegg.0500.igraphMetabolism.r | #!/usr/bin/env Rscript
library(dplyr, warn.conflicts=FALSE)
library(magrittr)
library(igraph)
args = commandArgs(T)
args = "~/newMeta4j2/misc/"
relationships <- list.files(args[1]) %>%
grep("rels$", ., value=T) %>%
paste(args[1], ., sep="/") ... | #!/usr/bin/env Rscript
library(dplyr, warn.conflicts=FALSE)
library(magrittr)
library(igraph)
args = commandArgs(T)
args = "~/newMeta4j2/misc/"
relationships <- list.files(args[1]) %>%
grep("rels$", ., value=T) %>%
paste(args[1], ., sep="/") ... | mit | R |
e4714d0894e7e981a06795be59d63a70ae19ecbd | Make themes into functions | 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_basic = function ()... | #' 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_basic = theme_minim... | apache-2.0 | R |
5170b82ec68caaaf9df7b42aadf174fd6d4a2f38 | add tbl_df class to lambda (fixes #19) | 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 envir Environment where variables can be f... | #' 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 |
64966a1e02b82f676c8ed7f89ab250481cb01148 | Update document. | snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3 | q3/docs/FolderEmptyAction.rd | q3/docs/FolderEmptyAction.rd | =begin
=FolderEmptyANV
ݑIĂtH_̑SẴbZ[W폜܂B̃AJEgɃS~iS~tO̗tH_jꍇɂ́ÃtH_ɃbZ[WړAȂꍇɂ͒ڃbZ[W폜܂B
AΏۂ̃bZ[WS~܂̓XptH_iXptO̗tH_jɂꍇAS~̗LɊւ炸ڃbZ[W폜܂B
==
Ȃ
==LȃEBhEEr[
*CEBhE
=end
| =begin
=FolderEmptyANV
ݑIĂtH_̑SẴbZ[W폜܂B
==
Ȃ
==LȃEBhEEr[
*CEBhE
=end
| mit | R |
6a7436d26bdf1073bd4ba577dc7bd98f7c846c60 | Update uvoz_tabel.r | ZavbiA/APPR-2017 | uvoz/uvoz_tabel.r | uvoz/uvoz_tabel.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
# Funkcija, ki uvozi število medalj po državah iz Wikipedije
uvozi.medalje <- function() {
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='wikitable sortable']") %... | mit | R |
449fe052a2b229dc18cd5e02a1a2a81d15199758 | Update get_length_and_gc_content.r code for latest bioc change | SANBI-SA/tools-iuc,pavanvidem/tools-iuc,natefoo/tools-iuc,loraine-gueguen/tools-iuc,nekrut/tools-iuc,jj-umn/tools-iuc,pjbriggs/tools-iuc,galaxyproject/tools-iuc,dpryan79/tools-iuc,galaxyproject/tools-iuc,pavanvidem/tools-iuc,abretaud/tools-iuc,nsoranzo/tools-iuc,davebx/tools-iuc,dpryan79/tools-iuc,gregvonkuster/tools-i... | tools/goseq/get_length_and_gc_content.r | tools/goseq/get_length_and_gc_content.r | # originally by Devon Ryan, https://www.biostars.org/p/84467/
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")
suppressPackag... | # originally by Devon Ryan, https://www.biostars.org/p/84467/
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")
suppressPackag... | mit | R |
c4e5e869b2f2faf4fd73f14d9f703bf071b74709 | Set up packages after loading | 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 |
68c15bc1e21d2ce0eecc7d31127cdd148de7bc3f | Add zoo lib | alexbbt/info370final,alexbbt/info370final | data-prep.r | data-prep.r | library(reshape2)
library(zoo)
#################
### Data Prep ###
#################
data <- read.csv('./data/training.csv')
# Factorize numeric data points
data$floors <- factor(data$floors)
data$waterfront <- as.logical(data$waterfront) # could just be a factor
data$view <- factor(data$view)
data$condition <- facto... | library(reshape2)
data <- read.csv('./data/training.csv')
data$floors <- factor(data$floors)
data$waterfront <- as.logical(data$waterfront) # could just be a factor
data$view <- factor(data$view)
data$condition <- factor(data$condition)
data$grade <- factor(data$grade)
data$yr_built <- factor(data$yr_built)
data$yr_r... | mit | R |
193874bda446c138272dc4691961c09435b2e3a4 | 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"),
tabsetPanel(
tabPanel("Dolg",
sliderInput(inputId="leto_1",label="Leto",min=2006,max=2014,value=2007,sep=""),
plotOutput("dolg")),
tabPanel("Deficit",
... | library(shiny)
shinyUI(
ui <- fluidPage(
titlePanel("Analiza dolga in primankljaja držav v Evropski uniji"),
tabsetPanel(
tabPanel("Dolg",
sliderInput(inputId="leto_1",label="Leto",min=2006,max=2014,value=2007,sep=""),
plotOutput("dolg")),
tabPanel("Deficit",
... | mit | R |
6fe2bb5e9bb4aec33bbc17bf8325cbc9d495ba5d | use biomart for lincs annotations | mschubert/narray,mschubert/narray | summarize.r | summarize.r | .b = import('../base')
.s = import('./split')
.m = import('./map')
.bi = import('./bind')
#' Summarize a matrix analogous to a grouped df in dplyr
#'
#' @param x A matrix
#' @param from Names that match the dimension `along`
#' @param to Names that this dimension should be summarized to
#' @param along Alo... | .b = import('../base')
.s = import('./split')
.m = import('./map')
.bi = import('./bind')
`%>%` = magrittr::`%>%`
#' Summarize a matrix analogous to a grouped df in dplyr
#'
#' @param x A matrix
#' @param from Names that match the dimension `along`
#' @param to Names that this dimension should be summarized... | apache-2.0 | R |
dd46db0bc7338c54072f7db072731763b126b2c3 | update scrapte30min for full path | isithot/isithotrightnow,isithot/isithotrightnow,isithot/isithotrightnow,isithot/isithotrightnow,isithot/isithotrightnow | cronscripts/scrape30min.r | cronscripts/scrape30min.r | #!/usr/bin/R
# File: scrape30min.r
# stefan contractor, mat lipson and james goldie
# Description:
# This is a script run every half hour to scrape current observations
# It is run through crontab, editable with: crontab
for (state in c("D", "N", "Q", "S", "T", "V", "W"))
{
download.file(
paste0("ftp://ftp.bom... | #!/usr/bin/R
# File: scrape30min.r
# stefan contractor, mat lipson and james goldie
# Description:
# This is a script run every half hour to scrape current observations
# It is run through crontab, editable with: crontab
for (state in c("D", "N", "Q", "S", "T", "V", "W"))
{
download.file(
paste0("ftp://ftp.bom... | mit | R |
95d10b76cd47acf49d73ae045fa987e4e0d3cb6e | Update uvoz.r | Anchiqua/APPR-2015-16 | uvoz/uvoz.r | uvoz/uvoz.r | # 2. faza: Uvoz podatkov
library(dplyr)
library(ggplot2)
require(jsonlite)
require(httr)
require(zoo)
#uvozimo podatke
r <- GET("http://www.nhl.com/stats/rest/grouped/skaters/season/skatersummary?cayenneExp=seasonId=20142015%20and%20gameTypeId=2")
text <- content(r, "text")
data <- fromJSON(content(r, "text"))
tabela ... | # 2. faza: Uvoz podatkov
#uvozimo podatke
require(jsonlite)
require(httr)
r <- GET("http://www.nhl.com/stats/rest/grouped/skaters/season/skatersummary?cayenneExp=seasonId=20142015%20and%20gameTypeId=2")
text <- content(r, "text")
data <- fromJSON(content(r, "text"))
tabela <- data.frame(data)
#omejimo na manj kategori... | mit | R |
61353b0bf0b1caf6cc7246474e6a597468c12fe7 | Update fRH.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/fRH.r | R/fRH.r | #' fRH
#'
#' Return relative humidity from air temperature (Celsius) and Dew point (Celsius);
#'
#' @param t numeric Vector or value of air temperature in Celsius degree.
#' @param td numeric Vector or value of dew point temperature in Celsius degree.
#' @return res numeric relative humidity value
#'
#'
#' @author Is... | #' fRH
#'
#' Return relative humidity from air temperature (Celsius) and Dew point (Celsius);
#'
#' @param t numeric Vector or value of air temperature in Celsius degree.
#' @param td numeric Vector or value of dew point temperature in Celsius degree.
