content large_stringlengths 0 6.46M | path large_stringlengths 3 331 | license_type large_stringclasses 2
values | repo_name large_stringlengths 5 125 | language large_stringclasses 1
value | is_vendor bool 2
classes | is_generated bool 2
classes | length_bytes int64 4 6.46M | extension large_stringclasses 75
values | text stringlengths 0 6.46M |
|---|---|---|---|---|---|---|---|---|---|
#################################################################
## calculate change in area % for scenarios
##################################################################
inimap<-raster('C:/Users/Vivienne Groner/Desktop/Vivienne/2020/SDM/Clivia_miniata_2020/predictors/MODIS/scen000/MODIS_LCType.grd')
endmap... | /calc_suitable_landcover.R | no_license | vgro/Groner_medicinal_plants | R | false | false | 1,452 | r | #################################################################
## calculate change in area % for scenarios
##################################################################
inimap<-raster('C:/Users/Vivienne Groner/Desktop/Vivienne/2020/SDM/Clivia_miniata_2020/predictors/MODIS/scen000/MODIS_LCType.grd')
endmap... |
\name{summary.OptimMCL.HCAR}
\alias{summary.OptimMCL.HCAR}
\alias{ranef.HCAR}
\title{Summary the output from the iterative procedure of maximising the
Monte Carlo likelihood.
}
\description{The summary function summarizes the output of the output from the
function \code{\link{OptimMCL.HCAR}} and the \code{ranef.HC... | /mclcar_0.1-8/man/summary.OptimMCL.HCAR.Rd | no_license | shazhe/mclcar | R | false | false | 2,230 | rd | \name{summary.OptimMCL.HCAR}
\alias{summary.OptimMCL.HCAR}
\alias{ranef.HCAR}
\title{Summary the output from the iterative procedure of maximising the
Monte Carlo likelihood.
}
\description{The summary function summarizes the output of the output from the
function \code{\link{OptimMCL.HCAR}} and the \code{ranef.HC... |
##overall goal here is simply to examine how household energy usage varies over a 2-day period
##in February, 2007. Your task is to reconstruct the following plots below, all of which were
##constructed using the base plotting system.
getwd()
setwd("~/JH Data Science/Exploratory Data Analysis/Week1 Peer Graded Assign... | /plot2.R | no_license | kum8ar/Coursera_JHU_ExploratoryDS_Project1 | R | false | false | 2,665 | r | ##overall goal here is simply to examine how household energy usage varies over a 2-day period
##in February, 2007. Your task is to reconstruct the following plots below, all of which were
##constructed using the base plotting system.
getwd()
setwd("~/JH Data Science/Exploratory Data Analysis/Week1 Peer Graded Assign... |
# Load packages, reserve a core for OS and other programs
library(parallel)
library(doParallel)
library(tidyverse)
library(rvest)
library("jiebaR")
cl <- makeCluster(detectCores() - 1) # convention to leave 1 core for OS
registerDoParallel(cl)
#Scrap data
content<-sapply(PDWebpageList, function(url){
tryCatch(
u... | /PDailyScratch.R | no_license | juan-qian/814-Political_Identity | R | false | false | 1,175 | r | # Load packages, reserve a core for OS and other programs
library(parallel)
library(doParallel)
library(tidyverse)
library(rvest)
library("jiebaR")
cl <- makeCluster(detectCores() - 1) # convention to leave 1 core for OS
registerDoParallel(cl)
#Scrap data
content<-sapply(PDWebpageList, function(url){
tryCatch(
u... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Pwr.r
\name{Pwr}
\alias{Pwr}
\title{Power for single-stage parallel-group RCT.}
\usage{
Pwr(pc, pt, Nc, alp = 0.05)
}
\arguments{
\item{pc}{Response probability in control group.}
\item{pt}{Response probability in treatment group.}
\item{Nc... | /man/Pwr.Rd | no_license | arsenionhacolo/InferenceBEAGSD | R | false | true | 813 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Pwr.r
\name{Pwr}
\alias{Pwr}
\title{Power for single-stage parallel-group RCT.}
\usage{
Pwr(pc, pt, Nc, alp = 0.05)
}
\arguments{
\item{pc}{Response probability in control group.}
\item{pt}{Response probability in treatment group.}
\item{Nc... |
# Assignment 6 Visualizing Data
# Accessing the Data API
library(wbstats)
library(ggplot2)
library(tidyr)
library(dplyr)
library(maps)
library(RColorBrewer)
options(scipen = 999)
# 1. Loading and Understanding the Data
#View(wbindicators())
top_10_co2_countries <- wb(country = "countries_only", indicator = c("EN.AT... | /A6_Visulization/analysis.R | no_license | BasedAbe/R-code | R | false | false | 6,778 | r | # Assignment 6 Visualizing Data
# Accessing the Data API
library(wbstats)
library(ggplot2)
library(tidyr)
library(dplyr)
library(maps)
library(RColorBrewer)
options(scipen = 999)
# 1. Loading and Understanding the Data
#View(wbindicators())
top_10_co2_countries <- wb(country = "countries_only", indicator = c("EN.AT... |
#` @import partykit
.list.rules.party <- function(x, i = NULL, ...) {
if (is.null(i)) i <- partykit::nodeids(x, terminal = TRUE)
if (length(i) > 1) {
ret <- sapply(i, .list.rules.party, x = x)
names(ret) <- if (is.character(i)) i else names(x)[i]
return(ret)
}
if (is.character(i) && !is.null(names(x... | /R/partykitModFuns.R | no_license | wpihongzhang/fiveSTAR | R | false | false | 2,150 | r | #` @import partykit
.list.rules.party <- function(x, i = NULL, ...) {
if (is.null(i)) i <- partykit::nodeids(x, terminal = TRUE)
if (length(i) > 1) {
ret <- sapply(i, .list.rules.party, x = x)
names(ret) <- if (is.character(i)) i else names(x)[i]
return(ret)
}
if (is.character(i) && !is.null(names(x... |
#' Get values from intersecting objects
#'
#' Extract values from intersecting sf objects
#'
#' @param x an sf object
#' @param y an sf object
#' @param x_id a column in x that uniquely identfies features
#' @param y_id a column in y that uniquely identfies features
#' @import sf
#' @import purrr
#' @import dplyr
#' @i... | /R/xy_intersection.R | permissive | MatthewJWhittle/spatialutils | R | false | false | 1,423 | r | #' Get values from intersecting objects
#'
#' Extract values from intersecting sf objects
#'
#' @param x an sf object
#' @param y an sf object
#' @param x_id a column in x that uniquely identfies features
#' @param y_id a column in y that uniquely identfies features
#' @import sf
#' @import purrr
#' @import dplyr
#' @i... |
###batting log wrangled in "substring.r"
###data was slightly edited from original. redo in R.
