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
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3a1d99b7f5649e102e3f38278303cd167f684dc8 | add 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 |
6c7011b7c229c5682acf3b868c5f60885532cfc3 | Revert "test" | JerryGuangXu/Spotify-Music-Data-Analysis,JerryGuangXu/Spotify-Music-Data-Analysis,GeorgiaTechGX/Spotify-Music-Data-Analysis,GeorgiaTechGX/Spotify-Music-Data-Analysis | plot.r | plot.r | ## scatterplot matrix example
p16 = ggplot(data=d,aes(x=album_popularity, y=track_popularity)) + geom_point(col=rgb(0,0,215,5,maxColorValue=255), pch=16) + geom_smooth(method=glm,se=TRUE,size=0.5,color="gold") + theme(panel.background = element_blank())
## barplot
ggplot(data=data, aes(fill=Class, y=Track_Num, x=reor... | ## scatterplot matrix exampledddd
p16 = ggplot(data=d,aes(x=album_popularity, y=track_popularity)) + geom_point(col=rgb(0,0,215,5,maxColorValue=255), pch=16) + geom_smooth(method=glm,se=TRUE,size=0.5,color="gold") + theme(panel.background = element_blank())
## barplot
ggplot(data=data, aes(fill=Class, y=Track_Num, x=... | mit | R |
e3c5b328881def42872de27b949de4072b448092 | Add brief description | mrcaps/wikimedia-analysis,mrcaps/wikimedia-analysis,mrcaps/wikimedia-analysis | plot.r | plot.r | #Create some basic summary plots for Wikimedia configuration changes
library(plyr)
library(ggplot2)
library(RColorBrewer)
library(grid)
library(scales)
setwd(dirname(sys.frame(1)$ofile))
theme_update(plot.margin = unit(c(0,0,0,0), "cm"))
times = read.csv("times.csv", header=FALSE)
times$date = as.Date(as.POSIXlt(tim... | library(plyr)
library(ggplot2)
library(RColorBrewer)
library(grid)
library(scales)
setwd(dirname(sys.frame(1)$ofile))
theme_update(plot.margin = unit(c(0,0,0,0), "cm"))
times = read.csv("times.csv", header=FALSE)
times$date = as.Date(as.POSIXlt(times$V1, origin="1970-01-01"), tz="America/New_York")
ggplot(times, aes... | bsd-3-clause | R |
628bba5c64e66d10c531e54312503390de030ac0 | Update sun_data.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/sun_data.r | R/sun_data.r | #' sun_data
#'
#' Calculate solar parameter for a location and a time.
#'
#' @param datetime Datetime in format YYYY-MM-DD HH:MM:SS.
#' @param numeric lat Latitude in decimal degrees.
#' @param numeric lon Longitude in decimal degrees.
#' @param character parameter Six solar parameter are available by name "azimuth",... | #' sun_data
#'
#' Calculate solar parameter for a location and a time.
#'
#' @param datetime Datetime in format YYYY-MM-DD HH:MM:SS.
#' @param numeric lat Latitude in decimal degrees.
#' @param numeric lon Longitude in decimal degrees.
#' @param character parameter Six solar parameter are available by name "azimuth",... | mit | R |
5a05c3a72bf5529050608f313d0198b8ee69da73 | correct to optimize calculation | 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 |
c774dcbb4c605b2bfaa1e5dec7c13c500b06fd19 | add Rcpp to required packages | 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('Rcpp',
'xml2',
'shiny',
... | #
# 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 |
9a9ecb3a93d661d7a90fd87e9b8d683591aa1125 | Disable vioplot install. | ryanlovett/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,ryanlovett/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 |
77d6e995baade6cf63e47f5359442771954d9d5a | Update zzz.r | syberia/syberia | R/zzz.r | R/zzz.r | .onAttach <- function(...) {
load_github_packages(.github_packages)
if (!exists('run')) makeActiveBinding('run', function() build_model, .GlobalEnv)
}
| .onAttach <- function(...) {
load_github_packages(.github_packages)
makeActiveBinding('run', function() build_model, .GlobalEnv)
}
| mit | R |
7abf56f8b3f60820ef5075f1d772b03bae8f67ec | fix arg, list name | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | tests/testthat/test-proxy.r | tests/testthat/test-proxy.r | context("proxy")
test_that("control flow", {
skip_on_os("windows")
# prerequesites
context = rzmq::init.context()
socket = rzmq::init.socket(context, "ZMQ_REP")
port = bind_avail(socket, 50000:55000)
Sys.sleep(0.5)
common_data = list(fun = function(x) x*2, const=list(), export=list(), seed... | context("proxy")
test_that("control flow", {
skip_on_os("windows")
# prerequesites
context = rzmq::init.context()
socket = rzmq::init.socket(context, "ZMQ_REP")
port = bind_avail(socket, 50000:55000)
Sys.sleep(0.5)
common_data = list(fun = function(x) x*2, const=list(), export=list(), seed... | apache-2.0 | R |
356858e12eafd3c340b06a4ab64ac93f2eb3e2ef | 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_gald'
host = 'baza.fmf.uni-lj.si'
user = 'javnost'
password = 'javnogeslo'
db = 'sem2017_zant'
host = 'baza.fmf.uni-lj.si'
user = 'javnost'
password = 'javnogeslo'
| db = 'sem2017_janp'
host = 'baza.fmf.uni-lj.si'
user = 'javnost'
password = 'javnogeslo' | mit | R |
3482364ab50713a199ce9c9f34a520e552e2949e | update tiles info | khufkens/daymetr | R/data.r | R/data.r | #' tile_outlines
#'
#' Large simple feature collection containing the outlines of all the
#' Daymet tiles available as well as projection information. This data
#' was converted from a shapefile as provided on the Daymet main website.
#'
#' @format SpatialPolygonDataFrame
#' \describe{
#' \item{TileID}{tile ID numb... | #' tile_outlines
#'
#' Large SpatialPolygonDataFrame containing the outlines of all the
#' Daymet tiles available as well as projection information. This data
#' was converted from a shapefile as provided on the Daymet main website.
#'
#' @format SpatialPolygonDataFrame
#' \describe{
#' \item{TileID}{tile ID number... | agpl-3.0 | R |
b82cb6ea04f9cc239d3fd26d70bb5bec0f1ff1d2 | Update slavicreview.r | YaleDHLab/lab-workshops,YaleDHLab/lab-workshops,YaleDHLab/lab-workshops,YaleDHLab/lab-workshops,YaleDHLab/lab-workshops | rstudio_dfrtopics/slavicreview.r | rstudio_dfrtopics/slavicreview.r | # download:
https://yale.box.com/s/icu69vs2m7ygww38lor7d3laoibpfk6x
#Create a new project in the folder that has the JSTOR data.
install.packages("devtools")
library(devtools)
install_github("agoldst/dfrtopics")
install.packages("dplyr")
install.packages("ggplot2")
install.packages("lubridate")
install.packages("stri... | # download:
https://yale.box.com/s/icu69vs2m7ygww38lor7d3laoibpfk6x
#Create a new project in the folder that has the JSTOR data.
install.packages("devtools")
install_github("agoldst/dfrtopics")
install.packages("dplyr")
install.packages("ggplot2")
install.packages("lubridate")
install.packages("stringr")
install.pack... | mit | R |
ba1b4e01898108de79645f0b285ecdc143d17257 | Update slavicreview.r | YaleDHLab/lab-workshops,YaleDHLab/lab-workshops,YaleDHLab/lab-workshops,YaleDHLab/lab-workshops,YaleDHLab/lab-workshops | rstudio_dfrtopics/slavicreview.r | rstudio_dfrtopics/slavicreview.r | # download:
https://yale.box.com/s/icu69vs2m7ygww38lor7d3laoibpfk6x
#Create a new project in the folder that has the JSTOR data.
install.packages("devtools")
install_github("agoldst/dfrtopics")
install.packages("dplyr")
install.packages("ggplot2")
install.packages("lubridate")
install.packages("stringr")
install.pack... | #Create a new project in the folder that has the JSTOR data.