#' @return res numeric relative humidity value
#'
#'
#' @author Is... | mit | R |
b3f7d28bcf9714b1b42ef587c09dc49a3b9408bc | Fix incorrect total calculation in run.r | metaeducation/ren-c-test,metaeducation/ren-c-test,rebolsource/rebol-test,rebolsource/rebol-test | run.r | run.r | Rebol [
Title: "Core tests run"
File: %core-tests-run.r
Author: "Ladislav Mecir"
Date: 18-Nov-2010/11:23:15+1:00
Purpose: "Core tests"
]
do %test-framework.r
; Example runner for the REBOL/Core tests which chooses
; appropriate flags depending on the interpreter version.
do-core-tests: has [
flags crash-flags ... | Rebol [
Title: "Core tests run"
File: %core-tests-run.r
Author: "Ladislav Mecir"
Date: 18-Nov-2010/11:23:15+1:00
Purpose: "Core tests"
]
do %test-framework.r
; Example runner for the REBOL/Core tests which chooses
; appropriate flags depending on the interpreter version.
do-core-tests: has [
flags crash-flags ... | apache-2.0 | R |
28af87384619bfef6524d93d9826cf963e071095 | Update run_irods_msvc_test.r | leesab/irods,leesab/irods,leesab/irods,leesab/irods,leesab/irods,leesab/irods,leesab/irods | examples/microservices/run_irods_msvc_test.r | examples/microservices/run_irods_msvc_test.r | test {
irods_msvc_test( "1", "2", "3", *out );
writeLine('stdout', *out);
}
input null
output ruleExecOut
| test {
irods_msvc_test( "1", "2", "3" );
}
input null
output ruleExecOut
| bsd-3-clause | R |
c6bbc4e69d16a897d5f3453ce3b4963ecffe8914 | fix construct | mschubert/narray,mschubert/narray | R/construct.r | R/construct.r | #' A wrapper around reshape2::acast using a more intuitive formula syntax
#'
#' @param formula A formula: value [+ value2 ..] ~ axis1 [+ axis2 + axis n ..]
#' @param data A data frame (TODO: handle envs, NULL, etc.)
#' @param fill Value to fill array with if undefined
#' @param fun.aggregate ... | #' A wrapper around reshape2::acast using a more intuitive formula syntax
#'
#' @param formula A formula: value [+ value2 ..] ~ axis1 [+ axis2 + axis n ..]
#' @param data A data frame (TODO: handle envs, NULL, etc.)
#' @param fill Value to fill array with if undefined
#' @param fun.aggregate ... | apache-2.0 | R |
e858818f6d0e898862a3d20aed4e47f5c0a98de9 | Set the values of all gobals to NA & print globals | jmousseau/Stain | R/slurm-job.r | R/slurm-job.r | #' NOAARequest R6 object.
#'
#' An interface to SLURM bash scripts and their submissions.
SlurmJob <- R6::R6Class("SlurmJob",
public = list(
main_file = NULL,
params = list(),
initialize = function(main_file, source_files = list()) {
if (!missing(main_file)) {
sel... | #' NOAARequest R6 object.
#'
#' An interface to SLURM bash scripts and their submissions.
SlurmJob <- R6::R6Class("SlurmJob",
public = list(
main_file = NULL,
params = list(),
initialize = function(main_file, source_files = list()) {
if (!missing(main_file)) {
sel... | mit | R |
c8f8c24786fc33f54d8a34fe1c423dfdaff300c4 | fix previous commit. | akr/clockcount,akr/clockcount | README.rd | README.rd | = clockcount
clockcount access processor specific clock counter.
== Usage
require 'clockcount'
p ClockCount()
== Sample Script to Mesure Clock Speed
% ruby sample.rb
0x18a9c616f16d5
0x18a9caca6f864 1.2640276924433[GHz] 3.97282828038034[day]
0x18a9cf9ac9d9c 1.29211869909757[GHz] 3.88646950425614[da... | = clockcount
clockcount access processor specific clock counter.
== Usage
require 'clockcount'
p ClockCount()
== Sample Script to Mesure Clock Speed
% ruby sample.rb
0x18a9c616f16d5
0x18a9caca6f864 1.2640276924433[GHz] 3.97282828038034[day]
0x18a9cf9ac9d9c 1.29211869909757[GHz] 3.88646950425614[da... | bsd-2-clause | R |
9062f268def25857880fdba5c74a2326f02a8316 | use array module for splitting | mschubert/narray,mschubert/narray | split.r | split.r | .s = import('./subset')
#' Splits and array along a given axis, either totally or only subsets
#'
#' @param X An array that should be split
#' @param along Along which axis to split; use -1 for highest dimension
#' @param subsets Whether to split each element or keep some together
#' @return A list ... | .s = import('./subset')
#' Splits and array along a given axis, either totally or only subsets
#'
#' @param X An array that should be split
#' @param along Along which axis to split
#' @param subsets Whether to split each element or keep some together
#' @return A list of arrays that combined make u... | apache-2.0 | R |
44545885689363dc02f94af0d154072145ed88d0 | remove margin, add method | 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 method The method to permute matrices with: "r0", "r1", "r2", "c0", "swap", "quasiswap"
#' @export
#' @examples
#' data(gopherlice)
#' library(ape)
... | #' 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 |
2a64fd9ef670b1bd5f6c6b9cecabf3aec984cde1 | fix regular expression | koji-to/effort_calculator,koji-to/effort_calculator,koji-to/effort_calculator | generate_git_log_main_sh.r | generate_git_log_main_sh.r | ######## generate .sh script for "git log" about main log
######## git log option: "%H%ae%ad%ce%cd"
shell.df<-read.csv("chromium_git_repo_tree.txt",header=F)
shell_top.df<-matrix(c("#!/bin/sh","logdir=\"`pwd`/git_log_main/\"","hmdir=\"`pwd`\""),3,1)
write.table(shell_top.df,"git_log_main.sh",row.names=F,col.names=F,q... | ######## generate .sh script for "git log" about main log
######## git log option: "%H%ae%ad%ce%cd"
shell.df<-read.csv("chromium_git_repo_tree.txt",header=F)
shell_top.df<-matrix(c("#!/bin/sh","logdir=\"`pwd`/git_log_main/\"","hmdir=\"`pwd`\""),3,1)
write.table(shell_top.df,"git_log_main.sh",row.names=F,col.names=F,q... | mit | R |
3f95cfc98de0dd9acea865c288d215aa57b81422 | fix genecloud error | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/Annotation/mafReport.r | lib/Annotation/mafReport.r | library(mafreport)
#https://github.com/PoisonAlien/maftools/issues/532
library("wordcloud")
devtools::source_gist(id = "https://gist.github.com/PoisonAlien/3f8752a89c1d63f64afe55b441621223")
mafFileList = parSampleFile1
#reportOutDir = "."
reportOutDir = getwd()
if(parFile1 != ''){
clinicalData = parFile1
#need ... | library(mafreport)
mafFileList = parSampleFile1
#reportOutDir = "."
