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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8601930956f902225375148b67aa54cdfe9bd7b4 | Use secure HTTPS CRAN mirror | 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 = 'https://cran.ma.imperial.ac.uk/'),
menu.graphics = FALSE, # Seriously, WHAT THE FUCK, R!?
import.path = '~/.R/modules',
devtools.name = 'Konrad Rudolph',
devtools.des... | options(pager = file.path(Sys.getenv('HOME'), '.R/pager.sh'),
# Imperial College London
repos = c(CRAN = 'http://cran.ma.imperial.ac.uk/'),
menu.graphics = FALSE, # Seriously, WHAT THE FUCK, R!?
import.path = '~/.R/modules',
devtools.name = 'Konrad Rudolph',
devtools.desc... | apache-2.0 | R |
390f66629d807c2ece12b2032c3382972ace402a | Add #!/bin/bash comment to submit bash script | jmousseau/Stain | R/slurm-bash-script.r | R/slurm-bash-script.r | #' SlurmBashScript R6 object.
#'
#' Generates the necessary bash script to submit through
#' the `sbatch` command.
SlurmBashScript <- R6::R6Class("SlurmBashScript",
public = list(
initialize = function(container, main_file, copy_back = c("*")) {
private$cat_main_file_magic(container$dir, main_fi... | #' SlurmBashScript R6 object.
#'
#' Generates the necessary bash script to submit through
#' the `sbatch` command.
SlurmBashScript <- R6::R6Class("SlurmBashScript",
public = list(
initialize = function(container, main_file, copy_back = c("*")) {
private$cat_main_file_magic(container$dir, main_fi... | mit | R |
d49d2cca527265b06f23fc7cc78dfbae95d3d7c9 | Remove completed TODO item | mattm/active-user-cohort-analysis | active-users.r | active-users.r | 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... | 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 |
fb5bcc7c182c803fed74738083e51e22f7fcb25a | Make summaries and use cpi | mkuzak/RIntroBayarea | R/RIntroBayarea.r | R/RIntroBayarea.r | library(plyr)
library(ggplot2)
library(ggmap)
library(dplyr)
library(mgcv)
# read in house sales data
path = system.file(package='RIntroBayarea')
sales_file <- paste0(path, "/extdata/house-sales.csv")
sales <- read.csv(sales_file, stringsAsFactors=FALSE)
# read in geolocation data
ad_file <- paste0(path, '/extdata/ad... | library(plyr)
library(ggplot2)
# read in house sales data
path = system.file(package='RIntroBayarea')
sales_file <- paste0(path, "/extdata/house-sales.csv")
sales <- read.csv(sales_file, stringsAsFactors=FALSE)
# read in geolocation data
ad_file <- paste0(path, '/extdata/addresses.csv')
ad <- read.csv(ad_file, string... | apache-2.0 | R |
841aef5e9879c55ed0b5ce0edbd569be5efdc565 | Add functions to generate test gene sets | klmr/codons,klmr/codons | scripts/translation-efficiency-test-sets.r | scripts/translation-efficiency-test-sets.r | define_relations = function (config) {
all_celltypes = unique(data$mrna_design(config)$Celltype)
healthy_celltypes = intersect(all_celltypes, c('Liver-Adult', 'E15.5'))
cancer_celltypes = setdiff(all_celltypes, healthy_celltypes)
all_relations = expand.grid(Codon = unique(all_celltypes),
... | define_relations = function (config) {
all_celltypes = unique(data$mrna_design(config)$Celltype)
healthy_celltypes = intersect(all_celltypes, c('Liver-Adult', 'E15.5'))
cancer_celltypes = setdiff(all_celltypes, healthy_celltypes)
all_relations = expand.grid(Codon = unique(all_celltypes),
... | apache-2.0 | R |
a0e15c6c5af83a803b2a6ac66978ff3c9efd16a5 | Update 2stations.r | data-henrik/db2-bluemix-r | 2stations.r | 2stations.r | ########### R script to analyze historic weather data for temperature
## Connection handle con to BLU for Cloud data warehouse is provided already
## For plotting, we are using ggplot2 package
##
## Data for multiple stations is shown in different colors
##
library(ggplot2)
library(ibmdbR)
## initialize DB2 connectio... | ########### R script to analyze historic weather data for temperature
## Connection handle con to BLU for Cloud data warehouse is provided already
## For plotting, we are using ggplot2 package
##
## Data for multiple stations is shown in different colors
##
library(ggplot2)
library(bluR)
## initialize DB2 connection ... | apache-2.0 | R |
1e022ab4eb2e24e8a1c91a3d6562c60acdc25be4 | make it also a unix command line script | teuben/astr288p,teuben/astr288p,teuben/astr288p | scripts/linearfit.r | scripts/linearfit.r | #! /usr/bin/env Rscript
#
# This is a script in the R language,
# Adapted from
# http://www.astro.umd.edu/~harris/ASTR610_F16/linearfit.r
#
# To run this within R, start R and type
# source('linearfit.r')
# and a plot should also appear on the screen.
#
# Or from the Unix commandline... | # This is a script in the R language,
# Adapted from
# http://www.astro.umd.edu/~harris/ASTR610_F16/linearfit.r
#
# To run this within R, start R and type
# source('linearfit.r')
# and a plot should also appear on the screen.
#
# Or from the Unix commandline
# Rscript linea... | mit | R |
f2ec23c6d0a01683d12e810b8fcf10915ba54363 | Update runShinyApp.r | xiaodaigh/shinydistro | windows/runShinyApp.r | windows/runShinyApp.r | options(browser = "./GoogleChromePortable/GoogleChromePortable.exe")
.libPaths("./R-Portable/App/R-Portable/library")
shiny::runApp("./yourApp/Shiny/",port=8888,launch.browser=TRUE)
| options(browser = "../../../../Apps/GoogleChromePortable/GoogleChromePortable.exe")
.libPaths("../library")
shiny::runApp("../../../../Apps/your_app/Shiny/",port=8888,launch.browser=TRUE)
| mit | R |
60156f33e3088821a4d8dd9cff5b64d0c2226341 | Fix inconsistency in DESeq col data | 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 |
61ddd576e62385d6a06fb04e97489d83ec54e96b | Update model_stage.r | syberia/syberia | R/model_stage.r | R/model_stage.r | #' Model stage for syberia models
#'
#' TODO: Document this more
#'
#' @param modelenv an environment. The persistent modeling environment.
#' @param model_parameters a list. Model-specific parameters, with the first
#' parameter always being the model keyword for the tundra container
#' (e.g., glm, gbm, etc.)
#... | #' Model stage for syberia models
#'
#' TODO: Document this more
#'
#' @param modelenv an environment. The persistent modeling environment.
#' @param model_parameters a list. Model-specific parameters, with the first
#' parameter always being the model keyword for the tundra container
#' (e.g., glm, gbm, etc.)
#... | mit | R |
055721446695f5d7bca914af3b92a3eafdc3b363 | Update sum-aggr-na.r | SwedishPensionsAgency/Hierarchy | R/sum-aggr-na.r | R/sum-aggr-na.r | #' Aggregate sum function
#'
#' ...
#'
#' @param ... arguments passed to the sum function
#'
#'
#' @export
sum_aggr_na <- function(x) {
if (length(x) == 1 && is.na(x)) {
sum(x, na.rm = FALSE)
} else {
sum(x, na.rm = TRUE)
}
}
| #' Aggregate sum function
#'
#' ...
#'
#' @param ... arguments passed to the sum function
#'
#'
#' @export
sum_aggr_na <- function(...) {
if (length(x) == 1 && is.na(x)) {
sum(..., na.rm = FALSE)
} else {
sum(..., na.rm = TRUE)
}
}
| agpl-3.0 | R |
5229e48d2659717670c83018d4e68c56cc042b92 | Add documentation to exported functions | klmr/ggplots | fonts.r | fonts.r | extrafontdb_path = try(system.file('metrics', package = 'extrafontdb', mustWork = TRUE), silent = TRUE)
# FIXME: Make this work with un-gzipped font metrics as well.
# FIXME: Make this work with incomplete fonts.
complete_font_set = paste0(c('-Regular', '-Bold', '-Italic', '-BoldItalic'), '.afm.gz')
rebuild_cache = fu... | extrafontdb_path = try(system.file('metrics', package = 'extrafontdb', mustWork = TRUE), silent = TRUE)