install.packages("devtools")
install_github("agoldst/dfrtopics")
install.packages("dplyr")
install.packages("ggplot2")
install.packages("lubridate")
install.packages("stringr")
install.packages("rJava")
install.packages("mallet")
library(devtools)
options... | mit | R |
a4d94d17fcca1f02fe34895ae9031150793515ce | Update module cache documentation | 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 |
57193474579d404f25590713089fd17a8aae75bc | Update documents. | snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3 | q3/docs/NewFunction.rd | q3/docs/NewFunction.rd | =begin
=@New
Boolean @New()
==
U蕪gpĐU蕪ɁAReLXgbZ[WVbZ[W̏ꍇTrueAȊȌꍇɂFalseԂ܂BȊO̎Ɏgpꂽꍇɂ͏FalseԂ܂BU蕪Ŋ̃bZ[WU蕪ݒ̏ꍇɁÅgp邱ƂŐVbZ[Wǂf邱Ƃł܂B
==
Ȃ
==G[
*̐ĂȂꍇ
==
Ȃ
==
# VbZ[W
@New()
# ̃bZ[W
@Not(@New())
=end
| =begin
=@New
Boolean @New()
==
U蕪ŐU蕪ŃReLXgbZ[WVbZ[W̏ꍇTrueAȊȌꍇɂFalseԂ܂BU蕪Ŋ̃bZ[WU蕪ݒ̏ꍇɁÅgp邱ƂŐVbZ[Wǂf邱Ƃł܂B
==
Ȃ
==G[
*̐ĂȂꍇ
==
Ȃ
==
# VbZ[Wǂׂ
@New()
=end
| mit | R |
c827073ddae9b67dc1fd4b4c2ef1c2a0a9194162 | Fix mistakes with renaming dtm in load()-function | HIIT/hybra-core,HIIT/hybra-core,HIIT/hybra-core,HIIT/hybra-core,HIIT/hybra-core | hybra/analysis/topicmodel/create_topics.r | hybra/analysis/topicmodel/create_topics.r | source('topics.r')
##source('stm.r')
args <- commandArgs(trailingOnly = TRUE)
dtm_path <- args[1]
if( ! grepl( '.rdata', dtm_path ) ) {
dtm_path <- paste( dtm, 'dtm.rdata', sep='' )
}
load( dtm_path )
k <- as.integer( args[2] )
model <- create_model( dtm , k )
path <- paste( dtm_path , 'topic-', args[2], '.rd... | source('topics.r')
##source('stm.r')
args <- commandArgs(trailingOnly = TRUE)
dtm <- args[1]
if( ! grepl( '.rdata', dtm ) ) {
dtm <- paste( dtm, 'dtm.rdata', sep='' )
}
load( dtm )
k <- as.integer( args[2] )
model <- create_model( dtm , k )
path <- paste( dtm , '/topic-', args[2], '.rdata' , sep = '' )
save( ... | mit | R |
55d76f43e82a2e09b195f7d19b3d7eeec9793b90 | Update 2013_PR_config.r | PSC-CoTC/PSC-FRAM-Admin,PSC-CoTC/PSC-FRAM-Admin | config/2013_PR_config.r | config/2013_PR_config.r | #note: here "pre.season" means "original BK post-season" for the Periodic Report comparison tables
run.year <- 2013
post.season.fram.db <- "./fram db/PeriodicReportdb/FramVS2-PSC-Coho-Backwards-redo 2010-2016 January 2019 products.mdb"
post.season.run.name <- "bc-bkCoho2013 step 3"
post.season.tamm <- "./fram db/Perio... |
run.year <- 2013
post.season.fram.db <- "./fram db/PeriodicReportdb/FramVS2-PSC-Coho-Backwards-redo 2010-2016 January 2019 products.mdb"
post.season.run.name <- "bc-bkCoho2013 step 3"
post.season.tamm <- "./fram db/PeriodicReportdb/updated2010-2016TAMMfiles/BK 2013 January 2019 redo step 3.xlsm"
post.season.tamm.fish... | mit | R |
828a96417ee339074c6ea55c3c3a81a25528ffd2 | Add the new metric 'virtual-screen-size to doc | giuliolunati/ren-c,codebybrett/ren-c,kealist/ren-c,rgchris/ren-c,rgchris/ren-c,codebybrett/ren-c,rgchris/ren-c,draegtun/ren-c,codebybrett/ren-c,rgchris/ren-c,giuliolunati/ren-c,hostilefork/rebol,hostilefork/rebol,mbk/ren-c,draegtun/ren-c,draegtun/ren-c,kealist/ren-c,hostilefork/rebol,kealist/ren-c,codebybrett/ren-c,giu... | src/boot/graphics.r | src/boot/graphics.r | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL Graphics"
Author: ["Richard Smolak" "Carl Sassenrath"]
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
Additional code modifications and improvements Copyright 2012 Saphirion AG
... | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL Graphics"
Author: ["Richard Smolak" "Carl Sassenrath"]
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
Additional code modifications and improvements Copyright 2012 Saphirion AG
... | apache-2.0 | R |
be5c2f6574d4d73265bd062ca46e0e610e061090 | use get_dim_plot | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/seurat_group_umap.r | lib/scRNA/seurat_group_umap.r | rm(list=ls())
outFile='AK6383'
parSampleFile1='fileList1.txt'
parSampleFile2=''
parSampleFile3=''
parFile1='C:/projects/nobackup/kirabo_lab/shengq2/20220506_6383_scRNA_human/seurat_merge_03_choose_res/result/AK6383.final.rds'
parFile2=''
parFile3=''
setwd('C:/projects/nobackup/kirabo_lab/shengq2/20220506_6383_scRNA_... | rm(list=ls())
outFile='AK6383'
parSampleFile1='fileList1.txt'
parSampleFile2=''
parSampleFile3=''
parFile1='C:/projects/nobackup/kirabo_lab/shengq2/20220506_6383_scRNA_human/seurat_merge_03_choose_res/result/AK6383.final.rds'
parFile2=''
parFile3=''
setwd('C:/projects/nobackup/kirabo_lab/shengq2/20220506_6383_scRNA_... | apache-2.0 | R |
5cbe21f1db413c853b692f15644f0b615f5e96a0 | Fix the variable names for usr and sys max times | fpavageau/poor-man-pidstat,fpavageau/poor-man-pidstat | pmtimes.r | pmtimes.r | #!/usr/bin/env r
# Copyright 2014 Frank Pavageau
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | #!/usr/bin/env r
# Copyright 2014 Frank Pavageau
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | apache-2.0 | R |
9b9f7c464da352b6ba010d1c880d881bdaeed577 | Update 2016_PR_config.r | PSC-CoTC/PSC-FRAM-Admin,PSC-CoTC/PSC-FRAM-Admin | config/2016_PR_config.r | config/2016_PR_config.r | #note: here "pre.season" means "original BK post-season" for the Periodic Report comparison tables
run.year <- 2016
post.season.fram.db <- "./fram db/PeriodicReportdb/FramVS2-PSC-Coho-Backwards-redo 2010-2016 January 2019 products.mdb"
post.season.run.name <- "bc-bkCoho2016 step 2"
post.season.tamm <- "./fram db/... |
run.year <- 2016
post.season.fram.db <- "./fram db/PeriodicReportdb/FramVS2-PSC-Coho-Backwards-redo 2010-2016 January 2019 products.mdb"
post.season.run.name <- "bc-bkCoho2016 step 2"
post.season.tamm <- "./fram db/PeriodicReportdb/updated2010-2016TAMMfiles/BK 2016 January 2019 redo.xlsm"
post.season.tamm.fishe... | mit | R |
2c593fc65a7debfae12a6723cb2d3a07ffd41a9e | Fix bug in GSEA DE | klmr/codons,klmr/codons | scripts/gsea.r | scripts/gsea.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
gsea_de = function (data, col_data, contrast, go_genes) {
stopifnot(inherits(go_... | 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
gsea_de = function (data, col_data, contrast, go_genes) {
stopifnot(inherits(go_... | apache-2.0 | R |
2c031551fc49828983a58d1dcc18d7c076c9ad84 | add dbh to output dataframe | benquist/Peru_Analyses,benquist/Peru_Analyses | per_tree_chem.r | per_tree_chem.r | library(gemtraits)
con = connect_gemtraits_db()
photosyn = get_photosyn(con)
library(plyr)
per_tree_chem = ddply(photosyn, .(tree_id), summarize, mean_c_percent = mean(c_percent, na.rm = T),
mean_n_percent = mean(n_percent, na.rm = T),
... | library(gemtraits)
con = connect_gemtraits_db()
photosyn = get_photosyn(con)
library(plyr)
per_tree_chem = ddply(photosyn, .(tree_id), summarize, mean_c_percent = mean(c_percent, na.rm = T),
mean_n_percent = mean(n_percent, na.rm = T))
| mit | R |
640cfc1808af24a78da7994b48996ec4705636a2 | scale essential genes | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/seurat_harmony.r | lib/scRNA/seurat_harmony.r | library(dplyr)
library(Seurat)
library(ggplot2)
library(ggpubr)
library(DT)
library(data.table)
library(cowplot)
library(scales)
library(stringr)
library(harmony)
library(patchwork)
require(data.table)
options(future.globals.maxSize= 10779361280)
random.seed=20200107
options_table<-read.table(parSampleFile1, sep="\t"... | library(dplyr)
library(Seurat)
library(ggplot2)
library(ggpubr)
library(DT)
library(data.table)
library(cowplot)
library(scales)
library(stringr)
library(harmony)
library(patchwork)
require(data.table)