library(rethinking)
library(tidyverse)
###
###
set.seed(1234)
options(mc.cores = parallel::detectCores())
###
m3 <- map2stan(
alist(
rdiff ~ dnorm( mu, sigma),
#likelihood function
mu <- A + B + C,
#varying ... | /Bayesian Baseball 2018/scripts/Modeling/Two Factor Models/battingpitching.r | no_license | blakeshurtz/Bayesian-Baseball | R | false | false | 1,471 | r | ###batting log wrangled in "substring.r"
###data was slightly edited from original. redo in R.
library(rethinking)
library(tidyverse)
###
###
set.seed(1234)
options(mc.cores = parallel::detectCores())
###
m3 <- map2stan(
alist(
rdiff ~ dnorm( mu, sigma),
#likelihood function
mu <- A + B + C,
#varying ... |
testlist <- list(ends = c(-1125300777L, 765849512L, -1760774663L, 791623263L, 1358782356L, -128659642L, -14914341L, 1092032927L, 1837701012L, 1632068659L), pts = c(1758370433L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,... | /IntervalSurgeon/inst/testfiles/rcpp_pile/AFL_rcpp_pile/rcpp_pile_valgrind_files/1609860123-test.R | no_license | akhikolla/updated-only-Issues | R | false | false | 728 | r | testlist <- list(ends = c(-1125300777L, 765849512L, -1760774663L, 791623263L, 1358782356L, -128659642L, -14914341L, 1092032927L, 1837701012L, 1632068659L), pts = c(1758370433L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,... |
% Generated by roxygen2 (4.1.0): do not edit by hand
% Please edit documentation in R/write.R
\name{write.cas}
\alias{write.cas}
\title{Write a SaTScan cas (case) file}
\usage{
write.cas(x, location, filename, userownames = FALSE)
}
\arguments{
\item{x}{Your data frame.}
\item{location}{Directory location where the fi... | /man/write.cas.Rd | no_license | skhan8/rsatscan | R | false | false | 775 | rd | % Generated by roxygen2 (4.1.0): do not edit by hand
% Please edit documentation in R/write.R
\name{write.cas}
\alias{write.cas}
\title{Write a SaTScan cas (case) file}
\usage{
write.cas(x, location, filename, userownames = FALSE)
}
\arguments{
\item{x}{Your data frame.}
\item{location}{Directory location where the fi... |
#Create sub-metering plot
library(lubridate)
library(grDevices)
elecpwconsump <- read.table("./household_power_consumption.txt",header = TRUE,sep = ";")
elecpwconsump$Date <- as.Date(as.character(elecpwconsump$Date),"%d/%m/%Y")
filteredelecdata <- subset(elecpwconsump,
as.POSIXlt(elecpwconsu... | /plot3.R | no_license | viseshraj/ExData_Plotting1 | R | false | false | 1,228 | r | #Create sub-metering plot
library(lubridate)
library(grDevices)
elecpwconsump <- read.table("./household_power_consumption.txt",header = TRUE,sep = ";")
elecpwconsump$Date <- as.Date(as.character(elecpwconsump$Date),"%d/%m/%Y")
filteredelecdata <- subset(elecpwconsump,
as.POSIXlt(elecpwconsu... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/add_WYD.R
\name{add_WYD}
\alias{add_WYD}
\title{Add Day of Year, Day of Water Year.}
\usage{
add_WYD(df, datecolumn)
}
\arguments{
\item{df}{a dataframe}
\item{datecolumn}{quoted, requires a POSIXct formatted date or datetime}
}
\description... | /man/add_WYD.Rd | permissive | ryanpeek/wateRshedTools | R | false | true | 1,271 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/add_WYD.R
\name{add_WYD}
\alias{add_WYD}
\title{Add Day of Year, Day of Water Year.}
\usage{
add_WYD(df, datecolumn)
}
\arguments{
\item{df}{a dataframe}
\item{datecolumn}{quoted, requires a POSIXct formatted date or datetime}
}
\description... |
# Functions that use the 'magick' package (ImageMagick) to combine separate brainview images into one image.
# Currently 'magick' is an optional dependency only.
#' @title Combine several brainview images into a new figure.