reportOutDir = getwd()
if(parFile1 != ''){
clinicalData = parFile1
#need also define clinicalFeatures in rCode
}else{
clinicalData = NULL
clinicalFeatures = NULL
}
if (!exists("genome")) {
genome="hg19"
}
interestedGenes = NULL
if(exists... | apache-2.0 | R |
bb08c1cdbd64dc8cc17e3c0cde8151c5110a0594 | Fix problems with rename due to bug in dplyr | petercarrjones/icc-data,petercarrjones/icc-data,petercarrjones/icc-data | load.r | load.r | #Load Packages
library(XML)
library(tidyr)
library(stringr)
library(magrittr)
library(plyr)
library(dplyr)
library(RWeka)
#Remove non-words from the raw icc texts
get_real_words <- function(word) {
word[!stringr::str_detect(word, "[^a-z ]")]
}
#' Remove unreasonable n-grams containing characters other than letters... | #Load Packages
library(XML)
library(tidyr)
library(stringr)
library(magrittr)
library(plyr)
library(dplyr)
library(RWeka)
#Remove non-words from the raw icc texts
get_real_words <- function(word) {
word[!stringr::str_detect(word, "[^a-z ]")]
}
#' Remove unreasonable n-grams containing characters other than letters... | mit | R |
7bd62e770c6ac4d8fe22931f34f10811b9c9f0e3 | Fix module finding | 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 |
299e87100adf447438188d7627185a655c3eab2d | Update 1.r | glor/R,glor/R | aufgaben/blatt06/1.r | aufgaben/blatt06/1.r | #6.1
# Unabhängigkeit der Observation gegeben
#Prüfen der Normalerverteilung mit Boxplot:
boxplot(cattle$Widerrist, cattle$Rumpf)
# —> Widerrist ist nicht normalerveteilt —> Spearman
cor(cattle, use = "all.obs", method = "spearman”)
#6.2
#Da hier bereits gerichtete Hypothesen sinnvoll sind:
# H0: Die Korrelat... | bsd-2-clause | R | |
da9de162b4f62000bdef86c0a68e5554cea60a6e | use mapreduce for uploaddata.r example | snowch/biginsight-examples,snowch/biginsight-examples | examples/BigR/uploaddata.r | examples/BigR/uploaddata.r | projdir <- Sys.getenv("projdir")
# connect.r will open the connection to the cluster
source( paste( projdir, "/connect.r", sep="" ) )
#################
# 1. Data loading
#################
# In order to try out any example, first run the following steps to upload
# the aforementioned dataset to a BigInsights cluster.... | projdir <- Sys.getenv("projdir")
# connect.r will open the connection to the cluster
source( paste( projdir, "/connect.r", sep="" ) )
#################
# 1. Data loading
#################
# In order to try out any example, first run the following steps to upload
# the aforementioned dataset to a BigInsights cluster.... | apache-2.0 | R |
e4de0aba1fb5ed379aeafd0e517b4ed4772efcb2 | Update 2.r | glor/R,glor/R | aufgaben/blatt02/2.r | aufgaben/blatt02/2.r | #Blatt 2
#2.1
sorte = c(rep(1,15), rep(2,12), rep(3, 20))
gewicht = c(6.22,5.75,6.4,4.6,3.25,4.5,4.8,5.88,5.8,6.1,5.58,6.01,5.62,6.72,8.55,4.28,7.7,6.4,7.77,7.37,4.2,7.05,6.45,8.93,5.9,5.94,6.39, 7.13,8.78,6.06,7.93,9.1,8,7.55,8.32,8.8,12.63,8.19,6.5,6.84,7.02,9.39,7.38,7.39,6.99,8.27,6.7)
tabelle = data.frame(So... | #Blatt 2
#2.1
sorte = c(rep(1,15), rep(2,12), rep(3, 20))
gewicht = c(6.22,5.75,6.4,4.6,3.25,4.5,4.8,5.88,5.8,6.1,5.58,6.01,5.62,6.72,8.55,4.28,7.7,6.4,7.77,7.37,4.2,7.05,6.45,8.93,5.9,5.94,6.39, 7.13,8.78,6.06,7.93,9.1,8,7.55,8.32,8.8,12.63,8.19,6.5,6.84,7.02,9.39,7.38,7.39,6.99,8.27,6.7)
tabelle = data.frame(So... | bsd-2-clause | R |
4e98dc48499ead94f8fb7345be79ab863c1b5b6f | 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 |
7f4fc6ca1a9471486676387e3d6e132d4309f684 | Update HSI_index.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/HSI_index.r | R/HSI_index.r | #' HSI_index
#'
#' Computes the Heat Strain Index. HSI is the ratio of the demand for sweat evaporation to capacity of evaporation (Ereq on Emax). This denotes also the percent of skin wettedness, which is a good predictor of warm discomfort.
#'
#' @param numeric t Air temperature in Celsius degrees.
#' @param numeric ... | #' HSI_index
#'
#' Computes the Heat Strain Index. HSI is the ratio of the demand for sweat evaporation to capacity of evaporation (Ereq on Emax). This denotes also the percent of skin wettedness, which is a good predictor of warm discomfort.
#'
#' @param numeric t Air temperature in Celsius degrees.
#' @param numeric ... | mit | R |
e2cd84ba600d3ac0e251b918488be89fd58f70f5 | Update 2017_report_config.r | PSC-CoTC/PSC-FRAM-Admin,PSC-CoTC/PSC-FRAM-Admin | config/2017_report_config.r | config/2017_report_config.r |
run.year <- 2017
post.season.fram.db <- "./fram db/Final pre and post databases/FramVS2-PSC-Coho-Backwards-redo 2010-2016 January 2019 products with BK2017 take2.mdb"
post.season.run.name <- "bc-BK Coho 2017 final take2"
post.season.tamm <- "./fram db/TAMM_Files_Postseason/BK Coho2017__Sht1Mtrx step 2 final take... |
run.year <- 2017
post.season.fram.db <- "./fram db/Final pre and post databases/FramVS2-PSC-Coho-Backwards-redo 2010-2016 January 2019 products with BK2017 take2.mdb"
post.season.run.name <- "bc-BK Coho 2017 final take2"
post.season.tamm <- "./fram db/TAMM_Files_Postseason/BK Coho2017__Sht1Mtrx step 2 final take... | mit | R |
b4602bc32e392091f67de5af7a0b785bd7437996 | Fix typos | HIIT/digivaalit-2015,HIIT/digivaalit-2015,HIIT/digivaalit-2015 | topics/topics.r | topics/topics.r | create_dtm <- function( path ) {
library(tm)
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 <-DocumentTermMatrix(a)
... | create_dtm <- function( path ) {
library(topicmodels)
library(tm)
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) )
stopwords("finnish")
a <- tm_map(a, removeWords, stopword... | mit | R |
0209d9d5c430a4d5e93c92ba7a7af64868466c5b | Update windspeed.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/windspeed.r | R/windspeed.r | #' windspeed
#'
#' @description Calculate meteorological wind speed.
#'
#' @param u numeric U zonal component
#' @param v numeric V meridian component
#' @return
#'
#' @references Istituto di Biometeorologia Firenze Italy.
#' @author Alfonso crisci \email{a.crisci@@ibimet.cnr.it} Marco Morabito \email{m.morabito@@... | #' windspeed
#'
#' @description Calculate meteorological wind speed.
#'
#' @param u numeric U zonal component
#' @param v numeric V meridian component
#' @return
#'
#' @references Istituto di Biometeorologia Firenze Italy.
#' @author Alfonso crisci \email{a.crisci@@ibimet.cnr.it} Marco Morabito \email{m.morabito@@... | mit | R |
16ac1dab6c3333df1a1eb041f5d09bda3001edb7 | test for CV and grid_search | chrinide/optunity,claesenm/optunity,chrinide/optunity,claesenm/optunity,chrinide/optunity,MarkAWard/optunity,MarkAWard/optunity,claesenm/optunity,chrinide/optunity,MarkAWard/optunity,MarkAWard/optunity,claesenm/optunity | wrappers/R/inst/tests/testthat/test-cv.r | wrappers/R/inst/tests/testthat/test-cv.r |
context("Cross-validation")
x <- matrix(runif(50*5), 50, 5)
y <- x[,1] + 0.5*x[,2] + 0.1*runif(50)
test_that("cv.setup can be created", {
cv <- cv.setup(x, y, score=score.neg.mse, num_folds = 10, num_iter = 2)
expect_equal( cv$supervised, TRUE )
expect_equal( nrow(cv$folds), 50 )
expect_equal( ncol(cv$folds)... |
context("Cross-validation")
x <- matrix(runif(50*5), 50, 5)
y <- x[,1] + 0.5*x[,2] + 0.1*runif(50)
test_that("cv.setup can be created", {
cv <- cv.setup(x, y, score=score.neg.mse, num_folds = 10, num_iter = 2)
expect_equal( cv$supervised, TRUE )
expect_equal( nrow(cv$folds), 50 )
expect_equal( ncol(cv$folds)... | bsd-3-clause | R |
51d83bcec5877c440b43cebe7338341a4285cb31 | Remove all output files after job completes | 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_dir, options) {
private$options <- options
private$cat_main_file_magic(... | #' SlurmBashScript R6 object.
#'
#' Generates the necessary bash script to submit through
#' the `sbatch` command.