# FIXME: Make this work with un-gzipped font metrics as well.
# FIXME: Make this work with incomplete fonts.
complete_font_set = paste0(c('-Regular', '-Bold', '-Italic', '-BoldItalic'), '.afm.gz')
rebuild_cache = fu... | apache-2.0 | R |
5d7e63a147d418d6be03671990d970e09712fa91 | Change dates so that they are consistent with used subset of data | 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 |
3548176c6ce28c4861011a17b0f4cd0ccbb5a967 | Fix terra tests | mnpopcenter/ripums,mnpopcenter/ripums | tests/testthat/test_terra.r | tests/testthat/test_terra.r | # Very basic tests for now
context("IPUMS Terra")
# This function helps find the data from the ipumsexamples package for us
ex_file <- function(x) {
system.file("extdata", x, package = "ipumsexamples")
}
test_that("Terra raster works", {
raster_file <- ex_file("2552_bundle.zip")
if (!file.exists(raster_file)) {... | # Very basic tests for now
context("IPUMS Terra")
# This function helps find the data from the ipumsexamples package for us
ex_file <- function(x) {
system.file("extdata", x, package = "ipumsexamples")
}
test_that("Terra raster works", {
raster_file <- ex_file("2552_bundle.zip")
if (!file.exists(raster_file)) {... | mpl-2.0 | R |
013ff0765a61b5c4c6fab4009f6bd73722ff6688 | Update 1.r | glor/R,glor/R | aufgaben/blatt02/1.r | aufgaben/blatt02/1.r | tapply(potato$Ertrag, INDEX=potato$Sorte, FUN=min) # minimum
tapply(potato$Ertrag, INDEX=potato$Sorte, FUN=max) # maximum
tapply(potato$Ertrag, INDEX=potato$Sorte, FUN=median) # median
tapply(potato$Ertrag, INDEX=potato$Sorte, FUN=mean) # mean
tapply(potato$Ertrag, INDEX=potato$Sorte, FUN=sd) # standardabweichung
tappl... | tapply(potato$Ertrag, INDEX=potato$Sorte, FUN=min) # minimum
tapply(potato$Ertrag, INDEX=potato$Sorte, FUN=max) # maximum
tapply(potato$Ertrag, INDEX=potato$Sorte, FUN=median) # median
tapply(potato$Ertrag, INDEX=potato$Sorte, FUN=mean) # mean
tapply(potato$Ertrag, INDEX=potato$Sorte, FUN=sd) # standardabweichung
tappl... | bsd-2-clause | R |
c6b9b1e4e251d12b4bf0a53461167ab15ed91472 | Change “RCU” and “RAA” to “CU” and “AA” in wobble TE | klmr/codons,klmr/codons | scripts/wobble_pairing.r | scripts/wobble_pairing.r | tai = import('./tai')
# Rules for wobble pairing
# Codon Anti i % 4 wobble_match_index
# TTT --- AAA (1, 2) 1 1
# X/
# TTC -/- GAA (1, 2) 2 -1
# /
# TTA --- TAA (1, 3) 3 -2
# /
# TTG --- CAA (3, 4) 0 -1
rc_anticodons = data.frame(Codon = tai$rc_anticodons) %>%
mutate(Or... | tai = import('./tai')
# Rules for wobble pairing
# Codon Anti i % 4 wobble_match_index
# TTT --- AAA (1, 2) 1 1
# X/
# TTC -/- GAA (1, 2) 2 -1
# /
# TTA --- TAA (1, 3) 3 -2
# /
# TTG --- CAA (3, 4) 0 -1
rc_anticodons = data.frame(Codon = tai$rc_anticodons) %>%
mutate(Or... | apache-2.0 | R |
817c035d3e79b4fd732165b686e30aee8abe5a3d | Update aggr-nodes.r | SwedishPensionsAgency/Hierarchy | R/aggr-nodes.r | R/aggr-nodes.r | #' Aggregate by
#'
#' A wrapper function to the path enumeration class to aggregate nodes.
#' The hierarchical data set must have a path enumerated column.
#'
#' @param data data frame
#' @param path column with path enumeration ids
#' @param metrics metric columns
#' @param ids node id (e.g. "1.2.1.3")
#' @param by ... | #' Aggregate by
#'
#' A wrapper function to the path enumeration class to aggregate nodes.
#' The hierarchical data set must have a path enumerated column.
#'
#' @param data data frame
#' @param path column with path enumeration ids
#' @param metrics metric columns
#' @param ids node id (e.g. "1.2.1.3")
#' @param by ... | agpl-3.0 | R |
87433754197c30e4fd1b31ee5049ee11dcf00a59 | Update active_runner.r | syberia/syberia | R/active_runner.r | R/active_runner.r | #' Fetch active stagerunner
#'
#' @export
active_runner <- function() {
syberiaStructure:::get_cache('last_stagerunner')
}
| #' Fetch active stagerunner
#'
#' @export
active_runner <- function() {
get_cache('last_stagerunner')
}
| mit | R |
4d9d2f500122db3d2b0436a235b3344dc0682e84 | Refactor del test Test-Voto | Arguggi/Relazione-Stat | R/test.r | R/test.r | suddividi <- function(lista,punti) {
split(lista,cut(lista,punti))
}
# Test Logica-Matematica
mateRange <- c(-5,19.99,34)
logicaRange <- c(-5,11,22,34)
# Divido i dati a seconda del voto in matematica e logica
logicaDivisi <- split(dati$Matematica,cut(dati$Logica,logicaRange))
test_mate <- sapply(logicaDivisi,s... | suddividi <- function(lista,punti) {
split(lista,cut(lista,punti))
}
# Test Logica-Matematica
mateRange <- c(-5,19.99,34)
logicaRange <- c(-5,11,22,34)
# Divido i dati a seconda del voto in matematica e logica
logicaDivisi <- split(dati$Matematica,cut(dati$Logica,logicaRange))
test_mate <- sapply(logicaDivisi,s... | mit | R |
98b204e5ab50aaa0b2d7448a683096264a2af0dc | verify data exists after uploading with bigr | 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")
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.
airfile <- system.file("extdata", "airline.zip", ... | apache-2.0 | R |
6bfe2e2d4da6e31066cd5fcadb38689d06f65b4e | check tglobe | 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 |
6ddf42d5cf36d59caffd5f6ea8fb59e3f7b0d3d5 | add t/sRNA ratio distribution | wangqinhu/tsRFinder,wangqinhu/tsRFinder,wangqinhu/tsRFinder,wangqinhu/tsRFinder | lib/draw_distribution.r | lib/draw_distribution.r | pdf(file="distribution.pdf", 6, 9)
# read length file
rls<-read.table("srna.len")
rlt<-read.table("trna.len")
rld[1:length(rls$V1),1]<-rls$V1
rld[1:length(rls$V1),2]<-rlt$V2
rld[1:length(rls$V1),3]<-rls$V2 - rlt$V2
# plot
layout(c(1:3))
par(mar=(c(4.5,5,2,1)))
barplot(rls$V2, col=2, main="Length distribution of sRNA re... | pdf(file="distribution.pdf", 6, 6)
# read length file
rls<-read.table("srna.len")
rlt<-read.table("trna.len")
# plot
layout(c(1,2))
par(mar=(c(4.5,5,2,1)))
barplot(rls$V2, col=2, main="Length distribution of sRNA reads", xlab="length (nt)", ylab="Frequency", names.arg=rls$V1)
par(mar=(c(4.5,5,2,1)))
barplot(rlt$V2, col... | mit | R |
7807344ee7d124c74f42c532d9ab35e1330a2971 | check clinical data | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/Annotation/mafReport.r | lib/Annotation/mafReport.r | library(mafreport)
mafFileList = parSampleFile1
reportOutDir = "."
if(parFile1 != ''){
clinicalData = parFile1
}else{
clinicalData = NULL
clinicalFeatures = NULL
}
if(!is.null(interestedGeneStr)) {
interestedGeneStr = gsub("\\s+", ",", interestedGeneStr)
interestedGenes = unlist(strsplit(inte... | library(mafreport)
mafFileList = parSampleFile1
reportOutDir = "."
clinicalData = parFile1
if(!is.null(interestedGeneStr)) {
interestedGeneStr = gsub("\\s+", ",", interestedGeneStr)
interestedGenes = unlist(strsplit(interestedGeneStr, ","))
}else{
interestedGenes = NULL
}
mafFiles = read.table(mafFi... | apache-2.0 | R |
602034c10d1cf01099a99c2ae8eb90365b74631d | use .onUnload, not .Last.Lib | RBigData/pbdADIOS,go-ski/pbdADIOS,RBigData/pbdADIOS,YupingLu/pbdADIOS,go-ski/pbdADIOS,RBigData/pbdADIOS,YupingLu/pbdADIOS,go-ski/pbdADIOS,RBigData/pbdADIOS,YupingLu/pbdADIOS | R/zzz.r | R/zzz.r | .onUnload <- function(libpath)
{
pbdADIOS::adios.finalize(pbdMPI::comm.rank())
}
| #' @export
.Last.lib <- function(libpath){
pbdADIOS::adios.finalize(pbdMPI::comm.rank())
}
| mpl-2.0 | R |
e44b7bb944359551e507d231d3a974ee633265a4 | test working chunk | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | tests/testthat/test-worker.r | tests/testthat/test-worker.r | context("worker")
context = rzmq::init.context()
socket = rzmq::init.socket(context, "ZMQ_REP")
rzmq::bind.socket(socket, "tcp://*:55443")
Sys.sleep(0.5)
start_worker = function(id="1", url="tcp://localhost:55443") {
p = parallel::mcparallel(worker(id, url, 1024))
msg = rzmq::receive.socket(socket)
testth... | context("worker")
context = rzmq::init.context()
socket = rzmq::init.socket(context, "ZMQ_REP")
rzmq::bind.socket(socket, "tcp://*:55443")
Sys.sleep(0.5)
start_worker = function(id="1", url="tcp://localhost:55443") {
p = parallel::mcparallel(worker(id, url, 1024))
msg = rzmq::receive.socket(socket)
testth... | apache-2.0 | R |
cc4820b19dd1be036a6af7f8fca9c74bc0303aa0 | Update ocir_7730.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/ocir_7730.r | R/ocir_7730.r | #' ocir_7730
#'
#' Calculate ocir index consisting in range of clothing insulation 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.
#' @param... | #' ocir_7730
#'
#' Calculate ocir index consisting in range of clothing insulation 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.
#' @param... | mit | R |
59263da3ae3c4bb4f502049ebcb50006303e31ca | Improve glove model | FTAsr/wordvet,FTAsr/wordvet,FTAsr/wordvet,FTAsr/wordvet | trainGloveModel.r | trainGloveModel.r |
##pre-requisites:
#library(devtools)
#load_all("text2vec")
#install("text2vec")
#build("text2vec")
print("started running trainGloveModel.r")
library("text2vec")
text8_file = "/data/wiki.shuffled-norm1-phrase1"
wiki = readLines(text8_file, n = 10000000, warn = FALSE)
# Create iterator over tokens
tokens <- space_... |
##pre-requisites:
#library(devtools)
#load_all("text2vec")
#install("text2vec")
#build("text2vec")
print("started running trainGloveModel.r")
library("text2vec")
text8_file = "/data/wordvet/wiki.shuffled-norm1-phrase1"
wiki = readLines(text8_file, n = 10000000, warn = FALSE)
# Create iterator over tokens
tokens <... | apache-2.0 | R |
ab11d9c78cb4a54955893967affb5b3fbc957944 | Add parameters messed when copypaste | 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(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 |
b626c5b75394fb41ea95691ceec2af7cfbdaa208 | Synchronize string token table with lexer errors | hostilefork/rebol,draegtun/ren-c,rgchris/ren-c,draegtun/ren-c,kealist/ren-c,kealist/ren-c,rgchris/ren-c,hostilefork/rebol,giuliolunati/ren-c,hostilefork/rebol,kealist/ren-c,codebybrett/ren-c,giuliolunati/ren-c,hostilefork/rebol,codebybrett/ren-c,codebybrett/ren-c,codebybrett/ren-c,giuliolunati/ren-c,draegtun/ren-c,rgch... | 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 |
56b3215751ef98ab9609668c06ed42d00858d8cd | Bump version for 3.1 beta | zsx/r3,Pointillistic/rebol-lang,zsx/r3,zsx/r3,Pointillistic/rebol-lang,Pointillistic/rebol-lang,Pointillistic/rebol-lang,zsx/r3 | src/boot/version.r | src/boot/version.r | 3.0.91.3.1
| 3.0.90.3.1
| apache-2.0 | R |
26a69321c78a46cfdbba872ec3e6f5de779f7cea | add tests | TobCap/lambdass,TobCap/lambdass | tests/testthat/test-test.r | tests/testthat/test-test.r | context("test for lambda syntax-sugar")
test_that("test", {
expect_equal(function(x) x, f.(x, x))
expect_equal(function(x, y) x + y, f.(x, y, x + y))
expect_error(f.(x = 1, y = x+1)) # body should not be named
expect_equal(function(..) .., ~~ ..)