#'
#' @description Create a new image from several image tiles, the exact layout depends on th... | /R/brainview_magick.R | permissive | haitaoge/fsbrain | R | false | false | 29,427 | r | # Functions that use the 'magick' package (ImageMagick) to combine separate brainview images into one image.
# Currently 'magick' is an optional dependency only.
#' @title Combine several brainview images into a new figure.
#'
#' @description Create a new image from several image tiles, the exact layout depends on th... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/deep.service.R
\name{deepAuction}
\alias{deepAuction}
\title{IEX Depth of Book}
\usage{
deepAuction(symbol)
}
\arguments{
\item{symbol}{a market symbol, one and only one symbol}
}
\description{
DEEP is used to receive real-time depth of book ... | /man/deepAuction.Rd | no_license | Sahanduiuc/iexcloudR | R | false | true | 1,188 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/deep.service.R
\name{deepAuction}
\alias{deepAuction}
\title{IEX Depth of Book}
\usage{
deepAuction(symbol)
}
\arguments{
\item{symbol}{a market symbol, one and only one symbol}
}
\description{
DEEP is used to receive real-time depth of book ... |
# Install relevant libraries ---------------------------------------------------
library(igraph)
library(ggplot2)
library(grid)
library(sf)
library(tidyverse)
library(tigris)
# Import trip data -------------------------------------------------------------
dir <- "/home/marion/PVDResearch/Data/mobilityData/cleanData"
#... | /scooterData/clusterInfomap.R | no_license | alicepaul/pvd_summer | R | false | false | 4,878 | r | # Install relevant libraries ---------------------------------------------------
library(igraph)
library(ggplot2)
library(grid)
library(sf)
library(tidyverse)
library(tigris)
# Import trip data -------------------------------------------------------------
dir <- "/home/marion/PVDResearch/Data/mobilityData/cleanData"
#... |
## __________________________________________________________
##
## RepresentationXGroup
##
## INPUT: x: Adjency matrix
## cluste: Vector of the classes
##
## Representation of the nodes and the corresponding groups after reorganization
## __________________________________________________________
Representatio... | /representations.R | no_license | docteurZ/cohsmix | R | false | false | 1,770 | r | ## __________________________________________________________
##
## RepresentationXGroup
##
## INPUT: x: Adjency matrix
## cluste: Vector of the classes
##
## Representation of the nodes and the corresponding groups after reorganization
## __________________________________________________________
Representatio... |
library(dfped)
### Name: doseRange
### Title: Dose-range for the paediatric population according to adult
### clearance, adult doses and paediatric clearance.
### Aliases: doseRange
### ** Examples
## Not run:
##D
##D ########
##D # Note: For this example we are using a paediatric database that we have... | /data/genthat_extracted_code/dfped/examples/doseRange.Rd.R | no_license | surayaaramli/typeRrh | R | false | false | 1,414 | r | library(dfped)
### Name: doseRange
### Title: Dose-range for the paediatric population according to adult
### clearance, adult doses and paediatric clearance.
### Aliases: doseRange
### ** Examples
## Not run:
##D
##D ########
##D # Note: For this example we are using a paediatric database that we have... |
# patient screening
# run MBO query:
# * Patients - by Medication (Generic)
# - Facility (Curr): HH HERMANN;HH Trans Care;HH Rehab;HH Clinics
# - Date Only - Admit (Start): 7/1/2012 12:00:00 AM # in 12 month increments
# - Date Only - Admit (End): 1/1/2017 12:00:00 AM
# - Medication (Generic)... | /src/01_screen-patients.R | no_license | bgulbis/DOAC_Warfarin_Readmission | R | false | false | 4,483 | r | # patient screening
# run MBO query:
# * Patients - by Medication (Generic)
# - Facility (Curr): HH HERMANN;HH Trans Care;HH Rehab;HH Clinics
# - Date Only - Admit (Start): 7/1/2012 12:00:00 AM # in 12 month increments
# - Date Only - Admit (End): 1/1/2017 12:00:00 AM
# - Medication (Generic)... |
testlist <- list(bytes1 = c(-1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,... | /mcga/inst/testfiles/ByteCodeMutation/libFuzzer_ByteCodeMutation/ByteCodeMutation_valgrind_files/1612802384-test.R | no_license | akhikolla/updatedatatype-list3 | R | false | false | 482 | r | testlist <- list(bytes1 = c(-1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prettify.R
\name{prettify_strings}
\alias{prettify_strings}
\alias{prettify_de}
\alias{prettify_en}
\title{Replace/prettify matching words/terms in one vector by another}
\usage{
prettify_strings(x, current = .trans_df$english,
new = .trans... | /man/prettify.Rd | permissive | fsolt/coalitions | R | false | true | 1,006 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prettify.R
\name{prettify_strings}
\alias{prettify_strings}
\alias{prettify_de}
\alias{prettify_en}
\title{Replace/prettify matching words/terms in one vector by another}
\usage{
prettify_strings(x, current = .trans_df$english,
new = .trans... |
#' Do a redundancy analysis
#'
#' Perform a redundancy analysis (RA) as proposed by \insertCite{Hair2016;textual}{cSEM}
#' with reference to \insertCite{Chin1998;textual}{cSEM}.
#'
#' RA is confined to PLS-PM, specifically PLS-PM with at least one construct
#' whose weights are obtained by mode B. In cSEM this is the c... | /R/postestimate_doRedundancyAnalysis.R | no_license | RicoDiel/cSEM | R | false | false | 3,348 | r | #' Do a redundancy analysis
#'
#' Perform a redundancy analysis (RA) as proposed by \insertCite{Hair2016;textual}{cSEM}
#' with reference to \insertCite{Chin1998;textual}{cSEM}.