options(future.globals.maxSize= 10779361280)
random.seed=20200107
options_table<-read.table(parSampleFile1, sep="\t"... | apache-2.0 | R |
3069f7a5c43e2787da696c7302f6247e1f7b3c08 | Update mtcars.r | bgweber/RServer,bgweber/RServer,bgweber/RServer,bgweber/RServer | tasks/userDemo/mtcars.r | tasks/userDemo/mtcars.r | str(mtcars)
print("Sleeping for 15 seconds")
Sys.sleep(15)
print("Saving RData file")
dir.create("/var/www/html/RServer/reports/mtcars")
save(mtcars, file = "/var/www/html/RServer/reports/mtcars/mtcars.RData")
fit <- lm(mpg~am + wt + hp, data = mtcars)
summary(fit)
print("Saving Model")
Sys.sleep(10)
save(fit, ... | str(mtcars)
print("Sleeping for 20 seconds")
Sys.sleep(15)
print("Saving RData file")
dir.create("/var/www/html/RServer/reports/mtcars")
save(mtcars, file = "/var/www/html/RServer/reports/mtcars/mtcars.RData")
fit <- lm(mpg~am + wt + hp, data = mtcars)
summary(fit)
print("Saving Model")
Sys.sleep(10)
save(fit, ... | bsd-3-clause | R |
6436d90ba31dadad613758a84faaf7527b028339 | Update BlankFilter.r | phnmnl/workflow-demo,phnmnl/workflow-demo,phnmnl/workflow-demo,phnmnl/workflow-demo | BlankFilter/BlankFilter.r | BlankFilter/BlankFilter.r | AdvancedBlankFilter <- function(blanks, samples, cutoff) {
blanks[is.na(blanks)] <- 0
samples[is.na(samples)] <- 0
blanks <- apply(blanks,1,median,na.rm=TRUE)
samples <- apply(samples,1,max,na.rm=TRUE)
to.remove <- which(blanks/samples >= cutoff)
return(to.remove)
}
######################
#
... | AdvancedBlankFilter <- function(blanks, samples, cutoff) {
blanks[is.na(blanks)] <- 0
samples[is.na(samples)] <- 0
blanks <- apply(blanks,1,median,na.rm=TRUE)
samples <- apply(samples,1,max,na.rm=TRUE)
to.remove <- which(blanks/samples >= cutoff)
return(to.remove)
}
######################
#
... | apache-2.0 | R |
70f0e132e9fee7d53448d95c33f3b1b5f4b08071 | Add articles optino to create codingjob | amcat/amcat-r | R/coding.r | R/coding.r | #' Create a new codingjob
#' @param conn the connection object from \code{\link{amcat.connect}}
#' @param project the project to add the articles to
#' @param articleset the article set id of an existing set, or the name of a new set to create
#' @param articlesarticle IDs to be added to this coding job. Ignored if art... | #' Create a new codingjob
#' @param conn the connection object from \code{\link{amcat.connect}}
#' @param project the project to add the articles to
#' @param articleset the article set id of an existing set, or the name of a new set to create
#' @param coder the ID of the coder to assign the job to
#' @param articlesc... | mit | R |
a629326172e914dbccee16d6850c48f68da2bb31 | add tests for overlay | kirillseva/stagerunner,syberia/stagerunner,robertzk/stagerunner,davluangu/stagerunner,davluangu/stagerunner,syberia/stagerunner,robertzk/stagerunner | inst/tests/test-overlay.r | inst/tests/test-overlay.r | context('stageRunner overlaying')
test_that('it can overlay a simple example correctly', {
sr1 <- stageRunner$new(cx <- new.env(), list(a = function(x) x$x <- 1, b = function(y) x$x <- 3))
sr2 <- stageRunner$new(cx, list(a = function(y) y$x <- 2))
sr1$overlay(sr2)
sr1$run(1)
expect_identical(cx$x, 2)
# Ch... | context('stageRunner overlaying')
test_that('it can overlay a complicated example correctly', {
#sr1 <- stageRunner$new(cx <- new.env(), list(c = function(x) x$x <- -1, a = function(x) { x$x <- 1; cat('setting x'); }, b = function(x) { x$x <- 2; cat('setting x to 2') }), remember = T)
#sr2 <- stageRunner$new(cx, l... | mit | R |
37d5164f57ff81adc4ba727b8e55cd4e350ba8c3 | Use sparse matrix to solve scale challenges. | HIIT/digivaalit-2015,HIIT/digivaalit-2015,HIIT/digivaalit-2015 | topics/topics.r | topics/topics.r | create_dtm <- function( path ) {
library(tm)
library(Matrix)
a <- Corpus( DirSource( path ) )
a <- tm_map(a, removeNumbers)
a <- tm_map(a , stripWhitespace)
a <- tm_map(a, removePunctuation)
a <- tm_map(a, content_transformer(tolower) )
a <- tm_map(a, removeWords, stopwords("finnish") )
dtm <-Docum... | 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)
... | mit | R |
a67de282746b7802124813f9413fa52cebd70cd3 | improve analyze-hydra-builds.r | Fuuzetsu/cabal2nix,bennofs/cabal2nix | doc/analyze-hydra-builds.r | doc/analyze-hydra-builds.r | # cabal2nix/doc/analyze-hydra-builds.r
#
# Generate the input file "builds.csv" by running
#
# sudo -u hydra psql -c "Copy (select b.project, b.jobset, b.job, b.timestamp, b.drvpath, b.system, b.buildstatus, b.size, b.closuresize, bs.type, bs.starttime, bs.stoptime, bs.machine from builds b left join buildsteps bs ... | # cabal2nix/doc/analyze-hydra-builds.r
#
# Generate the input file "builds.csv" by running
#
# sudo -u hydra psql -c "Copy (select * from Builds) to stdout With CSV HEADER;" >builds.csv
#
# on Hydra.
library(data.table)
builds <- within(as.data.table(read.csv("builds.csv", header=T, stringsAsFactors=F)), {
ti... | bsd-3-clause | R |
6f3c177f9d903b5e4b89a8763c67207a5911d97c | Remove delay from rulemsiservermonperf so msi is tested | PaulVanSchayck/irods,PaulVanSchayck/irods,PaulVanSchayck/irods,janiheikkinen/irods,janiheikkinen/irods,PaulVanSchayck/irods,janiheikkinen/irods,janiheikkinen/irods,PaulVanSchayck/irods,janiheikkinen/irods,PaulVanSchayck/irods,janiheikkinen/irods,janiheikkinen/irods,janiheikkinen/irods,janiheikkinen/irods,PaulVanSchayck... | iRODS/clients/icommands/test/rules3.0/rulemsiServerMonPerf.r | iRODS/clients/icommands/test/rules3.0/rulemsiServerMonPerf.r | acServerMonPerf {
#This microservice invokes a command in iRODS/server/bin/cmd
# irodsServerMonPerf - a perl script to get monitoring information
msiServerMonPerf("default","default");
msiServerMonPerf("verbose","default");
}
INPUT null
OUTPUT ruleExecOut
| acServerMonPerf {
#This microservice invokes a command in iRODS/server/bin/cmd
# irodsServerMonPerf - a perl script to get monitoring information
delay("<PLUSET>30s</PLUSET>< EF>1h</EF>") {
msiServerMonPerf("default","default");
}
}
INPUT null
OUTPUT ruleExecOut
| bsd-3-clause | R |
531c184cb5dbdcdf45bda2f0fd4ebe230d8945fd | Update tglob_sphere.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/tglob_sphere.r | R/tglob_sphere.r | #' Tglob_sphere
#'
#' Calculate the globe temperature having sphere diameter. The author of procedure is James C. Liljegren Decision and Information Sciences Division Argonne National Laboratory.
#'
#'
#' @param numeric t Air temperature in Celsius degrees.
#' @param numeric rh Air Relative humidity in percentage.
#' ... | #' Tglob_sphere
#'
#' Calculate the globe temperature having sphere diameter. The author of procedure is James C. Liljegren Decision and Information Sciences Division Argonne National Laboratory.
#'
#'
#' @param numeric t Air temperature in Celsius degrees.
#' @param numeric rh Air Relative humidity in percentage.
#' ... | mit | R |
6b098785d980e53576537da63742a55d1fb5ff56 | 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 |
65a6dd85762f0e4a04a1c03ca3bfe108afc20c49 | fix bug | syberia/syberia | R/import_stage.r | R/import_stage.r | #' Import data stage for Syberia model process.
#'
#' @param modelenv an environment. The current modeling environment.
#' @param import_options a list. The available import options. Will differ
#' depending on the adapter. (default is file adapter)
#' @export
import_stage <- function(modelenv, import_options) {
#... | #' Import data stage for Syberia model process.
#'
#' @param modelenv an environment. The current modeling environment.