expect_equal(function(._1, ._2) ._1 + ._2, ~~ ..1 + ..2... | context("test for lambda syntax-sugar")
test_that("test", {
expect_equal(function(x) x, f.(x, x))
expect_equal(function(x, y) x + y, f.(x, y, x + y))
# expect_equal(function(..) .., ~~ ..)
# expect_equal(function(._1, ._2) ._1 + ._2, ~~ ..1 + ..2)
expect_equal(function(x) x, x %->% x)
expect_equal(fu... | mit | R |
419ceb17e8dc171671dc293c8a9f1d2e5bc3a2be | optimize again, slightly | 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 |
c004cd50118a2942c136913892bcc8b31782e8c9 | Remove browser | tenforwardconsulting/crantastic,hadley/crantastic,tenforwardconsulting/crantastic,hadley/crantastic,tenforwardconsulting/crantastic,hadley/crantastic,tenforwardconsulting/crantastic | lib/r/update.r | lib/r/update.r | source("db.r")
source("package-info.r")
options(warn = 1)
## compare AP to EP and update db if necessary
update.packages <- function() {
known_versions <- load.packages()
latest <- latest.versions()
invisible(lapply(latest, function(pkg) {
try(update.package(pkg, known_versions))
}))
}
update.package <- ... | source("db.r")
source("package-info.r")
options(warn = 1)
## compare AP to EP and update db if necessary
update.packages <- function() {
known_versions <- load.packages()
latest <- latest.versions()
invisible(lapply(latest, function(pkg) {
try(update.package(pkg, known_versions))
}))
}
update.package <- ... | mit | R |
be75ec174377878fa9e08ddb8d1a3d74b4a5e9b0 | Support direct code for interactive R calls | klmr/modules,klmr/modules | tests/testthat/helper-callr.r | tests/testthat/helper-callr.r | rcmd = function (script_path) {
cmd = 'R CMD BATCH --slave --no-restore --no-save --no-timing'
output_file = 'output.rout'
on.exit(unlink(output_file))
system(paste(cmd, script_path, output_file))
readLines(output_file)
}
rscript = function (script_path) {
cmd = 'Rscript --slave --no-restore --... | rcmd = function (script_path) {
cmd = 'R CMD BATCH --slave --no-restore --no-save --no-timing'
output_file = 'output.rout'
on.exit(unlink(output_file))
system(paste(cmd, script_path, output_file))
readLines(output_file)
}
rscript = function (script_path) {
cmd = 'Rscript --slave --no-restore --... | apache-2.0 | R |
6ce787e564d92645d5c6dcc595fb34cb3ecead91 | Add algorithm (backend) to the shiny server function | isithot/isithotrightnow,isithot/isithotrightnow,isithot/isithotrightnow,isithot/isithotrightnow,isithot/isithotrightnow | server.r | server.r | library(shiny)
library(ggplot2)
# IsItHotRightNow.com
# Algorithm
# Libraries
library(jsonlite)
library(lubridate)
library(plotly)
# server logic: calc output based on inputs
function(input, output) {
# Get Data
# Get Climatology data
# Pre-made BOM statistics available in data/
BOMstats.raw <- read.csv("d... | library(shiny)
library(ggplot2)
# server logic: calc output based on inputs
function(input, output) {
# use reactive() to ensure that dataset is updated whenever
# inout$sampleSize changes
# dataset <- reactive({
# diamonds[sample(nrow(diamonds), input$sampleSize), ]
# })
# renderPlot() does the plot r... | mit | R |
8c917e2c2179e7fe4f02b098366f2323f1816053 | Update pp.r | robertzk/Ramd | R/pp.r | R/pp.r | # String interpolation in R!
#' export
pp <- function(..., envir = parent.frame(), sep = '', collapse = '') {
string <- list(...)
if (length(string) > 1)
return(paste(sapply(string,
function(s) { pp(s, envir = envir, sep = sep, collapse = collapse) }
), collapse = sep))
string <- string[[1]]
if (l... | # String interpolation in R!
pp <- function(..., envir = parent.frame(), sep = '', collapse = '') {
string <- list(...)
if (length(string) > 1)
return(paste(sapply(string,
function(s) { pp(s, envir = envir, sep = sep, collapse = collapse) }
), collapse = sep))
string <- string[[1]]
if (length(stri... | mit | R |
73861f89020939dee1925c6f9fdaf01cf133ae85 | update reference to github | leeper/leeper.github.io | code/r/coefpaste.r | code/r/coefpaste.r | # FUNCTION TO PRODUCE MEAN/SE OR MEAN/SD COMBINATIONS FOR PRINTING
# PRODUCES A VECTOR OF THE FORM "mean (SE)" FOR OUTPUT (e.g., IN xtable() )
# Copyright (C) 2012 Thomas J. Leeper
# This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published... | # FUNCTION TO PRODUCE MEAN/SE OR MEAN/SD COMBINATIONS FOR PRINTING
# PRODUCES A VECTOR OF THE FORM "mean (SE)" FOR OUTPUT (e.g., IN xtable() )
# Copyright (C) 2012 Thomas J. Leeper
# This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published... | mit | R |
64b340c5b98e0d76f9e9201eaca2159e9b7176fb | install map libraries if needed | hackoregon/nass-explore | getting-the-data.r | getting-the-data.r | #' ---
#' title: "Downloading NASS/ARMSDB data"
#' author: "M. Edward (Ed) Borasky"
#' date: "September 3, 2015"
#' output:
#' html_document:
#' keep_md: true
#' ---
#'
#' References:
#'
#' 1. NASS data: <http://challengefiles2.blob.core.windows.net/pdf/MSR_Innovation_challenge_NASS_description.pdf>
#' 2. ARMSDB ... | #' ---
#' title: "Downloading NASS/ARMSDB data"
#' author: "M. Edward (Ed) Borasky"
#' date: "September 3, 2015"
#' output:
#' html_document:
#' keep_md: true
#' ---
#'
#' References:
#'
#' 1. NASS data: <http://challengefiles2.blob.core.windows.net/pdf/MSR_Innovation_challenge_NASS_description.pdf>
#' 2. ARMSDB ... | agpl-3.0 | R |
374b20b809a963de30ab3fa10e831ccfd68517bc | annotate on GO and keggPathway only | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/Annotation/WebGestaltR.r | lib/Annotation/WebGestaltR.r | options(bitmapType='cairo')
library(WebGestaltR)
args = commandArgs(trailingOnly=TRUE)
organism = args[1] #hsapiens
sampleName=args[2]
geneFile = args[3]
outputDirectory = args[4]
interestGeneType = args[5]
referenceSet = args[6]
cat("organism=", organism, "\n")
cat("sampleName=", sampleName, "\n")
cat... | options(bitmapType='cairo')
library(WebGestaltR)
args = commandArgs(trailingOnly=TRUE)
organism = args[1] #hsapiens
sampleName=args[2]
geneFile = args[3]
outputDirectory = args[4]
interestGeneType = args[5]
referenceSet = args[6]
cat("organism=", organism, "\n")
cat("sampleName=", sampleName, "\n")
cat... | apache-2.0 | R |
34be0f03dbf60514a653dfdc1a20263a3669f2cd | Update vizualizacija.r | ZavbiA/APPR-2017 | vizualizacija/vizualizacija.r | vizualizacija/vizualizacija.r | # 3. faza: Vizualizacija podatkov
library(sp)
library(maptools)
library(digest)
gpclibPermit()
library(rvest)
library(gsubfn)
library(readr)
library(dplyr)
library(ggplot2)
library(tibble)
# Uvozim zemljevid.
zemljevid <- uvozi.zemljevid("http://www.naturalearthdata.com/http//www.naturalearthdata.com/download/50m/cul... | # 3. faza: Vizualizacija podatkov
library(sp)
library(maptools)
library(digest)
gpclibPermit()
library(rvest)
library(gsubfn)
library(readr)
library(dplyr)
library(ggplot2)
library(tibble)
# Uvozim zemljevid.
zemljevid <- uvozi.zemljevid("http://www.naturalearthdata.com/http//www.naturalearthdata.com/download/50m/cul... | mit | R |
95b8bc7050fe9213434ac2148906a03ab877f35d | update with links | davidmoten/rtree-3d,davidmoten/rtree-3d | src/main/r/source.r | src/main/r/source.r | #!/usr/bin/Rscript
#X11(type="Xlib")
library("plot3D")
for (i in 0:10 ) {
mat <- read.csv(file = paste("../../../target/out",i,".txt", sep=""), header = FALSE)
png(paste("../../../target/plot",i,".png",sep=""), height = 700, width =1000 )
box3D(
x0 = mat[,1], y0 = mat[,2], z0=mat[,3],
x1 = mat[,... | #!/usr/bin/Rscript
#X11(type="Xlib")
library("plot3D")
for (i in 0:10 ) {
mat <- read.csv(file = paste("../../../target/out",i,".txt", sep=""), header = FALSE)
png(paste("../../../target/plot",i,".png",sep=""), height = 700, width =1000 )
box3D(
x0 = mat[,1], y0 = mat[,2], z0=mat[,3],
x1 = mat[,4], y1 = mat... | apache-2.0 | R |
42850fa7ee42a9f2ef24e970e5a22b18eb451a85 | Fix error in tAI | klmr/codons,klmr/codons | scripts/tai.r | scripts/tai.r | # Based on the paper by Dos Reis & al, 2004
s = list(naive = c(0, 0, 0, 0, 0.5, 0.5, 0.75, 0.5, 0.5, 0.5),
ecoli = c(0, 0, 0, 0, 0.41, 0.28, 0.9999, 0.68, 0.89))
get_s = function (species)
if (species %in% names(s)) s[[species]] else s$naive
# Reverse complement of the anticodons, in the order of antico... | # Based on the paper by Dos Reis & al, 2004
s = list(naive = c(0, 0, 0, 0, 0.5, 0.5, 0.75, 0.5, 0.5, 0.5),
ecoli = c(0, 0, 0, 0, 0.41, 0.28, 0.9999, 0.68, 0.89))
get_s = function (species)
if (species %in% names(s)) s[[species]] else s$naive
# Reverse complement of the anticodons, in the order of antico... | apache-2.0 | R |
2450447fa0e4017706605e7d64ed3c926c1a2d7e | Update wetbulb_stull.r | alfcrisci/rBiometeo,alfcrisci/rBiometeo | R/wetbulb_stull.r | R/wetbulb_stull.r | #' wetbulb_stull
#'
#' Compute natural wetbulb temperature by using Stull empirical formulation
#'
#' @param numeric t Air temperature in Celsius degrees.