#'
#' RA is confined to PLS-PM, specifically PLS-PM with at least one construct
#' whose weights are obtained by mode B. In cSEM this is the c... |
context("im3d io")
test_that("we can read im3d files",{
expect_is(d<-read.im3d("testdata/nrrd/LHMask.nrrd"),'im3d')
expect_is(d,'array')
expect_true(is.integer(d))
expect_equal(sum(d!=0), 28669)
expect_equal(read.im3d("testdata/nrrd/LHMask.nhdr"), d)
expect_is(d0<-read.im3d("testdata/nrrd/LHMask.nrrd... | /tests/testthat/test-im3d.R | no_license | natverse/nat | R | false | false | 12,974 | r | context("im3d io")
test_that("we can read im3d files",{
expect_is(d<-read.im3d("testdata/nrrd/LHMask.nrrd"),'im3d')
expect_is(d,'array')
expect_true(is.integer(d))
expect_equal(sum(d!=0), 28669)
expect_equal(read.im3d("testdata/nrrd/LHMask.nhdr"), d)
expect_is(d0<-read.im3d("testdata/nrrd/LHMask.nrrd... |
trackSpeed <- function(dist, bin=5, interval=1){
v <- c()
for (i in 1:(length(dist)-bin)){
v[i] <- sum(dist[i:(i+bin-1)])/bin
}
return(v/interval)
} | /RImageBook/R/trackSpeed.R | no_license | tkatsuki/rimagebook | R | false | false | 166 | r | trackSpeed <- function(dist, bin=5, interval=1){
v <- c()
for (i in 1:(length(dist)-bin)){
v[i] <- sum(dist[i:(i+bin-1)])/bin
}
return(v/interval)
} |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/efficiency_algorithms.R
\name{SeqKL}
\alias{SeqKL}
\title{Sequential Kullback-Leibler based algorithm for the MNL model.}
\usage{
SeqKL(
des = NULL,
cand.set,
n.alts,
par.draws,
alt.cte = NULL,
no.choice = NULL,
wei... | /man/SeqKL.Rd | no_license | cran/idefix | R | false | true | 3,718 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/efficiency_algorithms.R
\name{SeqKL}
\alias{SeqKL}
\title{Sequential Kullback-Leibler based algorithm for the MNL model.}
\usage{
SeqKL(
des = NULL,
cand.set,
n.alts,
par.draws,
alt.cte = NULL,
no.choice = NULL,
wei... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/paws.configservice_package.R
\docType{package}
\name{paws.configservice-package}
\alias{paws.configservice}
\alias{paws.configservice-package}
\title{paws.configservice: AWS Config}
\description{
AWS Config provides a way to keep track of the... | /service/paws.configservice/man/paws.configservice-package.Rd | permissive | CR-Mercado/paws | R | false | true | 1,218 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/paws.configservice_package.R
\docType{package}
\name{paws.configservice-package}
\alias{paws.configservice}
\alias{paws.configservice-package}
\title{paws.configservice: AWS Config}
\description{
AWS Config provides a way to keep track of the... |
library(ggplot2)
library(dplyr)
setwd("C:/source/bio/project") # should be altered
NAME <- 'vsm.hg38' # should be altered
OUT_DIR <- 'results/'
bed_df <- read.delim(paste0('data/', NAME, '.bed'), as.is = TRUE, header = FALSE)
colnames(bed_df) <- c('chrom', 'start', 'end', 'name', 'score')
bed_df$len <- bed_df$end - ... | /src/not_filtered_peaks.r | no_license | qwerty-Bk/hse21_H3K27me3_ZDNA_human | R | false | false | 549 | r | library(ggplot2)
library(dplyr)
setwd("C:/source/bio/project") # should be altered
NAME <- 'vsm.hg38' # should be altered
OUT_DIR <- 'results/'
bed_df <- read.delim(paste0('data/', NAME, '.bed'), as.is = TRUE, header = FALSE)
colnames(bed_df) <- c('chrom', 'start', 'end', 'name', 'score')
bed_df$len <- bed_df$end - ... |
library(readr)
library(ggplot2)
library(jsonlite)
library(dplyr)
library(plyr)
library(tibble)
library(maps)
library(RCurl)
library(ggmap)
library(mapdata)
library(devtools)
library(lubridate)
library(DataExplorer)
library(ggpubr)
library(gridExtra)
library(tidyverse)
library(reshape2)
library(ggrepel)... | /LoL.R | no_license | RyanKirwan/Exploring-LoL-Datasets | R | false | false | 4,102 | r | library(readr)
library(ggplot2)
library(jsonlite)
library(dplyr)
library(plyr)
library(tibble)
library(maps)
library(RCurl)
library(ggmap)
library(mapdata)
library(devtools)
library(lubridate)
library(DataExplorer)
library(ggpubr)
library(gridExtra)
library(tidyverse)
library(reshape2)
library(ggrepel)... |
getwd()
mydata= read.csv('C:\\Users\\benve\\Documents\\university\\year3\\CS3002\\Labs\\Lab 1\\forestfires.csv',sep=',')
plot(mydata)
View(mydata)
#refer by column name
plot(mydata$temp, mydata$wind)
#refer by index
plot(mydata[,9],mydata[,11])
#histogram
hist(mydata$temp)
#line plots
plot(mydata$temp,type="l")... | /Lab 1/lab1.R | no_license | Benveer/cs3002-labs | R | false | false | 654 | r | getwd()
mydata= read.csv('C:\\Users\\benve\\Documents\\university\\year3\\CS3002\\Labs\\Lab 1\\forestfires.csv',sep=',')
plot(mydata)
View(mydata)
#refer by column name
plot(mydata$temp, mydata$wind)
#refer by index
plot(mydata[,9],mydata[,11])
#histogram
hist(mydata$temp)
#line plots
plot(mydata$temp,type="l")... |
# Definición del UI
shinyUI(basicPage(
fluidRow(
column(width = 4,
plotOutput("plot", height=300,
click = "plot_click", # Equiv, to click=clickOpts(id="plot_click")
hover = hoverOpts(id = "plot_hover", delayType = "throttle"),
brush = brushOpts(id = "plot_brush")