#' @param import_options a list. The available import options. Will differ
#' depending on the adapter. (default is file adapter)
#' @export
import_stage <- function(modelenv, import_options) {
#... | mit | R |
bb535d378ef9335a89d11b6368ab8240c7b18f36 | add unvotes | berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,ryanlovett/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", "2.0.0",
"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",
"... | bsd-3-clause | R |
84b51dc2236ed7f5a5f5d0aa3b7a3589980868cd | add text and remove custom function | hansthompson/shiny-server,hansthompson/shiny-server,hansthompson/shiny-server | CannabisRetailZoning/App.r | CannabisRetailZoning/App.r | library(rgeos)
library(rgdal)
library(leaflet)
library(geojsonio)
load("map.rda")
ui <- bootstrapPage(title = "Cannabis Cafe Zoning",
tags$head(includeScript("google-analytics.js")),
tags$style(type = "text/css", "html, body {width:100%;height:100%}"),
leafletOutput("map", width = "100%", height = "100%")... | library(rgeos)
library(rgdal)
library(leaflet)
load("map.rda")
spToGeoJSON <- function(x){
tf<-tempfile()
writeOGR(x, tf,layer = "geojson", driver = "GeoJSON")
js <- paste(readLines(tf), collapse=" ")
file.remove(tf)
return(js)
}
ui <- bootstrapPage(
tags$head(includeScript("google-analytics.js")),
... | mit | R |
09adf6547dfcb85efb84296498b531c10ffffabe | Fix for ARM | Pointillistic/rebol-lang,Pointillistic/rebol-lang,zsx/r3,Pointillistic/rebol-lang,Pointillistic/rebol-lang,zsx/r3,zsx/r3,zsx/r3 | make/tests/qsort.r | make/tests/qsort.r | REBOL []
recycle/torture
f: func [
a [integer!] "pointer to an integer"
b [integer!] "pointer to an integer"
][
i: make struct! compose/deep [
[raw-memory: (a)]
int32 i
]
j: make struct! compose/deep [
[raw-memory: (b)]
int32 i
]
case [
i/i = j/i [0... | REBOL []
recycle/torture
f: func [
a [integer!] "pointer to an integer"
b [integer!] "pointer to an integer"
][
i: make struct! compose/deep [
[raw-memory: (a)]
int32 i
]
j: make struct! compose/deep [
[raw-memory: (b)]
int32 i
]
case [
i/i = j/i [0... | apache-2.0 | R |
c1214f211e518a8d99364650dc04ffdae3d6c67d | Convert date times to POSIXct | IndyActuaries/epic-fhir,IndyActuaries/epic-fhir | r/load_data.r | r/load_data.r | #' ## Code Owners: Kyle Baird, Shea Parkes
#'
#' ### Objective:
#' * Load the data for analytics into native R data structures so it is easy to work with
#'
#' ### Developer Notes:
#' * <none>
path.dir.source <- '../data/'
#' ## LIBRARIES, LOCATIONS, LITERALS, ETC. GO ABOVE HERE
df.labs <- read.csv(
paste0(p... | #' ## Code Owners: Kyle Baird, Shea Parkes
#'
#' ### Objective:
#' * Load the data for analytics into native R data structures so it is easy to work with
#'
#' ### Developer Notes:
#' * <none>
path.dir.source <- '../data/'
#' ## LIBRARIES, LOCATIONS, LITERALS, ETC. GO ABOVE HERE
df.labs <- read.csv(
paste0(p... | mit | R |
d81abf05f2b38ff4e924b34bcc6a9c515259455f | remove duplication | robertzk/s3mpi | R/s3read.r | R/s3read.r | #' Read an R object in S3 by key
#'
#' Any type of object that can be serialized as an RDS file
#' is capable of being stored using this interface.
#'
#' @param name character. The key to grab from S3.
#' @param .path. The location of your S3 bucket.
#' @param cache logical. If true, use the local s3cache if available... | #' Read an R object in S3 by key
#'
#' Any type of object that can be serialized as an RDS file
#' is capable of being stored using this interface.
#'
#' @param name character. The key to grab from S3.
#' @param .path. The location of your S3 bucket.
#' @param cache logical. If true, use the local s3cache if available... | mit | R |
96894fb35ba768446ca32b7d44e6be74dc8cd161 | 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 |
7e90a2a4fa714fa056a837e6b73d75a91fe84eba | save rds for chipqc | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/QC/ChipseqQC.r | lib/QC/ChipseqQC.r | options(bitmapType='cairo')
options(expressions=102400)
args = commandArgs(trailingOnly = TRUE)
library(ChIPQC)
library(BiocParallel)
if(length(args) > 0){
configFile=args[1]
annotationName=args[2]
chromosomes=args[3]
}else{
configFile=r"(C:\projects\jonathan_brown\20210321_cutrun_6048_human\macs2callpeak_na... | options(bitmapType='cairo')
options(expressions=102400)
args = commandArgs(trailingOnly = TRUE)
library(ChIPQC)
library(BiocParallel)
if(length(args) > 0){
configFile=args[1]
annotationName=args[2]
chromosomes=args[3]
}else{
configFile=r"(C:\projects\jonathan_brown\20210321_cutrun_6048_human\macs2callpeak_na... | apache-2.0 | R |
ab3746193d502d91589ac4ed09951421134ea745 | update demo code | GilbertWatson/itsd-demo-project | mutliprocessingdemo.r | mutliprocessingdemo.r | require(snowfall)
#make some fake data
x <- data.frame(one = sample(x = seq(1, 100, 1),size = 2000000, replace = T),
two = sample(x = seq(1, 100, 1),size = 2000000, replace = T),
three = sample(x = seq(1, 100, 1),size = 2000000, replace = T),
four = sample(x = seq(1, 100... | require(snowfall)
#make some fake data
x <- data.frame(one = sample(x = seq(1, 100, 1),size = 2000, replace = T),
two = sample(x = seq(1, 100, 1),size = 2000, replace = T),
three = sample(x = seq(1, 100, 1),size = 2000, replace = T),
four = sample(x = seq(1, 100, 1),size... | mit | R |
aac27a9352becc76ce02d641648ea0ab89b70de6 | Fix instance where a vector might be used in an if clause | matijapretnar/projekt-tomo,ul-fmf/projekt-tomo,matijapretnar/projekt-tomo,matijapretnar/projekt-tomo,ul-fmf/projekt-tomo,matijapretnar/projekt-tomo,ul-fmf/projekt-tomo,ul-fmf/projekt-tomo,ul-fmf/projekt-tomo,matijapretnar/projekt-tomo,ul-fmf/projekt-tomo | web/problems/templates/r/library.r | web/problems/templates/r/library.r | {% load i18n %}.error <- FALSE
.errfun <- function(e) {
warning(e)
.error <<- TRUE
}
tryCatch({
library(rjson)
}, error = .errfun)
tryCatch({
library(httr)
}, error = .errfun)
if (.error) {
stop("{% trans 'Required libraries are unavailable. Please make sure that rjson and httr are available.' %}")... | {% load i18n %}.error <- FALSE
.errfun <- function(e) {
warning(e)
.error <<- TRUE
}
tryCatch({
library(rjson)
}, error = .errfun)
tryCatch({
library(httr)
}, error = .errfun)
if (.error) {
stop("{% trans 'Required libraries are unavailable. Please make sure that rjson and httr are available.' %}")... | agpl-3.0 | R |
973c83c6d927e0c7d1743bde851bd92aaa509cf5 | Add further path testing helper | klmr/modules,klmr/modules | inst/tests/helper-paths.r | inst/tests/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 |
955f79a7fc6c9ef0aa3533495bb7baa6615b5250 | add evaluation of similarity between resources based on set of consumers | 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 |
88893b7d4bdba03ef93491678ef1d5bd0322da34 | Update Corselect_Perch.r | awhitten/corselect | Examples/Corselect_Perch.r | Examples/Corselect_Perch.r | ################################################################################################
#
# Corselect.r - Simultaneous estimation of selectivity parameters for Gillnets & Cormorants
# Application to European Perch Data from Curonian Lagoon, Lithuania
#
# by Athol Whitten (awhitten@gmail.com)
# Melbourne, A... | ################################################################################################
#
# Corselect.r - Simultaneous estimation of selectivity parameters for Gillnets & Cormorants
# Application to European Perch Data from Curonian Lagoon, Lithuania
#
# by Athol Whitten (awhitten@gmail.com)
# Melbourne, A... | bsd-2-clause | R |
2322f1d7d467d7555ea56a029b9ea99c0c5ffbac | 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 |
80f818bc63b50b0b46e78872231b1178e93e1ccb | Fix multivariate sim code. | jtobin/bnp | finite-gaussian-mixture/src/simulation_multivariate.r | finite-gaussian-mixture/src/simulation_multivariate.r | require(ggplot2)
require(reshape2)
require(scatterplot3d)
source('fmm_multivariate_generative.r')
# 2d
config = list(
k = 4
, l = rep(0, 2)
, r = diag(0.05, 2)
, b = 2
, w = diag(1, 2)
, n = 10000
)
set.seed(42)
d = model(
config$k, config$l, config$r
, config$b, config$w, config$n
)
frame... | require(ggplot2)
require(reshape2)
require(scatterplot3d)
source('fmm_multivariate_generative.r')
# 2d
config = list(
m = 2
, v = 2
, k = 4
, n = 10000
)
set.seed(42)
d = model(config$m, config$k, config$v, config$n)
framed = lapply(d, function(mat) { data.frame(x = mat[,1], y = mat[,2]) })
melted... | mit | R |
e459985b72c44719cb985372385a6c8bf97b6e87 | Update vivo.query.r | mconlon17/vivo-r,mconlon17/vivo-r | sparql/vivo.query.r | sparql/vivo.query.r | vivo.query <- function(query, endpoint= 'http://localhost:8080/vivo/api/sparqlQuery',
email= 'vivo_root@school.edu', password= '*******', format="tsv",
ns = c(
"rdf","<http://www.w3.org/1999/02/22-rdf-syntax-ns#>",
"rdfs","<http://www.w3.org/2000/01/rdf-schema#>",
"xsd","<http://www.w3.org/2001/XMLSchem... | vivo.query <- function(query, endpoint= 'http://localhost:8080/vivo/api/sparqlQuery',
email= 'vivo_root@school.edu', password= 'v;bisons', format="tsv",
ns = c(
"rdf","<http://www.w3.org/1999/02/22-rdf-syntax-ns#>",
"rdfs","<http://www.w3.org/2000/01/rdf-schema#>",
"xsd","<http://www.w3.org/2001/XMLSche... | bsd-2-clause | R |
83a85b83cba6a782fd362f262a1d3ee405ff0a3d | Fix R script | NTAP/warpcore,NTAP/warpcore,NTAP/warpcore,NTAP/warpcore | scripts/analyze.r | scripts/analyze.r | #! /usr/bin/env Rscript
if ("data.table" %in% rownames(installed.packages()) == FALSE) {
install.packages("data.table", repos="http://cran.r-project.org")
}
library(data.table)
printf <- function(...) cat(sprintf(...))