#' @param numeric rh Air Relative humidity in percentage.
#' @param numeric press Air pressure in hPa or millibar.
#' @return Wet bulb temperature in Celsius degre... | mit | R | |
c4e40ad0b8f550bf6ad3a697db4e8ccf86766de8 | Update R3-GUI download URL used in LOAD-GUI | mbk/ren-c,kealist/ren-c,hostilefork/rebol,rgchris/ren-c,codebybrett/ren-c,mbk/ren-c,rgchris/ren-c,draegtun/ren-c,hostilefork/rebol,hostilefork/rebol,hostilefork/rebol,rgchris/ren-c,hostilefork/rebol,giuliolunati/ren-c,giuliolunati/ren-c,giuliolunati/ren-c,giuliolunati/ren-c,kealist/ren-c,rgchris/ren-c,codebybrett/ren-c... | src/mezz/rma-patches.r | src/mezz/rma-patches.r | REBOL [
Title: "REBOL Graphics - load-gui patch"
]
load-gui: func [
"Download current Spahirion's R3-GUI module from web."
/local data
][
print "Fetching GUI..."
either error? data: try [load http://development.saphirion.com/resources/r3-gui.r3] [
either data/id = 'protocol [print "Cannot load... | REBOL [
Title: "REBOL Graphics - load-gui patch"
]
load-gui: func [
"Download current Spahirion's R3-GUI module from web."
/local data
][
print "Fetching GUI..."
either error? data: try [load http://www.saphirion.com/development/downloads-2/files/r3-gui.r3] [
either data/id = 'protocol [print ... | apache-2.0 | R |
bdabe55b2a174c8e64d334a6563f9b99cd98157b | read from relative directory | davidmoten/rtree-3d,davidmoten/rtree-3d | src/main/r/source.r | src/main/r/source.r | #!/usr/bin/Rscript
#X11(type="Xlib")
library("plot3D")
mat <- read.csv(file = "../../../target/out.txt", header = FALSE)
png("../../../target/plot.png", height = 700, width =1000 )
box3D(
# x0 = runif(3), y0 = runif(3),print z0 = runif(3),
# x1 = runif(3), y1 = runif(3), z1 = runif(3),
x0 = mat[,1], y0 = mat[,2], z... | #!/usr/bin/Rscript
#X11(type="Xlib")
library("plot3D")
mat <- read.csv(file = "/home/dave/Development/ide/eclipse/workspace-4.4/rtree-3d/target/out.txt", header = FALSE)
png("../../../target/plot.png", height = 700, width =1000 )
box3D(
# x0 = runif(3), y0 = runif(3),print z0 = runif(3),
# x1 = runif(3), y1 = runif(3... | apache-2.0 | R |
bb8fdca74fe64b8d41f192288832e42a6d4a661c | Update uvoz.r | UrosKrampelj/APPR-2015-16 | uvoz/uvoz.r | uvoz/uvoz.r | library(rvest)
library(dplyr)
library(gsubfn)
html <- html_session("https://en.m.wikipedia.org/wiki/List_of_Chelsea_F.C._players#List_of_players") %>% read_html()
html_tabela <- html %>% html_nodes(xpath="//table[1]") %>% .[[1]]
tabela <- html_tabela %>% html_table()
tabela[grep(",", tabela[[1]]), 1] <- html_tabela %>... | library(rvest)
library(dplyr)
library(gsubfn)
html <- html_session("https://en.m.wikipedia.org/wiki/List_of_Chelsea_F.C._players#List_of_players") %>% read_html()
html_tabela <- html %>% html_nodes(xpath="//table[1]") %>% .[[1]]
tabela <- html_tabela %>% html_table()
tabela[grep(",", tabela[[1]]), 1] <- html_tabela %>... | mit | R |
c39edb28215eeed22ea8b47558579bffbc5a6162 | adjust figure after rename cluster | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/renameCluster.r | lib/scRNA/renameCluster.r |
library(Seurat)
library(ggplot2)
finalList<-readRDS(parFile1)
obj<-finalList$obj
newnames<-read.table(parSampleFile2, stringsAsFactors = F, sep="\t", header=F)
clusters<-data.frame("cell" = c(1:length(obj$seurat_clusters)), "seurat_clusters"=as.numeric(as.character(obj$seurat_clusters)), "cellactivity_cluste... |
library(Seurat)
library(ggplot2)
finalList<-readRDS(parFile1)
obj<-finalList$obj
newnames<-read.table(parSampleFile2, stringsAsFactors = F, sep="\t", header=F)
clusters<-data.frame("cell" = c(1:length(obj$seurat_clusters)), "seurat_clusters"=as.numeric(as.character(obj$seurat_clusters)), "cellactivity_clusters"=obj$... | apache-2.0 | R |
0a0bc3370867d5fad3fed55d02091e142ff5e7f1 | Update 1.r | glor/R,glor/R | aufgaben/blatt05/1.r | aufgaben/blatt05/1.r | #Anpassungstest, da untersucht wird, ob die tatsaechliche Anzahl mit der vermuteten, theoretischen Anzahl der Erbsen uebereinstimmt.
#1.2
#H0: Die Anzahl der Erbsen stimmt mit dem von Mendel aufgestellten Zahlenverhaeltnissen ueberein.
#H1: Die Anzahl stimmt nicht ueberein.
#1.3
chisq.test(c(60,16,20,4), c(9,3... | bsd-2-clause | R | |
e71f2b72fbe6bf88ca316a451d4eed3dd975028b | Update installRpackages.r | PascalLike/OSGeoLive,astroidex/OSGeoLive,PascalLike/OSGeoLive,astroidex/OSGeoLive,OSGeo/OSGeoLive,OSGeo/OSGeoLive,PascalLike/OSGeoLive,PascalLike/OSGeoLive,kalxas/OSGeoLive,PascalLike/OSGeoLive,OSGeo/OSGeoLive,guygriffiths/OSGeoLive,PascalLike/OSGeoLive,guygriffiths/OSGeoLive,OSGeo/OSGeoLive,OSGeo/OSGeoLive,guygriffith... | 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 |
5d58c8a1bc1d3745f0d8d60362769d01984503bb | use %||% list() here | syberia/syberia | R/model_stage.r | R/model_stage.r | #' Model stage for syberia models
#'
#' TODO: Document this more
#'
#' @param modelenv an environment. The persistent modeling environment.
#' @param model_parameters a list. Model-specific parameters, with the first
#' parameter always being the model keyword for the tundra container
#' (e.g., glm, gbm, etc.)
#... | #' Model stage for syberia models
#'
#' TODO: Document this more
#'
#' @param modelenv an environment. The persistent modeling environment.
#' @param model_parameters a list. Model-specific parameters, with the first
#' parameter always being the model keyword for the tundra container
#' (e.g., glm, gbm, etc.)
#... | mit | R |
22ad0254b969bf635e91be68db4f2eb925aa0529 | Update sum-aggr-na.r | SwedishPensionsAgency/Hierarchy | R/sum-aggr-na.r | R/sum-aggr-na.r | #' Aggregate sum function
#'
#' ...
#'
#' @param x data
#'
#'
#' @export
sum_aggr_na <- function(x) {
if (length(x) == 1 && is.na(x)) {
sum(x, na.rm = FALSE)
} else {
sum(x, na.rm = TRUE)
}
}
| #' Aggregate sum function
#'
#' ...