... | /programacion R/Shiny/click/ui.R | no_license | coalescencia/data-science | R | false | false | 776 | r | # Definición del UI
shinyUI(basicPage(
fluidRow(
column(width = 4,
plotOutput("plot", height=300,
click = "plot_click", # Equiv, to click=clickOpts(id="plot_click")
hover = hoverOpts(id = "plot_hover", delayType = "throttle"),
brush = brushOpts(id = "plot_brush")
... |
context("rbind.mids")
expect_warning(imp1 <<- mice(nhanes[1:13, ], m = 2, maxit = 1, print = FALSE))
test_that("Constant variables are not imputed by default", {
expect_equal(sum(is.na(complete(imp1))), 6L)
})
expect_warning(imp1b <<- mice(nhanes[1:13, ], m = 2, maxit = 1, print = FALSE, remove.constant = FA... | /tests/testthat/test-rbind.R | no_license | worldbank/mice | R | false | false | 3,215 | r | context("rbind.mids")
expect_warning(imp1 <<- mice(nhanes[1:13, ], m = 2, maxit = 1, print = FALSE))
test_that("Constant variables are not imputed by default", {
expect_equal(sum(is.na(complete(imp1))), 6L)
})
expect_warning(imp1b <<- mice(nhanes[1:13, ], m = 2, maxit = 1, print = FALSE, remove.constant = FA... |
# weighting edges
# the cells will be nodes
load("all_cells.rda")
# need the network
load("hybrid_cytokine_network.rda")
# need expression for each PAAD sample
load("paad_expr_cell_decon_and_clin.rda")
library("AnnotationDbi")
library("org.Hs.eg.db")
geneSymbols <- mapIds(org.Hs.eg.db, keys=rownames(paad), column... | /Code/archive/Src/Archive/edge_weighting.R | no_license | IlyaLab/Pan-Cancer-Cell-Cell-Comm-Net | R | false | false | 2,774 | r |
# weighting edges
# the cells will be nodes
load("all_cells.rda")
# need the network
load("hybrid_cytokine_network.rda")
# need expression for each PAAD sample
load("paad_expr_cell_decon_and_clin.rda")
library("AnnotationDbi")
library("org.Hs.eg.db")
geneSymbols <- mapIds(org.Hs.eg.db, keys=rownames(paad), column... |
# Create a package with state-level quarterly tax data
# 5/2/2018
# stabbr date source ic value level
# Note that historical state totals appear to be available only from around 1977 forward,
# but U.S. totals are available from the early 1960s.
# Package authoring with RStudio:
#
# http://r-pkgs.had.co.nz/
#
# S... | /data-raw/programs/OLD_get_latest_qtax_from_API.r | no_license | donboyd5/qtax | R | false | false | 6,315 | r | # Create a package with state-level quarterly tax data
# 5/2/2018
# stabbr date source ic value level
# Note that historical state totals appear to be available only from around 1977 forward,
# but U.S. totals are available from the early 1960s.
# Package authoring with RStudio:
#
# http://r-pkgs.had.co.nz/
#
# S... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/shmc.R
\name{sample_tmb_hmc}
\alias{sample_tmb_hmc}
\title{Draw MCMC samples from a model posterior using a static HMC sampler.}
\usage{
sample_tmb_hmc(iter, fn, gr, init, L, eps, warmup = floor(iter/2),
seed = NULL, chain = 1, thin = 1, co... | /man/sample_tmb_hmc.Rd | no_license | ChuangWan/adnuts | R | false | true | 2,562 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/shmc.R
\name{sample_tmb_hmc}
\alias{sample_tmb_hmc}
\title{Draw MCMC samples from a model posterior using a static HMC sampler.}
\usage{
sample_tmb_hmc(iter, fn, gr, init, L, eps, warmup = floor(iter/2),
seed = NULL, chain = 1, thin = 1, co... |
#Basic Machine Learning on kaggle titanic dataset
nomsg<-suppressMessages
nomsg(library(tidyverse))
nomsg(library(caret))
nomsg(library(mice))
nomsg(library(xgboost))
library(RANN)
library(caretEnsemble)
library(Amelia)
train<-read.csv("train.csv",stringsAsFactors = F)
train<-as.tibble(train)
#Remove cabin... | /titan with h2o.R | no_license | Nelson-Gon/Deepdeeph2o | R | false | false | 4,156 | r |
#Basic Machine Learning on kaggle titanic dataset
nomsg<-suppressMessages
nomsg(library(tidyverse))
nomsg(library(caret))
nomsg(library(mice))
nomsg(library(xgboost))
library(RANN)
library(caretEnsemble)
library(Amelia)
train<-read.csv("train.csv",stringsAsFactors = F)
train<-as.tibble(train)
#Remove cabin... |
###########################################################################################
### Filename: marginal.boxplot.R
### Creation Date: Friday, 13 November 2015 01:00 PM CST
### Last Modified: Thursday, 03 December 2015 08:30 AM CST
##########################################################################... | /R/marginal.boxplot.R | no_license | eheinzen/Ethan | R | false | false | 10,723 | r | ###########################################################################################
### Filename: marginal.boxplot.R
### Creation Date: Friday, 13 November 2015 01:00 PM CST
### Last Modified: Thursday, 03 December 2015 08:30 AM CST
##########################################################################... |
#' The butter function takes in a dataframe with 'words' and 'activation' columns, and
#' calls the spread function for a specific number of times to simulate the spread of
#' activation of a given initial activation space (specified in start_time) over time.