import <- function(file) {
dt <- data.table::fread(file)
dt[, nsec:=nsec/1000]
stats <- dt[ord... | #! /usr/bin/env Rscript
if ("data.table" %in% rownames(installed.packages(lib="~/.R")) == FALSE) {
install.packages("data.table", lib="~/.R",
repos="http://cran.r-project.org")
}
library(data.table, lib="~/.R")
printf <- function(...) cat(sprintf(...))
import <- function(file) {
dt <- data.table:... | bsd-2-clause | R |
30ae0ab08469c7eca1aabf8012537b9c1ac72f4b | save rdatafile before report | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/QC/ChipseqQC.r | lib/QC/ChipseqQC.r | options(bitmapType='cairo')
options(expressions=102400)
args = commandArgs(trailingOnly = TRUE)
library(ChIPQC)
configFile=args[1]
annotationName=args[2]
chromosomes=args[3]
cat("configFile=", configFile, "\n")
cat("annotationName=", annotationName, "\n")
cat("chromosomes=", chromosomes, "\n")
rdatafile = paste0(c... | options(bitmapType='cairo')
options(expressions=102400)
args = commandArgs(trailingOnly = TRUE)
library(ChIPQC)
configFile=args[1]
annotationName=args[2]
chromosomes=args[3]
cat("configFile=", configFile, "\n")
cat("annotationName=", annotationName, "\n")
cat("chromosomes=", chromosomes, "\n")
if(!is.na(chromosome... | apache-2.0 | R |
5ba42c687b3a6f7ff6a425fb7d404b5a0ca7f49e | Fix for ARM | codebybrett/ren-c,rgchris/ren-c,kealist/ren-c,hostilefork/rebol,kealist/ren-c,kealist/ren-c,hostilefork/rebol,mbk/ren-c,giuliolunati/ren-c,rgchris/ren-c,rgchris/ren-c,mbk/ren-c,codebybrett/ren-c,giuliolunati/ren-c,giuliolunati/ren-c,kealist/ren-c,giuliolunati/ren-c,hostilefork/rebol,kealist/ren-c,hostilefork/rebol,code... | make/tests/qsort.r | make/tests/qsort.r | REBOL []
recycle/torture
f: func [
a [integer!] "pointer to an integer"
b [integer!] "pointer to an integer"
][
i: make struct! compose/deep [
[raw-memory: (a)]
int32 i
]
j: make struct! compose/deep [
[raw-memory: (b)]
int32 i
]
case [
i/i = j/i [0... | REBOL []
recycle/torture
f: func [
a [integer!] "pointer to an integer"
b [integer!] "pointer to an integer"
][
i: make struct! compose/deep [
[raw-memory: (a)]
int32 i
]
j: make struct! compose/deep [
[raw-memory: (b)]
int32 i
]
case [
i/i = j/i [0... | apache-2.0 | R |
d714c6ed29b6f0876ad38db66351f81ac6efa298 | Call the SSL wrappers to access annotations instead of directly calling the AT variants: no annotations is equivalent to the empty list of annotations. Has-annotation tests whether the result of get-annotations is not the empty list. | metaborg/strategoxt,Apanatshka/strategoxt,Apanatshka/strategoxt,lichtemo/strategoxt,metaborg/strategoxt,metaborg/strategoxt,metaborg/strategoxt,lichtemo/strategoxt,Apanatshka/strategoxt,lichtemo/strategoxt,Apanatshka/strategoxt,lichtemo/strategoxt,metaborg/strategoxt,Apanatshka/strategoxt,lichtemo/strategoxt | ssl/spec/annotations.r | ssl/spec/annotations.r | \literate[annotations]
\begin{abstract}
This module defines primitives for getting and setting term
annotations. The preferred way to access annotations, however,
is through the term syntax t1{t2}, which allows matching and
building terms with annotations.
\end{abstract}
\begin{code}
module annotations
signat... | \literate[annotations]
\begin{abstract}
This module defines primitives for getting and setting term
annotations. The preferred way to access annotations, however,
is through the term syntax t1{t2}, which allows matching and
building terms with annotations.
\end{abstract}
\begin{code}
module annotations
signat... | apache-2.0 | R |
596ba93582e4633294cbb6d5c2a32d00d74bf12a | 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 |
7a19887e63223b3fc7659b86b399b8b199d650ee | Check edge case in compare_stage_keys | davluangu/stagerunner,robertzk/stagerunner,syberia/stagerunner,robertzk/stagerunner,kirillseva/stagerunner,davluangu/stagerunner,syberia/stagerunner | tests/testthat/test-compare_stage_keys.r | tests/testthat/test-compare_stage_keys.r | context('compare_stage_keys')
test_that("it gives FALSE when keys are incomparable", {
expect_false(compare_stage_keys("1/1", FALSE))
expect_false(compare_stage_keys(FALSE, "1/1"))
})
test_that("it gives TRUE when keys are identical", {
expect_true(compare_stage_keys(c(FALSE, TRUE), c(FALSE, TRUE)))
})
test_th... | context('compare_stage_keys')
test_that("it gives FALSE when keys are incomparable", {
expect_false(compare_stage_keys("1/1", FALSE))
expect_false(compare_stage_keys(FALSE, "1/1"))
})
test_that("it gives TRUE when keys are identical", {
expect_true(compare_stage_keys(c(FALSE, TRUE), c(FALSE, TRUE)))
})
test_th... | mit | R |
bbebfb9945db553728776afb3a205ded7a60a486 | Add na.rm = T to prevent NAs in variance calculation. | thehyve/heim-SmartR,thehyve/naa-SmartR,thehyve/heim-SmartR,thehyve/heim-SmartR,agapow/smartr,thehyve/heim-SmartR,agapow/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, na.rm = T) # Calculating variance per probe
df["SIGNIFICANCE"] <- variances
df["MEAN"] <- rowMeans... | 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["MEAN"] <- rowMeans(df[,3:ncol... | apache-2.0 | R |
e1ba1754465b857ba38c89698e905a621da4f506 | Update wbgt_full.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/wbgt_full.r | R/wbgt_full.r | #' wbgt_full
#'
#' Calculate wet bulb globe temperature index for outdoor environements by using globometric temperature and air pressure in hPa ( millibars).
#'
#
#' @param numeric t Air temperature in Celsius degrees.
#' @param numeric rh Air Relative humidity in percentage.
#' @param numeric tg Solar Radiation Radi... | mit | R | |
68462cee34fe6d4e91a67d917bc3de875a4f11c3 | Update vizualizacija.r | GalDrnovsek/APPR-2015-16 | vizualizacija/vizualizacija.r | vizualizacija/vizualizacija.r | # 3. faza: Izdelava zemljevida
# Uvozimo zemljevid.
#zemljevid <- uvozi.zemljevid("http://e-prostor.gov.si/fileadmin/BREZPLACNI_POD/RPE/OB.zip",
# "OB/OB", encoding = "Windows-1250")
# Preuredimo podatke, da jih bomo lahko izrisali na zemljevid.
#druzine <- preuredi(druzine, zemljevid, "OB... | # 3. faza: Izdelava zemljevida
# Uvozimo zemljevid.
#zemljevid <- uvozi.zemljevid("http://e-prostor.gov.si/fileadmin/BREZPLACNI_POD/RPE/OB.zip",