#'
#' @param ... arguments passed to the sum function
#'
#'
#' @export
sum_aggr_na <- function(x) {
if (length(x) == 1 && is.na(x)) {
sum(x, na.rm = FALSE)
} else {
sum(x, na.rm = TRUE)
}
}
| agpl-3.0 | R |
0141819bfdbe36615ab41e7e7e4bff0cc00941a2 | convert download routine from curl to httr | khufkens/phenor | R/download_berkeley_earth.r | R/download_berkeley_earth.r | #' Download Berkeley Earth Gridded mean daily temperature data
#'
#' @param path a path where to save the gridded data
#' @param year year to process (requires year - 1 to be present)
#' @return nothing is returned to the R working environment, files are
#' downloaded and stored on disk
#' @keywords phenology, model, d... | #' Download Berkeley Earth Gridded mean daily temperature data
#'
#' @param path a path where to save the gridded data
#' @param year year to process (requires year - 1 to be present)
#' @return nothing is returned to the R working environment, files are
#' downloaded and stored on disk
#' @keywords phenology, model, d... | agpl-3.0 | R |
d04a325c372d714313e6d23762d7d10028067d07 | check input file | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/clonotype_cluster.r | lib/scRNA/clonotype_cluster.r |
library("tools")
clonos<-read.csv(parFile1, stringsAsFactors=F)
clonos<-clonos[order(clonos$frequency, decreasing=T),]
clono_cells<-unique(clonos[,c("clonotype_id", "cells")])
if(file_ext(parFile2) == "rds"){
ct<-readRDS(parFile2)
ct$ident_celltype<-paste0(ct$orig.ident, ":", ct$seurat_cluster, ":", ct$... |
clonos<-read.csv(parFile1, stringsAsFactors=F)
clonos<-clonos[order(clonos$frequency, decreasing=T),]
clono_cells<-unique(clonos[,c("clonotype_id", "cells")])
ct<-read.csv(parFile2, row.names=1)
ct$ident_celltype<-paste0(ct$orig.ident, ":", ct$seurat_cluster, ":", ct$cellactivity_clusters)
clon_ic<-apply(clo... | apache-2.0 | R |
b3fc581d10b17779eb7f513b78bcf895438e53a5 | Add geom_label #chunks | jpalardy/dotfiles,jpalardy/dotfiles,jpalardy/dotfiles,jpalardy/dotfiles,jpalardy/dotfiles | chunks/chunks.r | chunks/chunks.r |
#-------------------------------------------------
# manual colors
#-------------------------------------------------
colors = c("val1"="red", "val2"="darkgreen")
scale_color_manual(values=colors)
#-------------------------------------------------
# labels
#-------------------------------------------------
# https:... |
#-------------------------------------------------
# manual colors
#-------------------------------------------------
colors = c("val1"="red", "val2"="darkgreen")
scale_color_manual(values=colors)
#-------------------------------------------------
# color brewer
#-------------------------------------------------
# ... | mit | R |
eae6b35eaec5fb48fb14dc16acb283d720f0c5d6 | add comment about multicore+multiprocess test | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | tests/testthat/test-5-qsys_impl.r | tests/testthat/test-5-qsys_impl.r | context("qsys implementations")
has_cmq = has_cmq()
has_network = has_connectivity(Sys.info()["nodename"])
avail = Sys.which(c("bsub", "qsub", "sbatch", "fake_scheduler.sh"))
avail = as.list(nchar(avail) != 0)
fx = function(x) x*2
test_that("local, explicit", {
w = workers(n_jobs=4, qsys_id="local")
r = Q(fx,... | context("qsys implementations")
has_cmq = has_cmq()
has_network = has_connectivity(Sys.info()["nodename"])
avail = Sys.which(c("bsub", "qsub", "sbatch", "fake_scheduler.sh"))
avail = as.list(nchar(avail) != 0)
fx = function(x) x*2
test_that("local, explicit", {
w = workers(n_jobs=4, qsys_id="local")
r = Q(fx,... | apache-2.0 | R |
ef5f0fb3af8588ec1b1c2dcbc351b3bdbbcdd8f0 | Add a second theme using Helvetica | 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 = theme_minim... | #' Pretty plotting module
export = import('./export', attach = 'export_from')
gg = import_package('ggplot2')
export_from(gg)
#
# Set a very minimal theme. Avoid chartjunk.
#
fonts = import('./fonts')
fonts$register_font('Roboto')
fonts$register_font('Roboto Condensed', 'RobotoCondensed')
theme_set(theme_minimal() ... | apache-2.0 | R |
aa8ed8dbd98fd84738d5335bc8414272da27ade0 | include importFrom %>% | khufkens/phenor | R/check_pep725_species.r | R/check_pep725_species.r | #' Checks if PEP725 species name or number exists or can be generated
#'
#' @param species A species to download, either specified by its
#' species number or species name.
#' @param list List all species numbers and names as verbose output
#' @return a validated list of species numbers, if not a warning is thrown
#' a... | #' Checks if PEP725 species name or number exists or can be generated
#'
#' @param species A species to download, either specified by its
#' species number or species name.
#' @param list List all species numbers and names as verbose output
#' @return a validated list of species numbers, if not a warning is thrown
#' a... | agpl-3.0 | R |
51f39d7902e3c9bba466f438ad7d36a809fe8c96 | add namemap | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/split_samples_summary.r | lib/scRNA/split_samples_summary.r | library(ggplot2)
library(reshape2)
args = commandArgs(trailingOnly=TRUE)
if (length(args) == 0) {
inputFile = "/scratch/cqs/paula_hurley_projects/20201208_scRNA_split/split_samples_summary/result/scRNA__fileList1.list"
nameMapFile = "/scratch/cqs/paula_hurley_projects/20201208_scRNA_split/split_samples_sum... | library(ggplot2)
library(reshape2)
args = commandArgs(trailingOnly=TRUE)
if (length(args) == 0) {
inputFile = "/scratch/cqs/alexander_gelbard_projects/20201202_5126_scRNA_split/split_samples_summary/result/scRNA_5126__fileList1.list"
outputPrefix = "/scratch/cqs/alexander_gelbard_projects/20201202_5126_scR... | apache-2.0 | R |
4bf5efbcb6bc7fc2622140a345a8cb4b994b75a3 | Add links to translations. | snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3 | web/en/index.rd | web/en/index.rd | =begin
=QMAIL3
==What's QMAIL3
QMAIL3 is a mail client which runs on Windows and Windows CE families. It has features:
*Supports POP3, SMTP, IMAP4, NNTP, RSS, Atom
*Supports several authentication mechanism, such as APOP, SMTP
*Supports SSL, STARTTLS
*Supports S/MIME
*Supports PGP/GnuPG (Windows version onl... | =begin
=QMAIL3
==What's QMAIL3
QMAIL3 is a mail client which runs on Windows and Windows CE families. It has features:
*Supports POP3, SMTP, IMAP4, NNTP, RSS, Atom
*Supports several authentication mechanism, such as APOP, SMTP
*Supports SSL, STARTTLS
*Supports S/MIME
*Supports PGP/GnuPG (Windows version onl... | mit | R |
e024a992dcdc8913572880ce778b5a830180225f | Add get_real_words function to remove non-words | petercarrjones/icc-data,petercarrjones/icc-data,petercarrjones/icc-data | load.r | load.r | #Load Packages
library(XML)
library(tidyr)
library(stringr)
library(magrittr)
library(dplyr)
library(RWeka)
#load OCR'd ICC Deceisions data into R
icc_dir <- "text"
files <- dir(icc_dir, "*.txt")
raw <- file.path(icc_dir, files) %>%
lapply(., scan, "character", sep = "\n")
names(raw) <- files
icc_texts <- lapply(ra... | #Load Packages
library(XML)
library(tidyr)
library(stringr)
library(magrittr)
library(dplyr)
library(RWeka)
#load OCR'd ICC Deceisions data into R
icc_dir <- "text"
files <- dir(icc_dir, "*.txt")
raw <- file.path(icc_dir, files) %>%
lapply(., scan, "character", sep = "\n")
names(raw) <- files
icc_texts <- lapply(ra... | mit | R |
8601c08bd3dc7efc2ee053c5d71d09322c606fa9 | fix variable names, add generalised source() call. | wikimedia-research/Blockr | main.r | main.r | # Copyright (c) 2013 Oliver Keyes
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, dis... | # Copyright (c) 2013 Oliver Keyes
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, dis... | mit | R |
ee750774b9b6b42ee740d10cfee5967338dc7565 | remove outdated comments | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | R/ssh_proxy.r | R/ssh_proxy.r | #' SSH proxy for different schedulers
#'
#' Do not call this manually, the SSH qsys will do that
#'
#' @param master_port The master address (tcp://ip:port)
ssh_proxy = function(master_port) {
# network forwarding most likely disabled, so set up local SSH forward
net_port = sample(8000:9999, 1)
cmd = sprin... | #' SSH proxy for different schedulers
#'
#' Do not call this manually, the SSH qsys will do that
#'
#' @param master_port The master address (tcp://ip:port)
ssh_proxy = function(master_port) {
# network forwarding most likely disabled, so set up local SSH forward
net_port = sample(8000:9999, 1)
cmd = sprin... | apache-2.0 | R |
0fbe4c22368612ec5ef7e7b366a78080fca1c9a1 | Update methylation-pcs.r | perishky/meffil,perishky/meffil | R/methylation-pcs.r | R/methylation-pcs.r | #' Compute principal components of a methylation matrix.
#'
#' @param beta Output from \code{\link{meffil.normalize.samples}()},
#' either a matrix or a GDS filename.
#' @param probe.range Default = 50000. How many probes to be used in calculating PCs.
#' @param sites Subset of CpG sites to consider (row names of beta)... | #' Compute principal components of a methylation matrix.
#'
#' @param beta Output from \code{\link{meffil.normalize.samples}()},
#' either a matrix or a GDS filename.
#' @param probe.range Default = 50000. How many probes to be used in calculating PCs.