#'
#' Note: butter.decay() is a modified function of butter.... | /R/butter.parallel.R | no_license | csqsiew/samr | R | false | false | 3,730 | r | #' The butter function takes in a dataframe with 'words' and 'activation' columns, and
#' calls the spread function for a specific number of times to simulate the spread of
#' activation of a given initial activation space (specified in start_time) over time.
#'
#' Note: butter.decay() is a modified function of butter.... |
dataRead <- "//mizazaycensql01/SCMBIR/Client Dashboard/DataIn"
setwd(dataRead)
tl <- list.files(getwd())
tl <- tl[grep("VoC", tl)]
tl <- tl[order(tl)]
tl <- tl[length(tl)]
VoC <- read.csv(tl)
FUNVOC <- function(PH, Metric){
VoC <- VoC[which(VoC$Product == PH),] ###
VoC$Date <- as.Date(VoC$Date, for... | /graphs/VoCGraph.R | no_license | andrubrown/ClientDashboard | R | false | false | 962 | r | dataRead <- "//mizazaycensql01/SCMBIR/Client Dashboard/DataIn"
setwd(dataRead)
tl <- list.files(getwd())
tl <- tl[grep("VoC", tl)]
tl <- tl[order(tl)]
tl <- tl[length(tl)]
VoC <- read.csv(tl)
FUNVOC <- function(PH, Metric){
VoC <- VoC[which(VoC$Product == PH),] ###
VoC$Date <- as.Date(VoC$Date, for... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/patchMatch.R
\name{polarDecomposition}
\alias{polarDecomposition}
\title{polar decomposition with reflection control}
\usage{
polarDecomposition(X)
}
\arguments{
\item{X}{matrix}
}
\value{
decomposition into P Z and approximation of X by \cod... | /man/polarDecomposition.Rd | no_license | stnava/patchMatchR | R | false | true | 563 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/patchMatch.R
\name{polarDecomposition}
\alias{polarDecomposition}
\title{polar decomposition with reflection control}
\usage{
polarDecomposition(X)
}
\arguments{
\item{X}{matrix}
}
\value{
decomposition into P Z and approximation of X by \cod... |
/R/NLo_parm.r | no_license | dpphat/partFilt | R | false | false | 1,492 | r | ||
timestamp <- Sys.time()
library(caret)
library(plyr)
library(recipes)
library(dplyr)
model <- "treebag"
#########################################################################
set.seed(2)
training <- twoClassSim(50, linearVars = 2)
testing <- twoClassSim(500, linearVars = 2)
trainX <- training[, -ncol(trainin... | /RegressionTests/Code/treebag.R | no_license | topepo/caret | R | false | false | 7,673 | r | timestamp <- Sys.time()
library(caret)
library(plyr)
library(recipes)
library(dplyr)
model <- "treebag"
#########################################################################
set.seed(2)
training <- twoClassSim(50, linearVars = 2)
testing <- twoClassSim(500, linearVars = 2)
trainX <- training[, -ncol(trainin... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sugsclusterProb.R
\name{sugsclusterProb}
\alias{sugsclusterProb}
\title{A function to compute the marginal probability of belong to an occupied cluster for the SUGS algorithm}
\usage{
sugsclusterProb(x, K, i, D, n, betaHat, phi, m, nu, S, lam... | /man/sugsclusterProb.Rd | no_license | ococrook/sugsvarsel | R | false | true | 1,173 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sugsclusterProb.R
\name{sugsclusterProb}
\alias{sugsclusterProb}
\title{A function to compute the marginal probability of belong to an occupied cluster for the SUGS algorithm}
\usage{
sugsclusterProb(x, K, i, D, n, betaHat, phi, m, nu, S, lam... |
library(queueing)
### Name: VT.o_MM1K
### Title: Returns the variance of the time spend in the M/M/1/K queueing
### model
### Aliases: VT.o_MM1K
### Keywords: M/M/1/K
### ** Examples
## create input parameters
i_mm1k <- NewInput.MM1K(lambda=5, mu=5.714, k=15)
## Build the model
o_mm1k <- QueueingModel(i_mm1k)
... | /data/genthat_extracted_code/queueing/examples/VT.o_MM1K.Rd.R | no_license | surayaaramli/typeRrh | R | false | false | 358 | r | library(queueing)
### Name: VT.o_MM1K
### Title: Returns the variance of the time spend in the M/M/1/K queueing
### model
### Aliases: VT.o_MM1K
### Keywords: M/M/1/K
### ** Examples
## create input parameters
i_mm1k <- NewInput.MM1K(lambda=5, mu=5.714, k=15)
## Build the model
o_mm1k <- QueueingModel(i_mm1k)
... |
library(varSelRF)
### Name: plot.varSelRF
### Title: Plot a varSelRF object
### Aliases: plot.varSelRF
### Keywords: tree classif
### ** Examples
x <- matrix(rnorm(25 * 30), ncol = 30)