# "OB/OB", encoding = "Windows-1250")
# Preuredimo podatke, da jih bomo lahko izrisali na zemljevid.
#druzine <- preuredi(druzine, zemljevid, "OB... | mit | R |
68506421ae0f10bc876c36ff6e827637c206283b | Use standard format for function names | lmullen/religious-statistics,lmullen/demographics-religion,lmullen/demographics-religion,lmullen/religious-statistics | functions/get.year.r | functions/get.year.r | # Function to get the year from our data, using lubridate
# Lincoln A. Mullen | lincoln@lincolnmullen.com | http://lincolnmullen.com
# MIT License <http://lmullen.mit-license.org/>
get_year <- function(date.string) {
require(lubridate)
result <- year(mdy(as.character(date.string)))
return(result)
}
| # Function to get the year from our data, using lubridate
# Lincoln A. Mullen | lincoln@lincolnmullen.com | http://lincolnmullen.com
# MIT License <http://lmullen.mit-license.org/>
get.year <- function(date.string) {
require(lubridate)
result <- year(mdy(as.character(date.string)))
return(result)
}
| mit | R |
c5f7478f6fb25fb9ef392b7e03b19222cda0febd | Remove slurm submission script SBATCH comments | 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 |
64aa2290de7cfd405c7829b8c8a942cb673d7f0c | change hard coded size to param with 1000 as default | wkmor1/voiWoodland | R/sens_prepost_BI.r | R/sens_prepost_BI.r | sens_prepost_BI <- function(dir, newdata, manage, param, n, size=1000, px=FALSE, verbose=FALSE) {
sensitivity_BI_obj <- vector('list', n)
preposts <- lapply(param,
function(x) pre_posterior(newdata[[manage]][, x], n, size)
)
for (i in seq_len(n)) {
inputs <- newdata
for (m i... | sens_prepost_BI <- function(dir, newdata, manage, param, n, verbose=FALSE) {
sensitivity_BI_obj <- vector('list', n)
preposts <- lapply(param,
function(x) pre_posterior(newdata[[manage]][, x], n, 1000)
)
for (i in seq_len(n)) {
inputs <- newdata
for (m in seq_along(param)) {... | mit | R |
63be0462c8923f6c0fca29943d56fe4531290162 | Remove explicit dependencies. | ryanlovett/datahub,ryanlovett/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,ryanlovett/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",
"barcode", "1.1", # dependency of gpairs
"vcd", "1.4-4", # dependency of gpairs
"gpairs", "1.2... | bsd-3-clause | R |
cae635c349c089582988c4bbdcd4693a90beee60 | Handle negative numbers >-1000 & < 0 | 1R151-1/R,fdryan/R | ggplot2_formatter.r | ggplot2_formatter.r | require(plyr)
require(scales)
# ---------------------------------------------------------------------------------------------
# Formatting functions for ggplot graph axis
# ---------------------------------------------------------------------------------------------
#' Human Numbers: Format numbers so they're legibl... | require(plyr)
require(scales)
# ---------------------------------------------------------------------------------------------
# Formatting functions for ggplot graph axis
# ---------------------------------------------------------------------------------------------
#' Human Numbers: Format numbers so they're legibl... | unlicense | R |
56dd63380765f7f0ede5b2d2b4f9129001aa6612 | fix indentation | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | R/create_worker_pool.r | R/create_worker_pool.r | #' Sets up workers for use in clustermq
#'
#' @param n_jobs Number of jobs to submit
#' @param data Set common data (function, constant args, seed)
#' @param template A named list of values to fill in template
#' @param log_worker Write a log file for each worker
#' @return An instance of the... | #' Sets up workers for use in clustermq
#'
#' @param n_jobs Number of jobs to submit
#' @param data Set common data (function, constant args, seed)
#' @param template A named list of values to fill in template
#' @param log_worker Write a log file for each worker
#' @return An instance of the... | apache-2.0 | R |
43a10f75184297681717499600ce38f162d3db3b | Add convience function to get s values | klmr/codons,klmr/codons | scripts/tai.r | scripts/tai.r | # Based on the paper by Dos Reis & al, 2004
s = list(naive = c(0, 0, 0, 0, 0.5, 0.5, 0.75, 0.5, 0.5, 0.5),
ecoli = c(0, 0, 0, 0, 0.41, 0.28, 0.9999, 0.68, 0.89))
get_s = function (species)
if (species %in% names(s)) s[[species]] else s$naive
# Reverse complement of the anticodons, in the order of antico... | # Based on the paper by Dos Reis & al, 2004
s = list(naive = c(0, 0, 0, 0, 0.5, 0.5, 0.75, 0.5, 0.5, 0.5),
ecoli = c(0, 0, 0, 0, 0.41, 0.28, 0.9999, 0.68, 0.89))
# Reverse complement of the anticodons, in the order of anticodons as given in
# Figure 1 of dos Reis & al.
rc_anticodons = c('TTT', 'TTC', 'TTA', ... | apache-2.0 | R |
060d5c2be510762a1a83426099fabfef171c5256 | Update utci_class7.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/utci_class7.r | R/utci_class7.r | #' utci_class7
#'
#' Calculate seven thermal classes 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 temperatur... | #' utci_class7
#'
#' Calculate seven thermal classes 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 temperatur... | mit | R |
9e0a1490d1e7fd9e17199897cefe24224c8f3576 | Refactor plotting code to a function | gadomski/rivlib-utils | scripts/chart-inclinations.r | scripts/chart-inclinations.r | library(ggplot2)
library(reshape2)
filenames <- c("Zuma/140123_202748_inclinations.txt",
"Zuma/140201_185848_inclinations.txt",
"Zuma/140226_163837_inclinations.txt",
"EastWall/140123_180026_inclination.txt",
"EastWall/140201_205741_inclination.txt")
plotInc... | library(ggplot2)
library(reshape2)
filenames <- c("140123_202748_inclinations.txt",
"140201_185848_inclinations.txt",
"140226_163837_inclinations.txt")
FILENAME_INDEX <- 3
inclinations <- read.csv(paste0("~/Code/rivlib-development/data/Zuma/", filenames[FILENAME_INDEX]))
inclinations <- ... | mit | R |
f4f7927f58bc372eb8e722ea1269a54bce3dd366 | Bump stat20data as in #2881. | 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", "2.2.0",
"infer", "1.0.0",
"patchwork", "1.1.1",
"tigris", "1.0",
"googlesheets4", "0.2.0",
"xaringanthemer", "0.4.0",
"... | bsd-3-clause | R |
c088e122ba1c591fb1712ef127f6095549c168e8 | Update uvoz_tabela1.r | ZavbiA/APPR-2017 | uvoz/uvoz_tabela1.r | uvoz/uvoz_tabela1.r | #tukaj opravim uvoz tabele iz wikipedije
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(xpat... | #tukaj opravim uvoz tabele iz wikipedije
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(xpat... | mit | R |
9527b9f9d22f6be0320688e580a831d980aa29eb | Fix qsort for 32-bit systems | zsx/r3,zsx/r3,Pointillistic/rebol-lang,Pointillistic/rebol-lang,Pointillistic/rebol-lang,zsx/r3,zsx/r3,Pointillistic/rebol-lang | make/tests/qsort.r | make/tests/qsort.r | REBOL []
recycle/torture
i386?: 4 = fifth system/version
f: func [
a [integer!] "pointer to an integer"
b [integer!] "pointer to an integer"
][
i: make struct! compose/deep [
[raw-memory: (a)]
int32 i
]
j: make struct! compose/deep [
[raw-memory: (b)]
int32 i
]... | REBOL []
recycle/torture
f: func [
a [integer!] "pointer to an integer"
b [integer!] "pointer to an integer"
][
i: make struct! compose/deep [
[raw-memory: (a)]
int32 i
]
j: make struct! compose/deep [
[raw-memory: (b)]
int32 i
]
case [
i/i = j/i [0]... | apache-2.0 | R |
a81570bf68ca2f03c445eb480f28eb56d2306fa6 | Make sure the output is a vector before injecting into raster format. | khufkens/phenor | R/shape_model_output.r | R/shape_model_output.r | #' (re)shape model output based upon the class of the input data
#' and valid model estimates. Mainly, reshapes data to a spatial
#' raster format when required.
#'
#' @param data input data generated using the format_*() functions
#' @param doy phenophase estimates as a doy value
#' @return raster or vector with esti... | #' (re)shape model output based upon the class of the input data
#' and valid model estimates. Mainly, reshapes data to a spatial
#' raster format when required.
#'
#' @param data input data generated using the format_*() functions
#' @param doy phenophase estimates as a doy value
#' @return raster or vector with esti... | agpl-3.0 | R |
56c9b2f22bd89467e55743e83ab1f600295ce72a | Modify path to be consistent with current folder layout | weecology/mete-energy,weecology/mete-energy | dist_par_est.r | dist_par_est.r | library(MASS)
trunc_weibull = function(x, k, lmd, lower_bound){
return (dweibull(x, k, lmd) / (1 - pweibull(lower_bound, k, lmd)))
}
trunc_weibull_par_est = function(x, lower_bound){
trunc_weibull_lb = function(x, k, lmd){
return (trunc_weibull(x, k, lmd, lower_bound))
}
weibull_est = as.numeric((fitdistr... | library(MASS)
trunc_weibull = function(x, k, lmd, lower_bound){
return (dweibull(x, k, lmd) / (1 - pweibull(lower_bound, k, lmd)))
}
trunc_weibull_par_est = function(x, lower_bound){
trunc_weibull_lb = function(x, k, lmd){
return (trunc_weibull(x, k, lmd, lower_bound))
}
weibull_est = as.numeric((fitdistr... | mit | R |
81b84ea421d0216c32a645ad6e08a2e8c62af005 | Bump version to prep for 3.1 alpha | zsx/r3,zsx/r3,zsx/r3,Pointillistic/rebol-lang,zsx/r3,Pointillistic/rebol-lang,Pointillistic/rebol-lang,Pointillistic/rebol-lang | src/boot/version.r | src/boot/version.r | 3.0.90.3.1
| 3.0.0.3.1
| apache-2.0 | R |
9a7ccb6c15c7d7ebfb6dad0b32e9853534f257db | improve analyze-hydra-builds.r | bennofs/cabal2nix,Fuuzetsu/cabal2nix | doc/analyze-hydra-builds.r | doc/analyze-hydra-builds.r | # cabal2nix/doc/analyze-hydra-builds.r
#
# Generate the input file "builds.csv" by running
#
# sudo -u hydra psql -c "Copy (select b.project, b.jobset, b.job, b.timestamp, b.drvpath, b.system, b.buildstatus, b.size, b.closuresize, bs.type, bs.starttime, bs.stoptime, bs.machine from builds b left join buildsteps bs ... | # cabal2nix/doc/analyze-hydra-builds.r
#
# Generate the input file "builds.csv" by running
#
# sudo -u hydra psql -c "Copy (select b.project, b.jobset, b.job, b.timestamp, b.drvpath, b.system, b.buildstatus, b.size, b.closuresize, bs.type, bs.starttime, bs.stoptime, bs.machine from builds b left join buildsteps bs ... | bsd-3-clause | R |
46a4681de179ed0c5feac7898b8e0cf115520567 | Fix demagrittr_source() | TobCap/demagrittr | R/demagrittr_source.r | R/demagrittr_source.r | #' Convert R's source file to non \%>\% code.