#' @param sites Subset of CpG sites to consider (row names of beta)... | artistic-2.0 | R |
4fd27dbe708d76c9b7d7939a9a0b9074227eb35b | Add document about FileUninstallAction. | snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3,snakamura/q3 | q3/docs/FileUninstallAction.rd | q3/docs/FileUninstallAction.rd | =begin
=FileUninstallANV
QMAIL3gp郌WXg폜܂B̓Iɂ́AHKEY_CURRENT_USER\Software\sn\q3ȉ̑SẴL[폜AȊOɎqL[ȂAHKEY_CURRENT_USER\Software\sn폜܂B
OSւ̃[NCAgƂĂ̓o^mailto URLւ̊֘AtȂǂ͍폜܂BCXg[ōs邱̐ݒ̓ACXg[ɂč폜܂B
==
Ȃ
==LȃEBhEEr[
*CEBhE
=end
| =begin
=FileUninstallANV
// TODO
=end
| mit | R |
19189e64bf6f43ce99ff6607055dbfa9a54f68f4 | Add likelihood plot. | jtobin/bnp | finite-gaussian-mixture/src/simulation_conditional.r | finite-gaussian-mixture/src/simulation_conditional.r | set.seed(42)
require(ggplot2)
require(reshape2)
source('fmm_conditional.r')
config = list(
k = 3
, a = 1
, l = 0
, r = 0.1
, b = 1
, w = 1
, n = 1000
)
origin = list(
p = mixing_model(config$k, config$a)
, m = location_model(config$k, config$l, config$r)
, s = precision_model(config$k, con... | set.seed(42)
require(ggplot2)
require(reshape2)
source('fmm_conditional.r')
config = list(
k = 3
, a = 1
, l = 0
, r = 0.1
, b = 1
, w = 1
, n = 500
)
origin = list(
p = mixing_model(config$k, config$a)
, m = location_model(config$k, config$l, config$r)
, s = precision_model(config$k, conf... | mit | R |
991ad55ade24635edf65673e02b0999785bcfe6e | bring back Ramd | syberia/syberia | R/config.r | R/config.r | .github_packages <- list(
list('productivus', 'robertzk'),
list('Ramd', 'robertzk'),
list('frost', 'robertzk'),
list('stagerunner', 'robertzk'),
list('mungebitsTransformations', 'robertzk'),
list('mungebits', 'robertzk'),
list('tundra', 'robertzk')
)
| .github_packages <- list(
list('productivus', 'robertzk'),
# list('Ramd', 'robertzk'),
list('frost', 'robertzk'),
list('stagerunner', 'robertzk'),
list('mungebitsTransformations', 'robertzk'),
list('mungebits', 'robertzk'),
list('tundra', 'robertzk')
)
| mit | R |
2e2e4b85fe697346860505c9cc0fdbb15f3989ca | simplify only 1-col arrays | 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 |
cbbf86d2de83dfecad5d383f7f4a4f2da1538405 | Update uvoz_tabele3.r | ZavbiA/APPR-2017 | uvoz/uvoz_tabele3.r | uvoz/uvoz_tabele3.r | library(rvest)
library(gsubfn)
library(readr)
library(dplyr)
# Funkcija, ki uvozi tabele slovenskih medalistov
link1 <- "http://www.olympic.si/olimpijski-wiki/olimpijske-igre"
stran1 <- html_session(link1) %>% read_html(encoding = "UTF-8")
tabele <- stran1 %>% html_nodes(xpath="//div[@id='vsebina259']/... | library(rvest)
library(gsubfn)
library(readr)
library(dplyr)
# Funkcija, ki uvozi tabele slovenskih medalistov
link1 <- "http://www.olympic.si/olimpijski-wiki/olimpijske-igre"
stran1 <- html_session(link1) %>% read_html(encoding = "UTF-8")
tabele <- stran1 %>% html_nodes(xpath="//div[@id='vsebina259']/... | mit | R |
03a29e86c2a0f19101044883ccf244b90bc5d76f | Move data files to top-level ./.data/ directory | jmousseau/Stain | R/slurm-bash-script.r | R/slurm-bash-script.r | #' SlurmBashScript R6 object.
#'
#' Generates the necessary bash script to submit through
#' the `sbatch` command.
SlurmBashScript <- R6::R6Class("SlurmBashScript",
public = list(
initialize = function(container, main_file, settings) {
private$settings <- settings
main_file <- paste... | #' SlurmBashScript R6 object.
#'
#' Generates the necessary bash script to submit through
#' the `sbatch` command.
SlurmBashScript <- R6::R6Class("SlurmBashScript",
public = list(
initialize = function(container, main_file, settings) {
private$settings <- settings
main_file <- paste... | mit | R |
edc6ff70a7a7956703b902a7ed0849882be59f29 | Add GitHub support | steinbaugh/seqcloudr,seqcloud/seqcloudR,steinbaugh/basejump | R/manage_pkg.r | R/manage_pkg.r | manage_bioc <- function(bioc_pkg) {
install_bioc_pkg <-
bioc_pkg[!(bioc_pkg %in% installed.packages()[, "Package"])]
if (length(install_bioc_pkg) > 0) {
source("https://bioconductor.org/biocLite.R")
biocLite()
biocLite(install_bioc_pkg)
}
invisible(lapply(bioc_pkg, require, character.only = TRUE... | manage_bioc <- function(bioc_pkg) {
install_bioc_pkg <-
bioc_pkg[!(bioc_pkg %in% installed.packages()[, "Package"])]
if (length(install_bioc_pkg) > 0) {
source("https://bioconductor.org/biocLite.R")
biocLite()
biocLite(install_bioc_pkg)
}
invisible(lapply(bioc_pkg, require, character.only = TRUE... | mit | R |
a9034c9208799867cf30e61c7689b3f82539a11c | Use correct assignment operators. | bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adventofcode,bertptrs/adv... | 2017/day-20/solution.r | 2017/day-20/solution.r | #!/usr/bin/env Rscript
data <- readLines("stdin")
cleaned <- gsub(" $", "", gsub("^[^0-9-]+", "", gsub("[^0-9-]+", " ", data)))
tc <- textConnection(cleaned)
input <- read.csv(tc, header=FALSE, sep=" ")
close(tc)
accs <- rowSums(abs(input[,7:9]))
speeds <- rowSums(abs(input[,4:6]))
perm <- order(accs, speeds)
prin... | #!/usr/bin/env Rscript
data <- readLines("stdin")
cleaned <- gsub(" $", "", gsub("^[^0-9-]+", "", gsub("[^0-9-]+", " ", data)))
tc <- textConnection(cleaned)
input <- read.csv(tc, header=FALSE, sep=" ")
close(tc)
accs <- rowSums(abs(input[,7:9]))
speeds <- rowSums(abs(input[,4:6]))
perm <- order(accs, speeds)
prin... | mit | R |
91d7fb3e4fccc0b9c14dc061eea20d935747e5a6 | Fix pipeline if only one sample is provided | ewels/NGI-RNAseq,ewels/NGI-RNAseq,ewels/NGI-RNAseq,ewels/NGI-RNAseq,ewels/NGI-RNAseq | bin/salmon_summarizedexperiment.r | bin/salmon_summarizedexperiment.r | #!/usr/bin/env Rscript
library(SummarizedExperiment)
## Create SummarizedExperiment (se) object from Salmon counts
args = commandArgs(trailingOnly=TRUE)
if (length(args) < 2) {
stop("Usage: salmon_se.r <coldata> <counts> <tpm>", call.=FALSE)
}
coldata = args[1]
counts_fn = args[2]
tpm_fn = args[3]
tx2gene = "s... | #!/usr/bin/env Rscript
library(SummarizedExperiment)
## Create SummarizedExperiment (se) object from Salmon counts
args = commandArgs(trailingOnly=TRUE)
if (length(args) < 2) {
stop("Usage: salmon_se.r <coldata> <counts> <tpm>", call.=FALSE)
}
coldata = args[1]
counts_fn = args[2]
tpm_fn = args[3]
tx2gene = "s... | mit | R |
9b46e568bba93ec17623bd704f4f2c4dc1410998 | Add dependencies to suggestions script | amcat/amcat,amcat/amcat,amcat/amcat,amcat/amcat,amcat/amcat,amcat/amcat | amcat/scripts/query/r_plugins/suggestions.r | amcat/scripts/query/r_plugins/suggestions.r | formfields = djangoFormFields(n = IntegerField(initial=50, required=T))
dependencies = c("corpustools", "knitr")
run = function(query, n, ...) {
a = get_text(...)
library(corpustools)
tc = create_tcorpus(a, doc_column = "id")
ass = tc$feature_associations(query=query)
result = knitr::kable(head(ass, n=n), fo... | formfields = djangoFormFields(n = IntegerField(initial=50, required=T))
run = function(query, n, ...) {
depends("corpustools", "knitr")
a = get_text(...)
library(corpustools)
tc = create_tcorpus(a, doc_column = "id")
ass = tc$feature_associations(query=query)
result = knitr::kable(head(ass, n=n), format="... | agpl-3.0 | R |
13b51bbec4c6c26dbafccc1166a0a7ddf2c7b00a | add more debugging | snowch/biginsight-examples,snowch/biginsight-examples | examples/BigR/install_packages.r | examples/BigR/install_packages.r | libdir <- Sys.getenv("libdir")
debug <- Sys.getenv("debug")
quiet=TRUE
if (debug) {
quiet=FALSE
}
.libPaths(libdir)
# create directory to hold libraries
dir.create(libdir)
# install libraries
install.packages('rJava', repos='http://cran.us.r-project.org', lib=libdir, quiet=quiet)
install.packages('base... | libdir <- Sys.getenv("libdir")
.libPaths(libdir)
# create directory to hold libraries
dir.create(libdir)
# install libraries
install.packages('rJava', repos='http://cran.us.r-project.org', lib=libdir, quiet=TRUE)
install.packages('base64enc', repos='http://cran.us.r-project.org', lib=libdir, quiet=TRUE)
inst... | apache-2.0 | R |
48682d2c892a917f02a3131be9737cd176ee635c | write meta file | shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl,shengqh/ngsperl | lib/scRNA/seurat_doublet_finder.r | lib/scRNA/seurat_doublet_finder.r |
source("scRNA_func.r")
library(dplyr)
library(Seurat)
library(ggplot2)
library(ggpubr)
library(DT)
library(data.table)
library(digest)
library(heatmap3)
library(cowplot)
library(scales)
library(stringr)
library(htmltools)
library(patchwork)
library(glmGamPoi)
library(DoubletFinder)
options(future.globals.maxSize= 107... |
source("scRNA_func.r")
library(dplyr)
library(Seurat)
library(ggplot2)
library(ggpubr)
library(DT)
library(data.table)
library(digest)
library(heatmap3)
library(cowplot)
library(scales)
library(stringr)
library(htmltools)
library(patchwork)
library(glmGamPoi)
library(DoubletFinder)
options(future.globals.maxSize= 107... | apache-2.0 | R |
7033a43247e2a63fcdbf96cd91008eec2deda989 | use array module for splitting | mschubert/clustermq,mschubert/clustermq,mschubert/clustermq | process_args.r | process_args.r | .split = import('../array/split')
.ll = import('../base/list')
#' @param fun the function to call
#' @param ... arguments to vectorise over
#' @param const arguments not to vectorise over
#' @param export objects to export to computing nodes
#' @param get returns ... | .ll = import('base/list')
#' @param fun the function to call
#' @param ... arguments to vectorise over
#' @param const arguments not to vectorise over
#' @param export objects to export to computing nodes
#' @param get returns the result of the run (default:T)
#' ... | apache-2.0 | R |
7ea5676e7a06bbb79f8c6a623d6953062a1da7aa | Add missing ggplot2 scale primitives | 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$register_font('Roboto Condensed', 'RobotoCondensed')
.theme_basic = theme_minim... | #' Pretty plotting module
export = import('./export', attach = 'export_from')
gg = import_package('ggplot2')
export_from(gg)
#
# Set a very minimal theme. Avoid chartjunk.
#
fonts = import('./fonts')
fonts$register_font('Roboto')
fonts$register_font('Roboto Condensed', 'RobotoCondensed')
.theme_basic = theme_minim... | apache-2.0 | R |
56620932f647a835a3daebe5c169c29833964c4b | Add common slurm setting parameters | jmousseau/Stain | R/slurm-settings.r | R/slurm-settings.r | #' SlurmSettings R6 object.