x[1:10, 1:2] <- x[1:10, 1:2] + 2
cl <- factor(c(rep("A", 10), rep("B", 15)))
rf.vs1 <- varSelRF(x, cl, ntree = 200, ntreeIterat ... | /data/genthat_extracted_code/varSelRF/examples/plot.varSelRF.Rd.R | no_license | surayaaramli/typeRrh | R | false | false | 391 | r | library(varSelRF)
### Name: plot.varSelRF
### Title: Plot a varSelRF object
### Aliases: plot.varSelRF
### Keywords: tree classif
### ** Examples
x <- matrix(rnorm(25 * 30), ncol = 30)
x[1:10, 1:2] <- x[1:10, 1:2] + 2
cl <- factor(c(rep("A", 10), rep("B", 15)))
rf.vs1 <- varSelRF(x, cl, ntree = 200, ntreeIterat ... |
context("test - getFpcScores")
context("1. test - getFpcScoresIN validate input")
yMat <- matrix(rnorm(36), 6, 6) %>>% ((. + t(.)) / 2)
diag(yMat) <- diag(yMat) + 0.5
eigRes <- eigen(yMat)
splitVar <- rep(1, 6)
allTimePnts <- 1:6
meanFunc <- rnorm(6)
test_that("test - getFpcScoresIN validate input", {
expect_error(r... | /tests/testthat/test-getFpcScores.R | permissive | alexchang2017/rfda | R | false | false | 3,863 | r | context("test - getFpcScores")
context("1. test - getFpcScoresIN validate input")
yMat <- matrix(rnorm(36), 6, 6) %>>% ((. + t(.)) / 2)
diag(yMat) <- diag(yMat) + 0.5
eigRes <- eigen(yMat)
splitVar <- rep(1, 6)
allTimePnts <- 1:6
meanFunc <- rnorm(6)
test_that("test - getFpcScoresIN validate input", {
expect_error(r... |
###################################################################################################
#' Objective Function Evaluation
#'
#' This function handles the evaluation of the objective function in \code{\link{spot}}.
#' This includes handling of the random number generator stream as well as the actual eva... | /R/objectiveFunctionEvaluation.R | no_license | bartzbeielstein/SPOT | R | false | false | 2,777 | r |
###################################################################################################
#' Objective Function Evaluation
#'
#' This function handles the evaluation of the objective function in \code{\link{spot}}.
#' This includes handling of the random number generator stream as well as the actual eva... |
# 1. write a function that take a vector as its argument and then calculate the mean of the vector
mean_calculator <- ... (x){
# calculate the sum of the vector
sum_x <- ...
# calculate the length of the vector
length_x <- ...
# calculate the mean
mean_x <- sum_x / length_x
# return the mean
...
... | /homeworks/homework1_advanced.R | permissive | Reihaneh-ahmadi/r_for_data_analysis | R | false | false | 1,618 | r |
# 1. write a function that take a vector as its argument and then calculate the mean of the vector
mean_calculator <- ... (x){
# calculate the sum of the vector
sum_x <- ...
# calculate the length of the vector
length_x <- ...
# calculate the mean
mean_x <- sum_x / length_x
# return the mean
...
... |
data(iris)
names(iris)
plot(iris$Petal.Width, iris$Sepal.Width, pch = 19, col = as.numeric(iris$Species))
legend(1, 4.5, legend = unique(iris$Species), col = unique(as.numeric(iris$Species)), pch = 19)
library(tree)
treel <- tree(Species ~ Sepal.Width + Petal.Width, data=iris)
summary(treel)
plot(treel)
text(treel)
plo... | /Problem Set 2/Question2Code.R | no_license | ackivo/RScripts | R | false | false | 1,389 | r | data(iris)
names(iris)
plot(iris$Petal.Width, iris$Sepal.Width, pch = 19, col = as.numeric(iris$Species))
legend(1, 4.5, legend = unique(iris$Species), col = unique(as.numeric(iris$Species)), pch = 19)
library(tree)
treel <- tree(Species ~ Sepal.Width + Petal.Width, data=iris)
summary(treel)
plot(treel)
text(treel)
plo... |
#' Run alignment procedure using Mplus
#'
#' Facilitates running frequentist alignmnet procedure in Mplus. It creates Mplus input and data from R data.frame, runs the input using Mplus, and provides its summaries back in R.
#'
#' @param model Character. Formula in Mplus format, e.g. "Factor1 BY item1 item2 item3 item... | /R/runAlignment.R | no_license | MaksimRudnev/MIE.package | R | false | false | 13,296 | r | #' Run alignment procedure using Mplus
#'
#' Facilitates running frequentist alignmnet procedure in Mplus. It creates Mplus input and data from R data.frame, runs the input using Mplus, and provides its summaries back in R.