SlurmBashScript <- R6::R6Class("SlurmBashScript",
public = list(
initialize = function(container_dir, options) {
private$options <- options
private$cat_main_file_magic(... | mit | R |
30064ce66674ca31d0bebf7c38c2a15fae3c0bf3 | Rename function | mattm/active-user-cohort-analysis | active-users.r | active-users.r | CSV_PATH = "data/complete.csv"
CSV_SEPARATOR = "\t"
Run <- function() {
activities <- LoadActivityData()
data <- AnalyzeActiveUserCohorts(activities)
PlotActiveUserCohorts(data)
}
LoadActivityData <- function() {
activities <- read.csv(CSV_PATH, sep = CSV_SEPARATOR,
col.names = c("user.id", "date"), header = FA... | CSV_PATH = "data/complete.csv"
CSV_SEPARATOR = "\t"
Run <- function() {
activities <- LoadActivityData()
data <- AnalyzeActiveUserCohorts(activities)
PlotActiveUserCohorts(data)
}
LoadActivityData <- function() {
activities <- read.csv(CSV_PATH, sep = CSV_SEPARATOR,
col.names = c("user.id", "date"), header = FA... | mit | R |
438e364ab7ffabc41d5b53bf519aca0492c84de5 | remove sink for port binding | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | R/bind_avail.r | R/bind_avail.r | #' Binds an rzmq to an available port in given range
#'
#' @param socket An rzmq socket object
#' @param range Numbers to consider (e.g. 6000:8000)
#' @param iface Interface to listen on
#' @param n_tries Number of ports to try in range
#' @return The port the socket is bound to
bind_avail = function(s... | #' Binds an rzmq to an available port in given range
#'
#' @param socket An rzmq socket object
#' @param range Numbers to consider (e.g. 6000:8000)
#' @param iface Interface to listen on
#' @param n_tries Number of ports to try in range
#' @return The port the socket is bound to
bind_avail = function(s... | apache-2.0 | R |
165c8937da5839706e357036192d9ed70794c839 | 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,sep=""),
sliderInput(inputId="leto_2",label="Leto",min=2006,max=2014,value... | 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,sep=""),
sliderInput(inputId="leto_2",label="Leto",min=2006,max=2014,value... | mit | R |
d8bbd95c40c67658f1de4316d0f4addce6dfe450 | order missed genes | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/scRNAMarkerGenes.r | lib/scRNA/scRNAMarkerGenes.r |
library(Seurat)
library(ggplot2)
library(patchwork)
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$Gene)
missGenes<-celltypes[!(celltypes... |
library(Seurat)
library(ggplot2)
finalList<-readRDS(parFile1)
geneFile<-parFile2
obj<-finalList$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$Gene %in% rownames... | apache-2.0 | R |
e3b93529179b1be8f9204b1acd51656969354aea | Fix plot legend. | danluu/BitFunnel,danluu/BitFunnel,danluu/BitFunnel,BitFunnel/BitFunnel,BitFunnel/BitFunnel,BitFunnel/BitFunnel,danluu/BitFunnel,BitFunnel/BitFunnel,danluu/BitFunnel,BitFunnel/BitFunnel,danluu/BitFunnel,BitFunnel/BitFunnel | src/Scripts/plot-qwords.r | src/Scripts/plot-qwords.r | library("ggplot2")
library("reshape")
setwd("~/dev/BitFunnel/src/Scripts")
queries <- read.csv(header=TRUE, file="/tmp/QueryPipelineStatistics.csv")
# Create column to graph vs. term position.
pos = seq(1, length(queries$quadwords))
df_temp <- data.frame(pos, queries$quadwords, queries$cachelines)
# Rename columns t... | 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... | mit | R |
92dc92a28f46d567570ed233652d227b4d62a6db | fix localhost timeout: takes ms, not s | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | tests/testthat/helper-util.r | tests/testthat/helper-util.r | send = function(sock, data) {
send_socket(sock, data)
}
recv = function(p, sock, timeout=3L) {
event = poll_socket(list(sock), timeout=timeout * 1000)
if (is.null(event))
return(recv(p, sock, timeout=timeout))
else if (event[1]) {
re = receive_multipart(sock)
if (length(re) == 1... | send = function(sock, data) {
send_socket(sock, data)
}
recv = function(p, sock, timeout=3L) {
event = poll_socket(list(sock), timeout=timeout * 1000)
if (is.null(event))
return(recv(p, sock, timeout=timeout))
else if (event[1]) {
re = receive_multipart(sock)
if (length(re) == 1... | apache-2.0 | R |
68f0146fdf7c84346a48fbb7195613a14e36b896 | Return WHAT-DIR location after a CD shell command | giuliolunati/ren-c,codebybrett/ren-c,hostilefork/rebol,rgchris/ren-c,hostilefork/rebol,draegtun/ren-c,draegtun/ren-c,giuliolunati/ren-c,draegtun/ren-c,kealist/ren-c,kealist/ren-c,codebybrett/ren-c,codebybrett/ren-c,hostilefork/rebol,rgchris/ren-c,kealist/ren-c,codebybrett/ren-c,hostilefork/rebol,codebybrett/ren-c,keali... | src/mezz/mezz-shell.r | src/mezz/mezz-shell.r | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: Shell-like Command Functions"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2... | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: Shell-like Command Functions"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2... | apache-2.0 | R |
150171d75bb5b6e2756d92fe7df653ff556a0276 | Fix typos | hadley/ggplot2-bayarea | 2-time-series.r | 2-time-series.r | library(ggplot2)
load("city-summary.rdata")
ggplot(bigsum, aes(date, price / 1e6)) +
geom_line() +
facet_wrap(~ city)
ggsave("cities-price.png", width = 8, height = 6, dpi = 128)
# Smoothing ------------------------------------------------------------------
library(mgcv)
smooth <- function(y, x) {
as.numeri... | library(ggplot2)
load("city-summary.rdata")
ggplot(bigsum, aes(date, price / 1e6)) +
geom_line() +
facet_wrap(~ city)
ggsave("cities-price.png", width = 8, height = 6, dpi = 128)
# Smoothing ------------------------------------------------------------------
library(mgcv)
smooth <- function(y, x) {
as.numeri... | mit | R |
44753dd99b53893084aa94f8ca3352044c30a8a2 | Fix `module_name` bug | klmr/modules,klmr/modules | R/module_cache.r | R/module_cache.r | #' Environment of loaded modules
#'
#' Each module is stored as an environment inside \code{.loaded_modules} with
#' the module’s code location path as its identifier. The path rather than the
#' module name is used because module names are not unique: two modules called
#' \code{a} can exist nested inside modules \cod... | #' Environment of loaded modules
#'
#' Each module is stored as an environment inside \code{.loaded_modules} with
#' the module’s code location path as its identifier. The path rather than the
#' module name is used because module names are not unique: two modules called
#' \code{a} can exist nested inside modules \cod... | apache-2.0 | R |
4bd825a323a5498d9d3576d79f947b2d2e50e444 | 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$leto_1), aes(x = Drzava, y = Dolg, fill=Dolg)) +
scale_fill_continuous(low = "#69b8f6", high = "#142d45") +
geom_bar(stat ="identity") +
theme(... |
library(shiny)
shinyServer(
server <- function(input, output) {
output$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... | mit | R |
e1468ef1fcfcb9799c170fefd5c05b28629d328e | Add RColorBrewer. | ryanlovett/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,berkeley-dsep-infra/datahub | deployments/r/image/extras.d/2019-fall-stat-131a.r | deployments/r/image/extras.d/2019-fall-stat-131a.r | #!/usr/bin/env Rscript
source("/tmp/install-class-libs.R")
class_name = "2019 Fall Stat 131a"
class_libs = c(
"cran/alluvial", "0.1-2",
"cran/DAAG", "1.22",
"cran/faraway", "1.0.7",
"cran/fdrtool", "1.2.15",
"cran/gpairs", "1.2",
"cran/gplots", "3.0.1.1",
"cran/hexbin", "1.27.3",
"cran/leaps", "2.9",
... | #!/usr/bin/env Rscript
source("/tmp/install-class-libs.R")
class_name = "2019 Fall Stat 131a"
class_libs = c(
"cran/alluvial", "0.1-2",
"cran/DAAG", "1.22",
"cran/faraway", "1.0.7",
"cran/fdrtool", "1.2.15",
"cran/gpairs", "1.2",
"cran/gplots", "3.0.1.1",
"cran/hexbin", "1.27.3",
"cran/leaps", "2.9",
... | bsd-3-clause | R |
653f18794e692938287a96fc01e550320a1e6ff4 | include new climate drivers in flattening routine | khufkens/phenor | R/flat_format.r | R/flat_format.r | #' Flatten the format as generated by format_phenocam()
#' and format_modis(). Flattening the file format allows
#' for substantial speed increases in optimization however
#' limits readability. Using the split functionality between
#' the format_*() functions and this function allows for easy
#' subsetting of datasets... | #' Flatten the format as generated by format_phenocam()
#' and format_modis(). Flattening the file format allows
#' for substantial speed increases in optimization however
#' limits readability. Using the split functionality between
#' the format_*() functions and this function allows for easy
#' subsetting of datasets... | agpl-3.0 | R |
e13dd2452f0eed2b48623d89825b56337a687f6c | Edit help description for HandleOvertime function | mattmills49/CFBWinProbability | R/HandleOvertime.r | R/HandleOvertime.r | #' Structure plays correctly for games that went into overtime
#'
#' This function takes in overtime plays and gets them in the same structure as
#' plays in regulation. This function is called from the DataPrep function. You
#' really won't need this function on it's own ever.
#' @param overtime a data frame contai... | #' Structure plays correctly for games that went into overtime
#'
#' This function takes in overtime plays and gets them in the same structure as
#' plays in regulation. This function is called from the DataPrep function.