#' @description read file and convert the code which uses %>%
#' to flatten code
#'
#' @param in_ file path of input.
#' @param out_ file path of output.
#' @param mode transformed mode.
#' @param ask ask to overwrite when `out_`` already exists
#'
#' @return no return. s... | #' Convert R's source file to non \%>\% code.
#' @description read file and convert the code which uses %>%
#' to flatten code
#'
#' @param in_ file path of input.
#' @param out_ file path of output.
#' @param ask ask to overwrite when `out_`` already exists
#'
#' @return no return. side effect on a file.
#'
#' @exam... | mit | R |
6e99d52506bc5fe6451df27a400af8a883c62162 | fix to number of trees in R | ryanbressler/ClassWar,ryanbressler/ClassWar | Rrf.r | Rrf.r |
library("foreign")
library("randomForest")
args<-(commandArgs(TRUE))
train<-read.arff(args[[1]])
test<-read.arff(args[[2]])
target<-args[[3]]
targets = colnames(train)==target
y = train[targets]
x = train[!targets]
ptm <- proc.time()
rf <- randomForest(x,as.factor(y[,1]),ntree=100)
print(cat("Total training tim... |
library("foreign")
library("randomForest")
args<-(commandArgs(TRUE))
train<-read.arff(args[[1]])
test<-read.arff(args[[2]])
target<-args[[3]]
targets = colnames(train)==target
y = train[targets]
x = train[!targets]
ptm <- proc.time()
rf <- randomForest(x,as.factor(y[,1]))
print(cat("Total training time (seconds... | bsd-3-clause | R |
8226f71740f1006d7f15b37a8aa253f0ba3e956a | debug armhf packaging | OwnYourData/app-allergy,OwnYourData/app-allergy | 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 |
547e7f07f44e848c36c6f42831df098c8d83196d | tweak graphics parameters for Figure 2 | khufkens/phenor | analysis/Figure_3_arrow_plot.r | analysis/Figure_3_arrow_plot.r | # Figure 3.
#
# Arrow plot comparing two model optimizations
# and the difference in model output.
# Mean differences are used across different runs within
# a given model.
library(phenor)
# quick comparison with default settings (1 random seed)
comparison = model_comparison(models = c("TT","PTT"),
... | # Figure 3.
#
# Arrow plot comparing two model optimizations
# and the difference in model output.
# Mean differences are used across different runs within
# a given model.
library(phenor)
# quick comparison with default settings (1 random seed)
comparison = model_comparison(models = c("TT","PTT"),
... | agpl-3.0 | R |
edf3e7caf0e84746fac7a970d648a147455f0a3f | comment on model env | syberia/syberia | R/export_stage.r | R/export_stage.r | #' Export stage for Syberia.
#'
#' Precise behavior depends on adapter.
#'
#' @param modelenv an environment. The current modeling environment.
#' @param export_options a list. The available export options. Will differ
#' depending on the adapter. (default is file adapter)
#' @export
export_stage <- function(modele... | #' Export stage for Syberia.
#'
#' Precise behavior depends on adapter.
#'
#' @param modelenv an environment. The current modeling environment.
#' @param export_options a list. The available export options. Will differ
#' depending on the adapter. (default is file adapter)
#' @export
export_stage <- function(modele... | mit | R |
95c79aeba50e56e1e5321c2c5621d687aa005efd | Update documents. | 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">))
AhX̎⊮̑ΏۂɂȂ̂́AAhX̃GgAOAhX荞GgAŋߎgp[AhXłB͂╶̃hCÃGg̖OAhXAAhX̃hCɊ܂܂ƁA⊮p̃hbv_EXg\܂BgpAhXIƓ͒̕ɒu܂B͂̂܂ܑƎIɌ₪i荞܂܂B
AhX̎⊮̓J[\L[̏㉺Xg̑IɎgp܂BXgɂESC܂B
AhXɓo^ĂȂ[AhXɃ[𑗐MƁÃAhXLA̎⊮ɌƂĎgp܂BftHgł͍ŐV10̃AhXL܂BLAhX̌((<qmail.xml|... | =begin
=AhX̎⊮
wb_GfBbgr[ŃAhX͂tB[hł́AAhX̎⊮s܂B
((<AhX̎⊮|"IMG:images/AddressAutoComplete.png">))
AhX̎⊮̑ΏۂɂȂ̂́AAhX̃GgAOAhX荞GgAŋߎgp[AhXłB͂ÃGg̖OAhXɊ܂܂((-ۂɂ́A[AhX̐擪hC̐擪AO̐擪ȂǂɂȂĂꍇ̂-))A⊮p̃hbv_EXg\܂BgpAhXIƓ͒̕ɒu܂B͂̂܂ܑƎIɌ₪i荞܂܂B
AhX̎⊮̓J[\L[̏㉺Xg̑IɎgp܂BXgɂESC܂B
AhXɓo^ĂȂ[AhXɃ[𑗐MƁÃAhXLA̎⊮ɌƂĎgp܂BftHgł͍ŐV10̃AhXL܂B... | mit | R |
4067bd38661b7c77ba18d8c20838c15f78dc25e4 | 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(axis.text.x = element_text(a... | mit | R |
41dd66c5c4884e27ff3d9d3b82e2c590f9774caf | check for DO_CHUNK msg id on worker | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | R/worker.r | R/worker.r | #' R worker submitted as cluster job
#'
#' Do not call this manually, the master will do that
#'
#' @param worker_id The ID of the worker (usually just numbered)
#' @param master The master address (tcp://ip:port)
#' @param memlimit Maximum memory before throwing an error
worker = function(worker_id, master, mem... | #' R worker submitted as cluster job
#'
#' Do not call this manually, the master will do that
#'
#' @param worker_id The ID of the worker (usually just numbered)
#' @param master The master address (tcp://ip:port)
#' @param memlimit Maximum memory before throwing an error
worker = function(worker_id, master, mem... | apache-2.0 | R |
3de7339d8ec37b8a517b674e3ccadc816744a67f | make sizes relative to configurable base_size | infotroph/DeLuciatoR | ggthemes.r | ggthemes.r | theme_ggEHD = function(base_size=18, ...){
(theme_bw(base_size=base_size) %+% theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.ticks.length = unit(-(base_size*0.75), "points"),
axis.ticks.margin = unit((base_size*1.5), "points"),
plot.margin = unit(base_size*c(1,1,1,1), "po... | theme_ggEHD = function(...){
(theme_bw() %+% theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.ticks.length = unit(-0.75, "lines"),
axis.ticks.margin = unit(1.5, "lines"),
plot.margin = unit(c(1,1,1,1), "lines"),
text=element_text( # Can we inherit some of these?
family... | mit | R |
d2f67865a30a5dcecc7a46485abcb4d043af2c8c | Add a few select MIME types | earl/rebol3 | scripts/shttpd.r | scripts/shttpd.r | REBOL [title: "A tiny static HTTP server" author: 'abolka date: 2009-11-04]
code-map: make map! [200 "OK" 400 "Forbidden" 404 "Not Found"]
mime-map: make map! [
"html" "text/html" "css" "text/css" "js" "application/javascript"
"gif" "image/gif" "jpg" "image/jpeg" "png" "image/png"
"r" "text/plain" "r3" "te... | REBOL [title: "A tiny static HTTP server" author: 'abolka date: 2009-11-04]
code-map: make map! [200 "OK" 400 "Forbidden" 404 "Not Found"]
mime-map: make map! ["html" "text/html" "jpg" "image/jpeg" "r" "text/plain"]
error-template: {
<html><head><title>$code $text</title></head><body><h1>$text</h1>
<p>Requeste... | apache-2.0 | R |
4d7ac55d078707651937be777dfc70178863d8c7 | Check range on final scaling parameter e in Rf. | khufkens/phenor | R/DP.r | R/DP.r | #' DormPhot model as defined in
#' Caffarra, Donnelly and Chuine 2011 (Clim. Res.)
#' parameter ranges are taken from Basler et al. 2016
#'
#' @param data input data (see reference for detailed description),
#' data should be formatted using flat_format()
#' @param par a vector of parameter values, this is functions sp... | #' DormPhot model as defined in
#' Caffarra, Donnelly and Chuine 2011 (Clim. Res.)
#' parameter ranges are taken from Basler et al. 2016
#'
#' @param data input data (see reference for detailed description),
#' data should be formatted using flat_format()
#' @param par a vector of parameter values, this is functions sp... | agpl-3.0 | R |
311e65897944028bfd65d74b07f6fc3c1297789e | Make data prep a function | alexbbt/info370final,alexbbt/info370final | data-prep.r | data-prep.r | library(reshape2)
library(zoo)
#################
### Data Prep ###
#################
data.prep <- function(path){
data <- read.csv(path, stringsAsFactors = FALSE)
# Factorize numeric data points
data$floors <- factor(data$floors)
data$waterfront <- as.logical(data$waterfront) # could just be a factor
dat... | library(reshape2)
library(zoo)
#################
### Data Prep ###
#################
data <- read.csv('./data/training.csv', stringsAsFactors = FALSE)
# Factorize numeric data points
data$floors <- factor(data$floors)
data$waterfront <- as.logical(data$waterfront) # could just be a factor
data$view <- factor(data$vi... | mit | R |
8077cd71f153d9e9483f2ece93cd87863f191b39 | allow "file", "filename", "name", and "path" to all reference the same thing | syberia/syberia | R/import_stage.r | R/import_stage.r | #' Import data stage for Syberia model process.