#'
#' An interface to SBATCH settings.
#'
#' @export
SlurmSettings <- R6::R6Class("SlurmSettings",
public = list(
nodes = NA,
cpus_per_task = NA,
time = NA,
memory = NA,
initialize = function(nodes = 1, cpus_per_task = 12,
... | #' SlurmSettings R6 object.
#'
#' An interface to SBATCH settings.
#'
#' @export
SlurmSettings <- R6::R6Class("SlurmSettings")
| mit | R |
13d46c627b5e7f0219768836b851e1288846e661 | Update ui.r | aleksandrov2/APPR-2015-16 | shiny/ui.r | shiny/ui.r | # This is the user-interface definition of a Shiny web application.
# You can find out more about building applications with Shiny here:
#
# http://www.rstudio.com/shiny/
#
library(shiny)
shinyUI(fluidPage(
plotOutput("prvi_graf"),
tableOutput("napoved.tabela"),
plotOutput("enajsti_graf")))
| # This is the user-interface definition of a Shiny web application.
# You can find out more about building applications with Shiny here:
#
# http://www.rstudio.com/shiny/
#
library(shiny)
source("lib/uvozi.zemljevid.r", encoding = "UTF-8")
source("podatki/podatki.r", encoding = "UTF-8")
source("uvoz/uvozi.r", encod... | mit | R |
224e90df74ab7edcb50e701d89b3ca532f4e157c | Move heatmap code inside a main function. | agapow/smartr,thehyve/naa-SmartR,thehyve/naa-SmartR,thehyve/heim-SmartR,thehyve/naa-SmartR,agapow/smartr,thehyve/heim-SmartR,thehyve/heim-SmartR,thehyve/heim-SmartR,agapow/smartr,agapow/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 <- subset(dataset,select=-c(Row.Label,Bio.marker)) # this will select all columns other than Row.Label,Bio.marker columns
measurements <- data.matrix(measureme... | library(gplots)
dataset <- loaded_variables[[1]] #dataframe with columns: Row.Label, Bio.marker, ASSAY_0001 ASSAY_0002 ...
measurements <- subset(dataset,select=-c(Row.Label,Bio.marker)) # this will select all columns other than Row.Label,Bio.marker columns
measurements <- data.matrix(measurements)
measurements <-... | apache-2.0 | R |
1032bb6c108e9d6f62159cdccc83e6caee925956 | Configure 2015 post season report | PSC-CoTC/PSC-FRAM-Admin,PSC-CoTC/PSC-FRAM-Admin | config/2015_report_config.r | config/2015_report_config.r |
run.year <- 2015
post.season.fram.db <- "./fram db/FramVS2-PSC-Coho-Backwards-for 2015.mdb"
post.season.run.name <- "bc-bkCoho2015 fw catch queets"
post.season.tamm <- "./fram db/coho BK 2015 in process no tami step 3.xlsm"
pre.season.fram.db <- "./fram db/CohoFRAMVB2015Pre&PostNew.mdb"
pre.season.run.name <- "bc-Co... |
run.year <- 2015
post.season.fram.db <- "./fram db/CohoFRAMVB2015Pre&PostNew.mdb"
post.season.run.name <- "bkCoho2015Post"
post.season.tamm <- "./fram db/Coho1523FinalwAttachCrevised and updated.xlsm"
pre.season.fram.db <- "./fram db/CohoFRAMVB2015Pre&PostNew.mdb"
pre.season.run.name <- "bc-Coho1523 Final"
pre.seaso... | mit | R |
fa0a0dcab4e3d723ffecdec2d7b642bf3b42bcaa | Add function for font embedding | klmr/ggplots | fonts.r | fonts.r | create_extrafontdb = function () {
extrafontdb_path = function ()
system.file('metrics', package = 'extrafontdb', mustWork = TRUE)
path = try(extrafontdb_path(), silent = TRUE)
# If extrafontdb doesn’t exist, this means that the extrafont package isn’t
# installed. Reinstalling it will re-crea... | create_extrafontdb = function () {
extrafontdb_path = function ()
system.file('metrics', package = 'extrafontdb', mustWork = TRUE)
path = try(extrafontdb_path(), silent = TRUE)
# If extrafontdb doesn’t exist, this means that the extrafont package isn’t
# installed. Reinstalling it will re-crea... | apache-2.0 | R |
a7ca3104ca70cfc5a46d2fad3fb778a50735732e | add new test for %then% | TobCap/walkast,TobCap/walkast | tests/testthat/test-then.r | tests/testthat/test-then.r | library(testthat)
context("walkast %then%")
test_that("walkast %then%", {
keep_source <- options()$keep.source
options(keep.source = FALSE)
on.exit(options(keep.source = keep_source))
add1 <- make_visitor(
leaf = function(x) if(is.numeric(x)) x + 1 else x
)
mul2 <- make_visitor(
leaf... | library(testthat)
context("walkast %then%")
test_that("walkast %then%", {
keep_source <- options()$keep.source
options(keep.source = FALSE)
on.exit(options(keep.source = keep_source))
add1 <- make_visitor(
leaf = function(x) if(is.numeric(x)) x + 1 else x
)
mul2 <- make_visitor(
leaf... | mit | R |
9ac884c54f71318b517bec146bdb7485e2e34ebc | add more debugging | snowch/biginsight-examples,snowch/biginsight-examples | examples/BigR/install_packages.r | examples/BigR/install_packages.r | libdir <- Sys.getenv("libdir")
debug <- Sys.getenv("debug")
quiet=TRUE
if (debug) {
quiet=FALSE
}
.libPaths(libdir)
# create directory to hold libraries
dir.create(libdir)
# install libraries
install.packages('rJava', repos='http://cran.us.r-project.org', lib=libdir, quiet=quiet)
install.packages('base... | libdir <- Sys.getenv("libdir")
debug <- Sys.getenv("debug")
quiet=TRUE
if (debug) {
quiet=FALSE
}
.libPaths(libdir)
# create directory to hold libraries
dir.create(libdir)
# install libraries
install.packages('rJava', repos='http://cran.us.r-project.org', lib=libdir, quiet=quiet)
install.packages('base... | apache-2.0 | R |
3a256b6df311064d6e77a4760986a5674bfed196 | Increase number of terms | FTAsr/wordvet,FTAsr/wordvet,FTAsr/wordvet,FTAsr/wordvet | trainGloveModel.r | trainGloveModel.r | args = commandArgs(trailingOnly=TRUE)
if (length(args) != 3) {
cat("trainGloveModel.R <size> <window> <iters>\n")
} else {
suppressMessages(library("text2vec"))
vectorSize <- as.numeric(args[1])
window <- as.numeric(args[2])
iters <- as.numeric(args[3])
print("started running trainGloveModel.r")
text... | args = commandArgs(trailingOnly=TRUE)
if (length(args) != 3) {
cat("trainGloveModel.R <size> <window> <iters>\n")
} else {
suppressMessages(library("text2vec"))
vectorSize <- as.numeric(args[1])
window <- as.numeric(args[2])
iters <- as.numeric(args[3])
print("started running trainGloveModel.r")
text... | apache-2.0 | R |
60c2ad502ef462a35ba899beb89f5e1af3bdfac8 | Support for Plotting WLP added. | felixlindemann/HNUORTools,felixlindemann/HNUORTools | R/01.class.e.HNU.GeoSituation.r | R/01.class.e.HNU.GeoSituation.r | setClass(
Class = "HNUGeoSituation",
representation=representation(
id = "character",
label = "character",
nodes = "list",
links = "list",
warehouses = "list",
customers = "list",
travelcosts = "numeri... | setClass(
Class = "HNUGeoSituation",
representation=representation(
id = "character",
label = "character",
nodes = "list",
links = "list",
warehouses = "list",
customers = "list",
travelcosts = "numeri... | mit | R |
32a7ec80317cbfe896ba386760ff651814149058 | Support arm64 | baku89/glslCanvas4AE,baku89/glslCanvas4AE,baku89/glslCanvas4AE,baku89/glslCanvas4AE | GLSLCanvasPiPL.r | GLSLCanvasPiPL.r | #include "AEConfig.h"
#include "AE_EffectVers.h"
#ifndef AE_OS_WIN
#include <AE_General.r>
#endif
resource 'PiPL' (16000) {
{ /* array properties: 12 elements */
/* [1] */
Kind {
AEEffect
},
/* [2] */
Name {
"GLSLCanvas"
},
/* [3] */
Category {
"Shader"
},
#ifdef AE_OS_WIN
#ifdef AE_PRO... | #include "AEConfig.h"
#include "AE_EffectVers.h"
#ifndef AE_OS_WIN
#include <AE_General.r>
#endif
resource 'PiPL' (16000) {
{ /* array properties: 12 elements */
/* [1] */
Kind {
AEEffect
},
/* [2] */
Name {
"GLSLCanvas"
},
/* [3] */
Category {
"Shader"
},
#ifdef AE_OS_WIN
#ifdef AE_PRO... | mit | R |
9a5a093e3761c14e876596f764e8e4854689438a | Install slidify | daigotanaka/kawaraban,daigotanaka/kawaraban,daigotanaka/kawaraban,daigotanaka/kawaraban | init.r | init.r | install.packages("devtools", dependencies = TRUE)
install.packages("methods", dependencies = TRUE)
install.packages("ggplot2", dependencies = TRUE)
install.packages("knitr", dependencies = TRUE)
install.packages("base64enc", dependencies = TRUE)
library(devtools)
options(unzip = "internal")
install_github('rCharts', 'r... | install.packages("methods", dependencies = TRUE)
install.packages("ggplot2", dependencies = TRUE)
install.packages("knitr", dependencies = TRUE)
install.packages("base64enc", dependencies = TRUE)
library(devtools)
options(unzip = "internal")
install_github("ramnathv/rCharts@dev")
| mit | R |
beda4161bd6074c8b0aa9bdf08637ad61739131b | Document function | klmr/modules,klmr/modules | R/export_submodule.r | R/export_submodule.r | #' Export a given submodule from the current module
#'
#' @param submodule character string of length 1 with the name of the submodule
#' @note Sometimes, a module may want to export all or some of its submodules in
#' bulk. Simply doing \code{import('submodul', attach = TRUE)} won’t work,
#' however, since \code{attac... | export_submodule = function (submodule) {
parent = parent.frame()
module = import(submodule)
expose_single = function (symbol)
assign(symbol, get(symbol, envir = module), envir = parent)
invisible(lapply(ls(module), expose_single))
}
| apache-2.0 | R |
18836f567ac4360f0a35bd1e228b839e0b6bfc85 | update testcase.r | skefi/SpatialStress,skefi/SpatialStress | R/testcase.r | R/testcase.r | source("R/functions.r")
inittest <- init_landscape(c("+","0","-"), c(0.5,0.4,0.1))
mapping(50,50)
summary(inittest)
parmstest <- list(
del = 0.9,
b = 0.8,
c_ = 0.2,
m0 = 0.05,
g = 0.2,
r = 0.01,
f = 0.9,
d = 0.1,
protect = 0.5
)
simtest <- ca(inittest, parmstest)
|
inittest <- init_landscape(c("+","0","-"), c(0.5,0.4,0.1))
mapping(50,50)
summary(inittest)
parmstest <- list(
del = 0.9,
b = 0.8,
c_ = 0.2,
m0 = 0.05,
g = 0.2,
r = 0.01,
f = 0.9,
d = 0.1,
protect = 0.5
)
simtest <- ca(inittest, parmstest)
update_grazing <- function(x_old, parms_temp, delta = 0.2, subs = 10, t... | mit | R |
160f3c9a0f10af854b7a79dbbefba87ec0e8fe2f | Update 1.r | glor/R,glor/R | aufgaben/blatt03/1.r | aufgaben/blatt03/1.r | #Blatt 3
#1.1 Datei lokal speichern
#1.2
maeuse = read.table(file="mice.txt", sep="t", dec=".", header=TRUE)
#1.3
boxplot(maeuse$speed ~ maeuse$health, date = maeuse, main = "kranke Maeuse" )
# Beide Gruppen sind normalverteilt, es gibt keine Aussreisser. (diese wuerden als Punkte ausserhalb der Boxen darge... | #Blatt 3
#1.1 Datei lokal speichern
#1.2
maeuse = read.table(file="mice.txt", sep="t", dec=".", header=TRUE)
#1.3
boxplot(maeuse$speed ~ maeuse$health, date = maeuse, main = "kranke Maeuse" )
# Beide Gruppen sind normalverteilt, es gibt keine Aussreisser. (diese wuerden als Punkte ausserhalb der Boxen darge... | bsd-2-clause | R |
5e28379377a4813db6d2fcfef435020a8299c372 | Update 1.r | glor/R,glor/R | aufgaben/blatt09/1.r | aufgaben/blatt09/1.r | #9.1.1 Nein, es ist keine Korrektur erforderlich.