#' @param overtime a data frame containing overtime plays from the CFB Stats play.csv file
#' @r... | mit | R |
116587b0c7671c344b3fb23910c2e0b8f10b4cdd | Update libraries.r | aleksandrov2/APPR-2015-16 | lib/libraries.r | lib/libraries.r | 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.
source("lib/uvozi.zemljevid.r", encoding = "UTF-8")
| library(knitr)
library(ggplot2)
library(dplyr)
require(gsubfn)
require(rvest)
require(xml2)
require(ggplot2)
library(sp)
library(maptools)
# Uvozimo funkcije za pobiranje in uvoz zemljevida.
source("lib/uvozi.zemljevid.r", encoding = "UTF-8") | mit | R |
4fe8ae6baea919b21c87ca5ddb9676d4cf1316e9 | update read-binary-fixes.r | amsa-code/risky,amsa-code/risky,amsa-code/risky,amsa-code/risky,amsa-code/risky | formats/src/test/resources/read-binary-fixes.r | formats/src/test/resources/read-binary-fixes.r | file = file("target/123456790.track","rb")
readSingle = function() readBin(file, single(), size=4, endian="big")
readInteger = function() readBin(file, integer(), size=4, endian="big")
readLong = function() {
a = readBin(file, integer(), size=4, endian="big")
b = readBin(file, integer(), size=4, endian="big")
# ... | file = file("target/123456790.track","rb")
readSingle = function() readBin(file, single(), size=4, endian="big")
readLong = function() readBin(file, integer(), size=8, endian="big")
readByte = function() readBin(file, integer(), size=1, endian="big")
readShort = function() readBin(file, integer(), size=2, endian="big")... | apache-2.0 | R |
e98988fcda86ce579a9bfa93f933258efe960a45 | Update test case for #66 | klmr/modules,klmr/modules | inst/tests/test-path.r | inst/tests/test-path.r | context('Find module path relative files')
test_that('module_file works in global namespace', {
expect_that(module_file(), equals(getwd()))
expect_true(nchar(module_file('run-all.r')) > 0)
throws_error(module_file('XXX-does-not-exist', mustWork = TRUE),
'no file found')
})
test_that('modu... | context('Find module path relative files')
test_that('module_file works in global namespace', {
expect_that(module_file(), equals(getwd()))
expect_true(nchar(module_file('run-all.r')) > 0)
throws_error(module_file('XXX-does-not-exist', mustWork = TRUE),
'no file found')
})
test_that('modu... | apache-2.0 | R |
30b171b8161aeddf672206c7a09b5ba28c4711b0 | Update steadman_class.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/steadman_class.r | R/steadman_class.r | #' steadman_class
#'
#' Computes the correspondent Steadman's apparent temperature class.
#'
#' @param numeric steadman_index Steadman index value.
#' @return class of apparent temperature.
#'
#'
#' @author Istituto di Biometeorologia Firenze Italy Alfonso Crisci \email{a.crisci@@ibimet.cnr.it}
#' @keywords class, ... | #' steadman_class
#'
#' Computes the correspondent Steadman's apparent temperature class.
#'
#' @param numeric steadman_index Steadman index value.
#' @return class of apparent temperature.
#'
#'
#' @author Istituto di Biometeorologia Firenze Italy Alfonso Crisci \email{a.crisci@@ibimet.cnr.it}
#' @keywords class, ... | mit | R |
496cbadbb69d76ac136839f1704d86de939d111e | comment out an unnecessary output | 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 |
fe8b3e0ab737901c19e08ef21411196e43aee48d | Bump version | giuliolunati/ren-c,kealist/ren-c,kealist/ren-c,hostilefork/rebol,mbk/ren-c,kealist/ren-c,mbk/ren-c,rgchris/ren-c,hostilefork/rebol,kealist/ren-c,giuliolunati/ren-c,codebybrett/ren-c,kealist/ren-c,hostilefork/rebol,draegtun/ren-c,rgchris/ren-c,mbk/ren-c,codebybrett/ren-c,rgchris/ren-c,codebybrett/ren-c,draegtun/ren-c,ho... | src/boot/version.r | src/boot/version.r | 3.0.0.3.1
| 2.101.0.3.1
| apache-2.0 | R |
525bb105ad6e41e78bf67c04f7931268b6919400 | 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){
if (file.exists(filePath) == TRUE){
filePath <- paste(c(str1,"/I",j,... | mit | R |
13089edcc2ce3d24e8fd257cf2cd1086354fc6d4 | Fix issue #55. | marksteele/basho_bench,mrallen1/basho_bench,GabrielNicolasAvellaneda/basho_bench,basho/basho_bench,basho/basho_bench,basho/basho_bench,mrallen1/basho_bench,mrallen1/basho_bench,fogfish/basho_bench,marksteele/basho_bench,mrallen1/basho_bench,basho/basho_bench,GabrielNicolasAvellaneda/basho_bench,fogfish/basho_bench,Gabr... | priv/common.r | priv/common.r | # Load all the necessary packages, installing missing ones when necessary
packages.to.install <- c("plyr", "grid", "getopt", "proto", "ggplot2")
for(p in packages.to.install)
{
print(p)
if (suppressWarnings(!require(p, character.only = TRUE))) {
install.packages(p, repos = "http://lib.sta... | # Load all the necessary packages, installing missing ones when necessary
packages.to.install <- c("plyr", "grid", "getopt", "proto", "ggplot2")
for(p in packages.to.install)
{
print(p)
if (suppressWarnings(!require(p, character.only = TRUE))) install.packages(p, repos = "http://lib.stat.cmu.edu/R/CR... | apache-2.0 | R |
d9212982953dca671b821fa2c1d7502da1dd9bea | Add symlink for stat20data. | berkeley-dsep-infra/datahub,ryanlovett/datahub,ryanlovett/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub | deployments/stat20/image/r-packages/2022-spring-stat-20.r | deployments/stat20/image/r-packages/2022-spring-stat-20.r | #!/usr/bin/env Rscript
source("/tmp/class-libs.R")
class_name = "2022 Spring Stat 20"
class_libs = c(
"swirl", "2.4.5",
"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",
"palmerp... | #!/usr/bin/env Rscript
source("/tmp/class-libs.R")
class_name = "2022 Spring Stat 20"
class_libs = c(
"swirl", "2.4.5",
"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",
"palmerp... | bsd-3-clause | R |
1a4ca27ac28d547cb311180363cb65418a79c42d | update openintro version | berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,ryanlovett/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", "2.0.0",
"infer", "1.0.0",
"patchwork", "1.1.1",
"tigris", "1.0",
"googlesheets4", "0.2.0",
"xaringanthemer", "0.4.0",
"... | bsd-3-clause | R |
52a7d03f1fc43ff252f3d8f2900fb0e6c524ae3a | add library(png) | AndySouth/coverage | coverage_starting.r | coverage_starting.r | #coverage_starting.r
#andy south 11/5/2016
#first go at creating some coverage visualisations
#git remote add origin git@github.com:AndySouth/coverage.git
#but because i set to wrong one first
#git remote set-url origin git@github.com:AndySouth/coverage.git
#git pull origin master
#git push -u origin master
dfv <... | #coverage_starting.r
#andy south 11/5/2016
#first go at creating some coverage visualisations
#git remote add origin https://github.com/AndySouth/coverage.git
#git push -u origin master
dfv <- data.frame(
man = 0.7,
cow = 0.3,
indoor = 0.6,
outdoor = 0.4
)
dfv <- data.frame(
man = 0.8,
cow = 0.2,
in... | mit | R |
380f39303ea5684e3b0b6ccff875dcd353d7a066 | Update vizualizacija.r | nastja88/APPR-2017 | vizualizacija/vizualizacija.r | vizualizacija/vizualizacija.r | # 3. faza: Vizualizacija podatkov
library(ggplot2)
library(dplyr)
library(sp)
library(maptools)
library(digest)
gpclibPermit()
uvozi.zemljevid <- function(url, pot.zemljevida, mapa = "../zemljevidi",
encoding = "UTF-8", force = FALSE) {
ime.zemljevida <- digest(url, algo = "sha1")
map ... | # 3. faza: Vizualizacija podatkov
library(ggplot2)
library(dplyr)
library(sp)
library(maptools)
library(digest)
gpclibPermit()
source(lib/uvozi.zemljevid.r)
uvozi.zemljevid("http://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/cultural/ne_110m_admin_0_countries.zip",