#'
#' @param modelenv an environment. The current modeling environment.
#' @param import_options a list. The available import options. Will differ
#' depending on the adapter. (default is file adapter)
#' @export
import_stage <- function(modelenv, import_options) {
#... | #' Import data stage for Syberia model process.
#'
#' @param modelenv an environment. The current modeling environment.
#' @param import_options a list. The available import options. Will differ
#' depending on the adapter. (default is file adapter)
#' @export
import_stage <- function(modelenv, import_options) {
#... | mit | R |
af13f62da56c902aae5f5257ebf575a3daf7818d | Fix bugs | HIIT/digivaalit-2015,HIIT/digivaalit-2015,HIIT/digivaalit-2015 | topics/check_k.r | topics/check_k.r | source('topics.r')
print( commandArgs(trailingOnly=TRUE) )
for( path in commandArgs(trailingOnly=TRUE) ) {
df = data.frame( k = integer(), ll =integer() )
for( f in list.files(path) ){
load( paste(path, f, sep = '') )
k <- model@k
ll <- check_fitness_model( model )
row = c(k, ll)
df[ nrow(df)+1,]... | source('topics.r')
df = data.frame( k = integer(), ll =integer() )
for( path in commandArgs(trailingOnly=TRUE) ) {
for( f in list.files(path) ){
load( paste(path, f, sep = '') )
k <- model@k
ll <- check_fitness_model( model )
row = c(k, ll)
df[ nrow(df)+1,] <- row
}
print("Examinging", path )
... | mit | R |
b9ae41ea5342b6a8faa499db18cba5b5cfb04962 | Revert "s/#/'/g" | raviqqe/tisp,tisp-lang/tisp,tisp-lang/tisp,raviqqe/tisp,raviqqe/tisp | examples/data.r | examples/data.r | ; Dictionary
(let d {"foo" 1 "bar" 2})
; Set
(let s '{1 2 3})
; List
(let l [1 2 3])
; Array?
;(let l '[1 2 3])
; Closure
(let l '(+ #1 #2))
| ; Dictionary
(let d {"foo" 1 "bar" 2})
; Set
(let s '{1 2 3})
; List
(let l [1 2 3])
; Array?
;(let l '[1 2 3])
; Closure
(let l '(+ '1 '2))
| mit | R |
d6f1dc0ae392f9c0ea05460b32befc172df8dfaf | Add na.strings fix | 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 |
8c915311ebad9b6f6ba904bdb36570579c7e3daf | 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 |
78b66fe1d57650c13849d6a06c5c8fff86c8b419 | 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 |
1b2206ce1d00b8655e8449ca693cb900e15f950b | update get_percentiles_DGAP_all.r with deletion of _A and _B suffix from name column of input file | ibn-salem/position_effect,ibn-salem/position_effect,ibn-salem/position_effect | get_percentiles_DGAP_all.r | get_percentiles_DGAP_all.r | ########################################################################################################################
### Calculate percentiles of phenomatch scores for the analyzed gene values per DGAP case
### Input: phenomatch and max_phenomatch scores file. Remember to delete the _A and _B from the file before ... | ########################################################################################################################
### Calculate percentiles of phenomatch scores for the analyzed gene values per DGAP case
### Input: phenomatch and max_phenomatch scores file. Remember to delete the _A and _B from the file before ... | mit | R |
c0ae89a11d69bc1a1d329a29f17b927beabd2af7 | Make script work with several folders | HIIT/digivaalit-2015,HIIT/digivaalit-2015,HIIT/digivaalit-2015 | topics/check_k.r | topics/check_k.r | source('topics.r')
df = data.frame( k = integer(), ll =integer() )
for( path in commandArgs(trailingOnly=TRUE) ) {
for( f in list.files(path) ){
load( paste(path, f, sep = '') )
k <- model@k
ll <- check_fitness_model( model )
row = c(k, ll)
df[ nrow(df)+1,] <- row
}
print("Examinging", path )
... | source('topics.r')
df = data.frame( k = integer(), ll =integer() )
path <- commandArgs(trailingOnly=TRUE)[0]
for( f in list.files(path) ){
load(f)
k <- model@k
ll <- check_fitness_model( model )
row = c(k, ll)
df[ nrow(df)+1,] <- row
}
print("Best fit log likelihood", which.max( df$ll ) )
print("Best fit k", d... | mit | R |
aca8027422cd95e5241625036afbc1648f902e45 | read obj | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/seurat_doublet_finder.r | lib/scRNA/seurat_doublet_finder.r |
library(Seurat)
library(DoubletFinder)
options(future.globals.maxSize= 10779361280)
random.seed=20200107
min.pct=0.5
logfc.threshold=0.6
options_table<-read.table(parSampleFile1, sep="\t", header=F, stringsAsFactors = F)
myoptions<-split(options_table$V1, options_table$V2)
by_sctransform<-ifelse(myoptions$by_sctran... |
library(Seurat)
library(DoubletFinder)
options(future.globals.maxSize= 10779361280)
random.seed=20200107
min.pct=0.5
logfc.threshold=0.6
options_table<-read.table(parSampleFile1, sep="\t", header=F, stringsAsFactors = F)
myoptions<-split(options_table$V1, options_table$V2)
by_sctransform<-ifelse(myoptions$by_sctran... | apache-2.0 | R |
5db83a8aa19598fa1439c7fb06a7882244f4ef09 | Make thread graph shorter for paper submission. | danluu/BitFunnel,BitFunnel/BitFunnel,BitFunnel/BitFunnel,BitFunnel/BitFunnel,danluu/BitFunnel,BitFunnel/BitFunnel,danluu/BitFunnel,BitFunnel/BitFunnel,BitFunnel/BitFunnel,danluu/BitFunnel,danluu/BitFunnel,danluu/BitFunnel | src/Scripts/plot-qps.r | src/Scripts/plot-qps.r | library("ggplot2")
setwd("~/dev/BitFunnel/src/Scripts")
args = commandArgs(trailingOnly=TRUE)
if (length(args) != 2) {
stop("Required args: inputFilename, outputFilename", call.=FALSE)
}
inputName = args[1]
outputName = args[2]
print("Reading input")
df <- read.csv(header=TRUE, file=inputName)
print("Creating plo... | library("ggplot2")
setwd("~/dev/BitFunnel/src/Scripts")
args = commandArgs(trailingOnly=TRUE)
if (length(args) != 2) {
stop("Required args: inputFilename, outputFilename", call.=FALSE)
}
inputName = args[1]
outputName = args[2]
print("Reading input")
df <- read.csv(header=TRUE, file=inputName)
print("Creating plo... | mit | R |
450cfb97eeb4c378e8729d036abbca64f2ff0a0b | Update test.r | snowch/biginsight-examples,snowch/biginsight-examples | examples/BigR/test.r | examples/BigR/test.r |
# 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.or... |
# 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', li... | apache-2.0 | R |
a6bba11b689c2524268af95a9d5b2c420b87f44e | Copy recursively for source and input files | 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 |
aae69435b61af4957d8b236518f3278ac4c7cf9e | add evaluation of similarity between resources based on set of consumers | david-beauchesne/Predict_interactions | Script/similarity_taxon.r | Script/similarity_taxon.r | #Similarity matrix as a single functions
similarity_taxon <- function(S0, wt, taxa) {
# Note: the similarity on the diagonal has to be set to 1 since it's all the same species.
# taxa is either resource or consumer
similarity.matrix <- matrix(nrow = nrow(S0), ncol = nrow(S0), dimnames = list(S0[, 'taxon'],... | #Similarity matrix as a single functions
similarity_taxon <- function(S0, wt) {
# Note: the similarity on the diagonal has to be set to 1 since it's all the same species.
similarity.matrix <- matrix(nrow = nrow(S0), ncol = nrow(S0), dimnames = list(S0[, 'taxon'], S0[, 'taxon']))
taxonomy <- vector("list",... | mit | R |
b988e8dbe0d7f58aa2a15a01bfe682407cdd7cf2 | Make scale larger. | thomaskrause/graphANNIS,thomaskrause/graphANNIS,thomaskrause/graphANNIS,thomaskrause/graphANNIS,thomaskrause/graphANNIS,thomaskrause/graphANNIS,thomaskrause/graphANNIS | evaluation/evaluate-csv.r | evaluation/evaluate-csv.r | bench_getaql <- function(x, querydir) {
aqlFile <- ""
group <- x[1]
problemSpace = as.numeric(x[2])
if(problemSpace == 0) {
corpus <- sub("_[^_]+$", "", group)
fn <- substr(group, nchar(corpus)+2, nchar(group))
aqlFile <- paste(querydir, "/", corpus,"/", fn, ".aql", sep='')
} else {
aqlFi... | bench_getaql <- function(x, querydir) {
aqlFile <- ""
group <- x[1]
problemSpace = as.numeric(x[2])
if(problemSpace == 0) {
corpus <- sub("_[^_]+$", "", group)
fn <- substr(group, nchar(corpus)+2, nchar(group))
aqlFile <- paste(querydir, "/", corpus,"/", fn, ".aql", sep='')
} else {
aqlFi... | apache-2.0 | R |
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