#9.1.2 Bei einer initialen Vermutung (die neue Polymerase ist besser/schlechter), bräuchte ich nur zwei Vergleiche durchführen (mit geplanten Kontrasten). (Alt-Polymerase gegen Neu-Polymerasen in Gruppe, dann die Neu-Polymerasen gegeneinander). Bei keiner Vermutung mus... | bsd-2-clause | R | |
cd1c7094f51c2bd78144808d2c8c7c2d643a6818 | add rename functionality | wikimedia-research/Blockr | functions.r | functions.r | # functions.r centralises miscellaneous functions used throughout the Blockr project
#
# Copyright (c) 2013 Oliver Keyes
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restrict... | # functions.r centralises miscellaneous functions used throughout the Blockr project
#
# Copyright (c) 2013 Oliver Keyes
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restrict... | mit | R |
f1b627b375cb0f90b116a1db5e5c4a070fb069de | set progress bar to 1 when done | XSEDEScienceGateways/TAG,wrathematics/TAG,XSEDEScienceGateways/textgateway,XSEDEScienceGateways/TAG,wrathematics/TAG,XSEDEScienceGateways/textgateway,XSEDEScienceGateways/TAG,wrathematics/TAG,XSEDEScienceGateways/textgateway | inst/tag/shiny/pages/analyse/lda.r | inst/tag/shiny/pages/analyse/lda.r | output$analyse_lda_fit <- renderUI(
sidebarLayout(
sidebarPanel(
h5("Latent Dirichlet Allocation"),
sliderInput("lda_ntopics", "Number of Topics", min=1, max=20, value=3),
selectizeInput("lda_method", "Method", c("Gibbs", "VEM"), "Gibbs"),
actionButton("lda_button_fit", "Fit"),
rende... | output$analyse_lda_fit <- renderUI(
sidebarLayout(
sidebarPanel(
h5("Latent Dirichlet Allocation"),
sliderInput("lda_ntopics", "Number of Topics", min=1, max=20, value=3),
selectizeInput("lda_method", "Method", c("Gibbs", "VEM"), "Gibbs"),
actionButton("lda_button_fit", "Fit"),
rende... | agpl-3.0 | R |
de2d8578140ca9c97fb63c518c0f6fbfe3ffdaf2 | Update banner | Pointillistic/rebol-lang,Pointillistic/rebol-lang,zsx/r3,zsx/r3,Pointillistic/rebol-lang,Pointillistic/rebol-lang,zsx/r3,zsx/r3 | src/mezz/mezz-banner.r | src/mezz/mezz-banner.r | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: Startup Banner"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2.0
See: http://www.apache.org/licenses/LICENS... | REBOL [
System: "REBOL [R3] Language Interpreter and Run-time Environment"
Title: "REBOL 3 Mezzanine: Startup Banner"
Rights: {
Copyright 2012 REBOL Technologies
REBOL is a trademark of REBOL Technologies
}
License: {
Licensed under the Apache License, Version 2.0
See: http://www.apache.org/licenses/LICENS... | apache-2.0 | R |
e113ec361d4f9c6c69cfaa7f1f395d8638234e2c | Fix species name for optimised 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))
# 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', ... | # 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),
human = 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 |
720ce77caf9aff7a594b81bbcd6bd721c79e243b | fix PRINT compilation test | NikolayShubenkovProgSchool/red,vehar/red,vehar/red,rheber/red,rheber/red,iArnold/red,NikolayShubenkovProgSchool/red,iArnold/red,red-eco/red,red-eco/red | red-system/tests/source/compiler/print-test.r | red-system/tests/source/compiler/print-test.r | REBOL [
Title: "Test print function from Red/System programs"
File: %print-test.r
License: "BSD-3 - https://github.com/dockimbel/Red/blob/master/BSD-3-License.txt"
]
change-dir %../ ;; revert to tests/ directory from runnable/
~~~start-file~~~ "print"
--test-- "p1"
--compile-and-r... | REBOL [
Title: "Test print function from Red/System programs"
File: %print-test.r
License: "BSD-3 - https://github.com/dockimbel/Red/blob/master/BSD-3-License.txt"
]
change-dir %../ ;; revert to tests/ directory from runnable/
~~~start-file~~~ "print"
--test-- "p1"
--compile-and-r... | bsd-3-clause | R |
62130e5eaaed098ba2b821bb055272e761387fee | Update test.r | xiaodaigh/teradata.dplyr | test/test.r | test/test.r | #library("teradataR")
library("RODBC")
library("dplyr")
library("assertthat")
#con <- tdConnect(dsn, uid = uid, pwd = pwd, database = database)
#a <- td.data.frame(test_table)
# tdQuery('select count(*) from udparm.ao_sovn')
#td.stats(a, "Delinquency")
#tdClose()
#a1 <- as.td.data.frame(a, tableName = "ao_sovn2", d... | #library("teradataR")
library("RODBC")
library("dplyr")
library("assertthat")
#con <- tdConnect(dsn, uid = uid, pwd = pwd, database = database)
#a <- td.data.frame(test_table)
# tdQuery('select count(*) from airlines')
#tdClose()
#a1 <- as.td.data.frame(a, tableName = "airlines", database = "")
st <- src_teradata(h... | mit | R |
b8592591ea702b2f12ead53677bfe603d0bc5940 | fix up the plot a bit | rhansen/rpstir,rhansen/rpstir,rhansen/rpstir,rhansen/rpstir,rhansen/rpstir | bin/rpki-statistics/plots/run-times-over-time.r | bin/rpki-statistics/plots/run-times-over-time.r | data <- read.table('run-times-over-time.dat', sep="\t", header=TRUE)
data$Start <- as.POSIXlt(read.table('times.dat', sep="\t", header=TRUE)$Start)
png('run-times-over-time.png', width=1600, height=1200, pointsize=24)
plot(data$Start, data$Duration/60, type="o",
main="Combined Fetch and Validation Times",
xlab... | data <- read.table('run-times-over-time.dat', sep="\t", header=TRUE)
data$Start <- as.POSIXlt(read.table('times.dat', sep="\t", header=TRUE)$Start)
png('run-times-over-time.png')
plot(data)
dev.off()
| bsd-3-clause | R |
058184685c60ab82a54a7c869bef9ceac2d059ae | Remove trailing slash | berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,berkeley-dsep-infra/datahub,ryanlovett/datahub,ryanlovett/datahub,ryanlovett/datahub | deployments/r/image/extras.d/ph-w250fg.r | deployments/r/image/extras.d/ph-w250fg.r | #!/usr/bin/env Rscript
# From https://github.com/berkeley-dsep-infra/datahub/issues/881
print("Installing packages for PHW250F+G")
source("/tmp/class-libs.R")
# dplyr requires 0.2.1...cran only has 0.2.0
print("Installing assertthat...")
devtools::install_github('hadley/assertthat', ref='v0.2.1', upgrade_dependencies... | #!/usr/bin/env Rscript
# From https://github.com/berkeley-dsep-infra/datahub/issues/881
print("Installing packages for PHW250F+G")
source("/tmp/class-libs.R")
# dplyr requires 0.2.1...cran only has 0.2.0
print("Installing assertthat...")
devtools::install_github('hadley/assertthat', ref='v0.2.1', upgrade_dependencies... | bsd-3-clause | R |
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