"ne_110m_... | mit | R |
c15904a562eb1630329ab4e1dbc0d8f25557ce65 | Fix x axis label | johnrfleck/water-tools | gauge_daily_five_year_boxplot.r | gauge_daily_five_year_boxplot.r | # box plot of daily flows at selected gauges, in five year bins
# Uses USGS dataRetrieval package
# tutorial here: https://owi.usgs.gov/R/dataRetrieval.html#1
# Albuquerque gauge to use as example: 08330000
# uses log scale - easier to visualize given variability, particularly
# at low end
library(dataRetrieval)
libra... | # box plot of daily flows at selected gauges, in five year bins
# Uses USGS dataRetrieval package
# tutorial here: https://owi.usgs.gov/R/dataRetrieval.html#1
# Albuquerque gauge to use as example: 08330000
# uses log scale - easier to visualize given variability, particularly
# at low end
library(dataRetrieval)
libra... | mit | R |
1bc452892677b3c1b5a0f4aa2c72eed44258de78 | Change the way JSON is served back to writing a file to the disk. | agapow/smartr,thehyve/heim-SmartR,agapow/smartr,thehyve/heim-SmartR,thehyve/heim-SmartR,agapow/smartr,thehyve/naa-SmartR,thehyve/naa-SmartR,thehyve/heim-SmartR,thehyve/naa-SmartR,agapow/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]] # 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"]... | apache-2.0 | R |
dd6761cc1cf448ff5810942735520f5b977a044d | Install ottr | berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,ryanlovett/datahub | deployments/publichealth/image/r-packages/ph-142.r | deployments/publichealth/image/r-packages/ph-142.r | #!/usr/bin/env Rscript
# From https://github.com/berkeley-dsep-infra/datahub/issues/881
print("Installing packages for PH142")
source("/tmp/class-libs.R")
class_name = "PH142"
class_libs = c(
"fGarch", "3042.83.2",
"SASxport", "1.7.0",
"googlesheets", "0.3.0",
"googledrive", "1.0.1",
"ggrepel", "0.9.0",
... | #!/usr/bin/env Rscript
# From https://github.com/berkeley-dsep-infra/datahub/issues/881
print("Installing packages for PH142")
source("/tmp/class-libs.R")
class_name = "PH142"
class_libs = c(
"fGarch", "3042.83.2",
"SASxport", "1.7.0",
"googlesheets", "0.3.0",
"googled... | bsd-3-clause | R |
f688f341e52417b0952ba675ed4cc49fa0ecdf06 | Set new dimension tile | SteveViss/OuranosDB,SteveViss/OuranosDB | prg/fcts_hdf.r | prg/fcts_hdf.r | check_res <- function(lon,lat){
rs = 0
if(all(dim(lat) == dim(lon)) == FALSE){
write("lat/lon lattices with different dimensions...", stderr())
}
reso <- round(get_res(lon,lat),digit=3)
if(round((range(lat)[2]-range(lat)[1])/nrow(lat),digit=3) != reso){
write("lat resolution is not... | check_res <- function(lon,lat){
rs = 0
if(all(dim(lat) == dim(lon)) == FALSE){
write("lat/lon lattices with different dimensions...", stderr())
}
reso <- round(get_res(lon,lat),digit=3)
if(round((range(lat)[2]-range(lat)[1])/nrow(lat),digit=3) != reso){
write("lat resolution is not... | mit | R |
961c9bf4398e4b23a7416ccd2143ed40fa848d2a | Update zzz.r | syberia/syberia | R/zzz.r | R/zzz.r | .onAttach <- function(...) {
load_github_packages(.github_packages)
if (exists('run', envir = .GlobalEnv, inherits = FALSE)) rm('run', envir = .GlobalEnv)
makeActiveBinding('run', function() build_model, .GlobalEnv)
}
| .onAttach <- function(...) {
load_github_packages(.github_packages)
if (exists('run')) rm('run')
makeActiveBinding('run', function() build_model, .GlobalEnv)
}
| mit | R |
113b7ca2f2ef4504ac35237bfd4d373fe8659dbb | Modify formatting | a-holm/MachinelearningAlgorithms,a-holm/MachinelearningAlgorithms | Regression/RandomForestRegression/regularRandomForestRegression.r | Regression/RandomForestRegression/regularRandomForestRegression.r | # Random Forest Regression for machine learning.
#
# Random forest algorithm is a supervised classification algorithm. As the name
# suggest, this algorithm creates the forest with a number of decision trees.
#
# In general, the more trees in the forest the more robust the forest looks like.
# In the same way in the ... | # Random Forest Regression for machine learning.
#
# Random forest algorithm is a supervised classification algorithm. As the name
# suggest, this algorithm creates the forest with a number of decision trees.
#
# In general, the more trees in the forest the more robust the forest looks like.
# In the same way in the ... | mit | R |
31db0fbf13b806eeeca24d7beeb78dc5aa3a6379 | Remove extra print statement | mattm/active-user-cohort-analysis | active-users.r | active-users.r | CSV_PATH = "data/complete.csv"
CSV_SEPARATOR = "\t"
Run <- function() {
activities <- LoadActivityData()
data <- AnalyzeActiveUserCohorts(activities)
PlotActiveUserCohorts(data)
}
LoadActivityData <- function() {
activities <- read.csv(CSV_PATH, sep = CSV_SEPARATOR,
col.names = c("user.id", "date"), header = FA... | CSV_PATH = "data/test-data.csv"
CSV_SEPARATOR = "\t"
Run <- function() {
activities <- LoadActivityData()
data <- AnalyzeActiveUserCohorts(activities)
PlotActiveUserCohorts(data)
}
LoadActivityData <- function() {
activities <- read.csv(CSV_PATH, sep = CSV_SEPARATOR,
col.names = c("user.id", "date"), header = F... | mit | R |
61afa27681597e4cefdad6ef78c18b9bb78364dc | Add example with convexity issue. | mcmtroffaes/improb-redux | improb-redux-example-1.r | improb-redux-example-1.r | source("improb-redux.r")
pmfs = c(
0.5, 0.5,
0.8, 0.2)
getexpectations = getexpectationsfunc(2, pmfs) # 2 = size of possibility space
getlowerprevisions = getlowerprevisionsfunc(getexpectations)
getupperprevisions = getupperprevisionsfunc(getexpectations)
isgammamaximin = isgammamaxisomethingfunc(getlowerprevisions... | source("improb-redux.r")
pmfs = c(
0.5, 0.5,
0.8, 0.2)
getexpectations = getexpectationsfunc(2, pmfs) # 2 = size of possibility space
getlowerprevisions = getlowerprevisionsfunc(getexpectations)
getupperprevisions = getupperprevisionsfunc(getexpectations)
isgammamaximin = isgammamaxisomethingfunc(getlowerprevisions... | mit | R |
5ec3a25554f2d3e8c633f0b39454a19d54b130aa | update quickstart to user more modern R libraries | shapiromatron/bmds-server,shapiromatron/bmds-server,shapiromatron/bmds-server,shapiromatron/bmds-server | docs/quickstart.r | docs/quickstart.r | # Load required libraries
library(httr)
library(dplyr)
library(jsonlite)
# Set the URL root to the address where BMDS server is currently running:
url_root <- Sys.getenv('BMDS_SERVER_URL', 'http://bmds-server.com')
# Create a data-frame that has two continuous dose-response datasets:
datasetsDf = data.frame(
id=... | # Load required libraries
library(httr)
library(plyr)
library(rjson)
# Set the URL root to the address where BMDS server is currently running
url_root <- Sys.getenv('BMDS_SERVER_URL', 'http://bmds-server.com')
# Create an example BMDS job. This example uses uses BMDS v2.6.0.1. with two
# dichotomous datasets:
inputs ... | mit | R |
260f65d8ce392620988001488f7f6e8454535e83 | remove shift option | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/Annotation/getGeneLocus.r | lib/Annotation/getGeneLocus.r |
require(biomaRt)
require(stringr)
params_def=read.table(parSampleFile1, stringsAsFactor=F)
params<-split(params_def$V1, params_def$V2)
host=params$host
dataset=params$dataset
symbolKey=params$symbolKey
genesStr<-params$genesStr
addChr<-params$add_chr=="1"
if(!file.exists(genesStr)){
genesStr = gsub(",", " ", gene... |
require(biomaRt)
require(stringr)
params_def=read.table(parSampleFile1, stringsAsFactor=F)
params<-split(params_def$V1, params_def$V2)
host=params$host
dataset=params$dataset
symbolKey=params$symbolKey
genesStr<-params$genesStr
shift<-as.numeric(params$shift)
addChr<-params$add_chr=="1"
if(!file.exists(genesStr)){
... | apache-2.0 | R |
ddb11edde2671bceedecae7a22fed28483c8b56e | Add plots. | jtobin/bnp | finite-gaussian-mixture/src/simulation_multivariate_conditional.r | finite-gaussian-mixture/src/simulation_multivariate_conditional.r | require(ggplot2)
require(gridExtra)
require(reshape2)
source('fmm_multivariate_conditional.r')
dimension = 2
config = list(
k = 3
, m = dimension
, a = 1
, l = rep(0, dimension)
, r = diag(0.05, dimension)
, b = 2
, w = diag(1, dimension)
, n = 1000
)
set.seed(222)
d = list(
t(replicate(250... | require(ggplot2)
require(gridExtra)
require(reshape2)
source('fmm_multivariate_conditional.r')
dimension = 2
config = list(
k = 3
, m = dimension
, a = 1
, l = rep(0, dimension)
, r = diag(0.05, dimension)
, b = 2
, w = diag(1, dimension)
, n = 1000
)
set.seed(222)
d = list(
t(replicate(250... | mit | R |
bff788a5200edc64aa0f7d1c4f15531476ff51b7 | add palmerpenguins | ryanlovett/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,ryanlovett/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", "2.0.0",
"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", "2.0.0",
"infer", "1.0.0",
"patchwork", "1.1.1",
"tigris", "1.0",
"googlesheets4", "0.2.0",
"xaringanthemer", "0.4.0"
)
cla... | bsd-3-clause | R |
0c8a281a4e27d5c20ac131185d0ee72038a5a491 | add bootStepAIC R package | felipenoris/AWSFinance,felipenoris/math-server-docker,felipenoris/math-server-docker,felipenoris/AWSFinance | libs/r-packages.r | libs/r-packages.r |
pkgs <- c(
"alabama",
"base64enc",
"bootStepAIC",
"caret",
"cubature",
"data.table",
"DEoptim",
"devtools",
"doParallel",
"doSNOW",
"dplyr",
"dyn",
"dynlm",
"extrafont",
"feather",
"fAsianOptions",
"fAssets",
"fBasics",
"fBonds",
"fCopulae",
"fExoticOptions",
"fExtremes",
"fGarch",
"fImport",
... |
pkgs <- c(
"alabama",
"base64enc",
"caret",
"cubature",
"data.table",
"DEoptim",
"devtools",
"doParallel",
"doSNOW",
"dplyr",
"dyn",
"dynlm",
"extrafont",
"feather",
"fAsianOptions",
"fAssets",
"fBasics",
"fBonds",
"fCopulae",
"fExoticOptions",
"fExtremes",
"fGarch",
"fImport",
"fMultivar",
"f... | mit | R |
e6a67f50974550d270ac67aad31915bc85ad815f | Install vioplot via install.packages. | ryanlovett/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,ryanlovett/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub | deployments/r/image/extras.d/2019-fall-stat-131a.r | deployments/r/image/extras.d/2019-fall-stat-131a.r | #!/usr/bin/env Rscript
source("/tmp/class-libs.R")
class_name = "2019 Fall Stat 131a"
class_libs = c(
"alluvial", "0.1-2",
"latticeExtra", "0.6-28",
"DAAG", "1.22",
"faraway", "1.0.7",
"fdrtool", "1.2.15",
"gpairs", "1.2",
"gplots", "3.0.1.1",
"hexbin", "1.27.3",
"leaps", "2.9",
"NMF", "0.21.0",
... | #!/usr/bin/env Rscript
source("/tmp/class-libs.R")
class_name = "2019 Fall Stat 131a"
class_libs = c(
"alluvial", "0.1-2",
"latticeExtra", "0.6-28",
"DAAG", "1.22",
"faraway", "1.0.7",
"fdrtool", "1.2.15",
"gpairs", "1.2",
"gplots", "3.0.1.1",
"hexbin", "1.27.3",
"leaps", "2.9",
"NMF", "0.21.0",
... | bsd-3-clause | R |
3854465ab62558ce63768c0fe2e965618d3dd03e | change busyIndicator class to shiny-busy | vrann/ShinySky,vrann/ShinySky,vrann/ShinySky,vrann/ShinySky,vrann/ShinySky | R/busy-indicator.r | R/busy-indicator.r | #' busyIndicator
#'
#' A busy indicator
#'
#' @param text The text to show
#' @param img An anitmated gif
#' @param wait The amount of time to wait before showing the busy indicator. The
#' default is 1000 which is 1 second.
#'
#' @export
busyIndicator <- function(text = "Calculation in progress..",img = "shinys... | #' busyIndicator
#'
#' A busy indicator
#'
#' @param text The text to show
#' @param img An anitmated gif
#' @param wait The amount of time to wait before showing the busy indicator. The
#' default is 1000 which is 1 second.
#'
#' @export
busyIndicator <- function(text = "Calculation in progress..",img = "shinys... | mit | R |
648ba41c4df23f7eb9af388afc59808546024f90 | Simplify tests | TobCap/demagrittr | tests/testthat/test-dplyr-adhoc.r | tests/testthat/test-dplyr-adhoc.r | context("adhoc dplyr")
suppressMessages(library("dplyr"))
test_that("equiv value3", {
e1 <- quote(iris %>% filter(Sepal.Width %>% `>`(4.3)))
expect_identical(eval(e1), eval(demagrittr(e1, FALSE)))
e2 <- quote(filter(iris, Sepal.Width %>% `>`(4.3)))
expect_identical(eval(e2), eval(demagrittr(e2, FALSE)))
})
| context("adhoc dplyr")
suppressMessages(library("magrittr"))
suppressMessages(library("dplyr"))
test_that("equiv value3", {
e1 <- quote(iris %>% filter(Sepal.Width %>% is_greater_than(4.3)))
expect_identical(eval(e1), eval(demagrittr(e1, FALSE)))
e2 <- quote(filter(iris, Sepal.Width %>% is_greater_than(... | mit | R |
fb6e55470b8cca7e53ecf745bf41fc07639ebd58 | Put variance in significance field. | thehyve/heim-SmartR,thehyve/naa-SmartR,agapow/smartr,thehyve/heim-SmartR,thehyve/heim-SmartR,agapow/smartr,thehyve/heim-SmartR,thehyve/naa-SmartR,agapow/smartr,thehyve/naa-SmartR,agapow/smartr | web-app/HeimScripts/heatmap/run.r | web-app/HeimScripts/heatmap/run.r | library(jsonlite)
library(reshape2)
main <- function(max_rows=50){
df <- loaded_variables[[1]] # SmartR does not support multiple HDD nodes yet
if(ncol(df) > 3){
variances <- apply(df[,3:ncol(df)],1,var) # Calculating variance per probe
df["SIGNIFICANCE"] <- variances
df <- df[with(df, order(-SIGNIFIC... | library(jsonlite)
library(reshape2)
main <- function(max_rows=50){
df <- loaded_variables[[1]] # SmartR does not support multiple HDD nodes yet
if(ncol(df) > 3){
variances <- apply(df[,3:ncol(df)],1,var) # Calculating variance per probe
df["variance"] <- variances
df <- df[with(df, order(-variance)), ... | apache-2.0 | R |
1bdef2de0c99fad79226423bedd0c35e6bf33190 | Update installRpackages.r | PascalLike/OSGeoLive,OSGeo/OSGeoLive,astroidex/OSGeoLive,kalxas/OSGeoLive,PascalLike/OSGeoLive,OSGeo/OSGeoLive,PascalLike/OSGeoLive,guygriffiths/OSGeoLive,kalxas/OSGeoLive,OSGeo/OSGeoLive,PascalLike/OSGeoLive,kalxas/OSGeoLive,astroidex/OSGeoLive,kalxas/OSGeoLive,OSGeo/OSGeoLive,OSGeo/OSGeoLive,guygriffiths/OSGeoLive,gu... | app-conf/R/installRpackages.r | app-conf/R/installRpackages.r | core <- c("classInt", "DCluster", "deldir", "geoR", "gstat", "maptools",
"RandomFields", "raster", "RColorBrewer", "rgdal", "sp", "spatstat",
"spdep", "splancs","spgrass6", "rgeos","ncdf", "RSAGA")
#optional <- c("ade4", "adehabitat", "adehabitatHR", "adehabitatHS", "adehabitatLT", "adehabitatMA", "ads", "akima", "ash... | core <- c("classInt", "DCluster", "deldir", "geoR", "gstat", "maptools",
"RandomFields", "raster", "RColorBrewer", "rgdal", "sp", "spatstat",
"spdep", "splancs","spgrass6", "rgeos","ncdf", "RSAGA")
#optional <- c("ade4", "adehabitat", "adehabitatHR", "adehabitatHS", "adehabitatLT", "adehabitatMA", "ads", "akima", "ash... | lgpl-2.1 | R |
6a294ec8324b00540bfd9d0393a1c4fac27a13ef | Add an onDetach todo. | syberia/syberia | R/zzz.r | R/zzz.r | .onAttach <- function(...) {
if (!isTRUE(getOption("syberia.silent"))) {
packageStartupMessage(paste0("Loading ", crayon::red("Syberia"), "...\n"))
}
# We want to initialize a Syberia project in the current working directory
# because 9 times out of 10 this is what the user wants.
#
# However, this h... | .onAttach <- function(...) {
if (!isTRUE(getOption("syberia.silent"))) {
packageStartupMessage(paste0("Loading ", crayon::red("Syberia"), "...\n"))
}
# We want to initialize a Syberia project in the current working directory
# because 9 times out of 10 this is what the user wants.
#
# However, this h... | mit | R |
7163b9a48f640d2f9ca360e2c472f0f23b4e83af | add a todo for smart interpolation test | robertzk/syberiaStructure | inst/tests/test-syberia_models.r | inst/tests/test-syberia_models.r | context('syberia_models')
local({
syberia_objects <- force(syberia_objects)
environment(syberia_objects) <- new.env(parent = environment(syberia_objects))
environment(syberia_objects)$is.syberia_project <- function(...) TRUE
environment(syberia_objects)$file.exists <- function(...) TRUE
environment(syberia_o... | context('syberia_models')
local({
syberia_objects <- force(syberia_objects)
environment(syberia_objects) <- new.env(parent = environment(syberia_objects))
environment(syberia_objects)$is.syberia_project <- function(...) TRUE
environment(syberia_objects)$file.exists <- function(...) TRUE
environment(syberia_o... | mit | R |
8f568546b45952dd20ab7b1eb6043e65120ac6a2 | set size of figures to reduce responsivity problems | 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$plot_feed <- rende... | #coverage/inst/shiny/coverage1/server.r
#andy south 12/5/16
#https://andysouth.shinyapps.io/coverage1/
library(shiny)
#library(devtools)
#install_github('AndySouth/coverage')
library(coverage)
library(png)
shinyServer(function(input, output, session) {
################################
output$plot_feed <- rende... | mit | R |
c1411519e5651f63c0c63b4a9534f5091e9f27e2 | Refactor heatmap making and modularize processing the dataframe. | thehyve/naa-SmartR,agapow/smartr,thehyve/naa-SmartR,thehyve/heim-SmartR,thehyve/heim-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)
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)
}
... | library(gplots)
main <- function(){
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 Row.Label,Bio.marker columns
measurements <- data.matr... | apache-2.0 | R |
3614abb4e122793463f37db1892cf5788ffe0628 | add download section. | akr/clockcount,akr/clockcount | README.rd | README.rd | = clockcount
clockcount access processor specific clock counter.
== Usage
require 'clockcount'
p ClockCount()
== Sample Script to Mesure Clock Speed
% ruby sample.rb
0x18a9c616f16d5
0x18a9caca6f864 1.2640276924433[GHz] 3.97282828038034[day]
0x18a9cf9ac9d9c 1.29211869909757[GHz] 3.88646950425614[da... | = clockcount
clockcount access processor specific clock counter.
== Usage
require 'clockcount'
p ClockCount()
== Sample Script to Mesure Clock Speed
% ruby sample.rb
0x171faf0c3cbed
0x171fb3e46f666 1.30258316772774[GHz]
0x171fb8a2981c2 1.27298907227854[GHz]
0x171fbd7ae77dc 1.30054508000412[GHz]
0x... | bsd-2-clause | R |
a13ec08701ceed17a41cd34693dcc4fb81f1e8de | add in dep_var | syberia/tundra,robertzk/tundra | R/tundra_ensemble.r | R/tundra_ensemble.r | #' Tundra ensemble wrapper
fetch_submodel <- function(model_parameters) {
stopifnot(length(model_parameters) > 0 && is.character(model_parameters[[1]]))
if (!exists(model_fn <- paste0('tundra_', model_parameters[[1]])))
stop("Missing tundra container for keyword '", model_parameters[[1]], "'")
get(model_fn)(m... | #' Tundra ensemble wrapper
fetch_submodel <- function(model_parameters) {
stopifnot(length(model_parameters) > 0 && is.character(model_parameters[[1]]))
if (!exists(model_fn <- paste0('tundra_', model_parameters[[1]])))
stop("Missing tundra container for keyword '", model_parameters[[1]], "'")
get(model_fn)(m... | mit | R |
dd207be399ced6d80a0169bcd288f30c34ec1668 | include commands to recreate empty plot_table.RDS | david-beauchesne/SurveyTool | init.r | init.r | # Run init.r before other scripts
rm(list=ls())
# for use in R console.
# set own relevant directory if working in R console, otherwise ignore if in terminal
setwd("/Users/davidbeauchesne/Dropbox/PhD/Misc/SurveyTool")
# -----------------------------------------------------------------------------
# PROJECT:
# Surv... | # Run init.r before other scripts
rm(list=ls())
# for use in R console.
# set own relevant directory if working in R console, otherwise ignore if in terminal
setwd("/Users/davidbeauchesne/Dropbox/PhD/Misc/SurveyTool")
# -----------------------------------------------------------------------------
# PROJECT:
# Surv... | mit | R |
81232bd349217c71494a87677cdc51cd993fe68c | use yaml::yaml.load_file() instead of servr::jekyll_config() | yutannihilation/allYourFigureAreBelongToUs,yutannihilation/allYourFigureAreBelongToUs,yutannihilation/allYourFigureAreBelongToUs,yutannihilation/allYourFigureAreBelongToUs | knit.r | knit.r | #! /usr/bin/env Rscript
# This script is a forked version of https://github.com/yihui/knitr-jekyll/blob/gh-pages/build.R
"
Usage: knit.r INPUT OUTPUT
" -> doc
opts <- docopt::docopt(doc)
ifile <- opts[["INPUT"]]
ofile <- opts[["OUTPUT"]]
#----------------------------
# fall back on '/' if baseurl is... | #! /usr/bin/env Rscript
# This script is a forked version of https://github.com/yihui/knitr-jekyll/blob/gh-pages/build.R
"
Usage: knit.r INPUT OUTPUT
" -> doc
opts <- docopt::docopt(doc)
ifile <- opts[["INPUT"]]
ofile <- opts[["OUTPUT"]]
#----------------------------
# fall back on '/' if baseurl is... | mit | R |
e59acd2faf385c83e3d9739193eadb89418bc52d | remove init | snoweye/pbdMPI,snoweye/pbdMPI,snoweye/pbdMPI | inst/examples/test_spmd/allgather.r | inst/examples/test_spmd/allgather.r | ### SHELL> mpiexec -np 2 Rscript --vanilla [...].r
suppressMessages(library(pbdMPI, quietly = TRUE))
.comm.size <- comm.size()
.comm.rank <- comm.rank()
N <- 5
x.total <- N * .comm.size
x <- matrix((1:N) + N * .comm.rank, nrow = 1)
y <- allgather(x)
comm.print(y)
y <- allgather(as.integer(x), integer(x.total))
comm.p... | ### SHELL> mpiexec -np 2 Rscript --vanilla [...].r
suppressMessages(library(pbdMPI, quietly = TRUE))
init()
.comm.size <- comm.size()
.comm.rank <- comm.rank()
N <- 5
x.total <- N * .comm.size
x <- (1:N) + N * .comm.rank
y <- allgather(matrix(x, nrow = 1))
comm.print(y)
y <- allgather(as.integer(x), integer(x.total))... | mpl-2.0 | R |
da7a1f281707702b3d4d1a1d1d24504a531da9fd | Add more cleaning techniques | ixaxaar/handyR | clean.r | clean.r |
# Identify the dataset
names(dat) = normVarNames(names(dat))
# Lower case variable names.
vars = names(dat)
target = "rain_tomorrow"
risk = "risk_mm"
id = c("date", "location")
# Ignore the IDs and the risk variable.
ignore = c(id, if (exists("risk")) risk)
# Ignore variables which are completely missing.
mvc = sapp... |
# Identify the dataset
names(dat) <- normVarNames(names(dat))
# Lower case variable names.
vars <- names(dat)
target <- "rain_tomorrow"
risk <- "risk_mm"
id <- c("date", "location")
# Ignore the IDs and the risk variable.
ignore <- c(id, if (exists("risk")) risk)
# Ignore variables which are completely missing.
mvc ... | mit | R |
d654895d59c6d491eea64874840231124033cf33 | remove unnecessary print | robertzk/s3mpi | R/s3store.r | R/s3store.r | #' Store an R object in S3 by key
#'
#' Any type of object that can be serialized as an RDS file
#' is capable of being retrieved using this interface.
#'
#' @export
#' @param obj ANY. An R object to save to S3.
#' @param name character. The S3 key to save to.
#' @param .path character. The S3 prefix, e.g., "s3://yourb... | #' Store an R object in S3 by key
#'
#' Any type of object that can be serialized as an RDS file
#' is capable of being retrieved using this interface.
#'
#' @export
#' @param obj ANY. An R object to save to S3.
#' @param name character. The S3 key to save to.
#' @param .path character. The S3 prefix, e.g., "s3://yourb... | mit | R |
7db04f6b27320a8fc5c5d0f73e83b7a561a8f995 | Correct the example in the comment | rgchris/ren-c,kealist/ren-c,giuliolunati/ren-c,draegtun/ren-c,hostilefork/rebol,codebybrett/ren-c,codebybrett/ren-c,kealist/ren-c,kealist/ren-c,draegtun/ren-c,hostilefork/rebol,giuliolunati/ren-c,giuliolunati/ren-c,giuliolunati/ren-c,giuliolunati/ren-c,rgchris/ren-c,codebybrett/ren-c,hostilefork/rebol,hostilefork/rebol... | src/boot/strings.r | src/boot/strings.r | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "Low-level strings"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2.0.
See: http://www.ap... | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "Low-level strings"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2.0.
See: http://www.ap... | apache-2.0 | R |
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