#'
#' @param model Character. Formula in Mplus format, e.g. "Factor1 BY item1 item2 item3 item... |
# Here is the start of the credits
#
fluidRow(
column(3,
div(
img(src='emilogo.jpg', height=140,width=200),
... | /footer_credits.R | no_license | EMIConsulting/evalwaterfallr_shiny | R | false | false | 2,115 | r | # Here is the start of the credits
#
fluidRow(
column(3,
div(
img(src='emilogo.jpg', height=140,width=200),
... |
testlist <- list(A = structure(c(2.32784507357645e-308, 9.53818252170339e+295, 1.22810536108214e+146, 4.12396251261199e-221, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ), .Dim = 5:6), B = structure(0, .Dim = c(1L, 1L)))
result <- do.call(multivariance:::match_rows,testlist)
str(resul... | /multivariance/inst/testfiles/match_rows/AFL_match_rows/match_rows_valgrind_files/1613107002-test.R | no_license | akhikolla/updatedatatype-list3 | R | false | false | 322 | r | testlist <- list(A = structure(c(2.32784507357645e-308, 9.53818252170339e+295, 1.22810536108214e+146, 4.12396251261199e-221, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ), .Dim = 5:6), B = structure(0, .Dim = c(1L, 1L)))
result <- do.call(multivariance:::match_rows,testlist)
str(resul... |
library(rgl)
mydir = "/Users/shehjarsadhu/Desktop/Spring2020/STA441/Final_Project/wisdm-dataset/raw/phone/accel"
myfiles = list.files(path=mydir, pattern="*.txt", full.names=TRUE)
tbl <- sapply(myfiles, read.table, comment.char=";",sep=",")
exercise = "A"
subset(tbl[[4]], tbl[[2]] == "A")
watch_gyro_df1 <- rea... | /group_project_STA441.R | no_license | sadhushehjar/Multivariate-statistics-in-R | R | false | false | 11,678 | r |
library(rgl)
mydir = "/Users/shehjarsadhu/Desktop/Spring2020/STA441/Final_Project/wisdm-dataset/raw/phone/accel"
myfiles = list.files(path=mydir, pattern="*.txt", full.names=TRUE)
tbl <- sapply(myfiles, read.table, comment.char=";",sep=",")
exercise = "A"
subset(tbl[[4]], tbl[[2]] == "A")
watch_gyro_df1 <- rea... |
mp_setapikey("../manifesto_apikey.txt")
contains_factors <- function(mpds) {
mpds %>%
lapply(class) %>%
magrittr::equals("factor") %>%
any()
}
mpds_large_enough <- function(mpds) {
expect_more_than(nrow(mpds), 3800)
expect_more_than(ncol(mpds), 130)
expect_true(all(c("country", "countryname",
... | /tests/testthat/testmaindataset.R | no_license | kbenoit/manifestoR | R | false | false | 6,270 | r | mp_setapikey("../manifesto_apikey.txt")
contains_factors <- function(mpds) {
mpds %>%
lapply(class) %>%
magrittr::equals("factor") %>%
any()
}
mpds_large_enough <- function(mpds) {
expect_more_than(nrow(mpds), 3800)
expect_more_than(ncol(mpds), 130)
expect_true(all(c("country", "countryname",
... |
context('Readers')
test_that('Test 1: CSV Data file', {
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project, minimal = FALSE))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
suppressMessages(load.... | /tests/testthat/test-readers.R | no_license | tomliptrot/ProjectTemplate | R | false | false | 40,039 | r | context('Readers')
test_that('Test 1: CSV Data file', {
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project, minimal = FALSE))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
suppressMessages(load.... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sample_binary.R
\name{int_to_bin}
\alias{int_to_bin}
\title{Converts integer to vector of zeros and ones}
\usage{
int_to_bin(x)
}
\arguments{
\item{x}{a numeric vector of positive integers}
}
\value{
a matrix in which each column corresponds ... | /man/int_to_bin.Rd | permissive | fboehm/xu2012 | R | false | true | 411 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sample_binary.R
\name{int_to_bin}
\alias{int_to_bin}
\title{Converts integer to vector of zeros and ones}
\usage{
int_to_bin(x)
}
\arguments{
\item{x}{a numeric vector of positive integers}
}
\value{
a matrix in which each column corresponds ... |
#' summary.freqlist
#'
#' Summarize the \code{freqlist} object.
#'
#' @param object an object of class \code{\link{freqlist}}
#' @param ... For \code{summary.freqlist}, these are passed to \code{\link{as.data.frame.freqlist}} (and hence to
#' \code{\link{freq.control}}). For the print method, these are
#' additiona... | /R/summary.freqlist.R | no_license | umarfaruk9/arsenal | R | false | false | 3,379 | r | #' summary.freqlist
#'
#' Summarize the \code{freqlist} object.
#'
#' @param object an object of class \code{\link{freqlist}}
#' @param ... For \code{summary.freqlist}, these are passed to \code{\link{as.data.frame.freqlist}} (and hence to
#' \code{\link{freq.control}}). For the print method, these are
#' additiona... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/linear_regression.R
\docType{class}
\name{linreg-class}
\alias{linreg-class}
\alias{linreg}
\title{LinearRegression class}
\value{
class
}
\description{
LinearRegression class containing information about relevant results from the linear regr... | /man/linreg-class.Rd | no_license | senseiyukisan/732A94-Lab4 | R | false | true | 1,163 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/linear_regression.R
\docType{class}
\name{linreg-class}
\alias{linreg-class}
\alias{linreg}
\title{LinearRegression class}
\value{
class
}
\description{
LinearRegression class containing information about relevant results from the linear regr... |
testlist <- list(phi = numeric(0), x = c(1.36656528938164e-311, -1.65791256519293e+82, 1.29418168595419e-228, -1.85353502606261e+293, 8.08855267383463e-84, -4.03929894096111e-178, 6.04817943207006e-103, -1.66738461804717e-220, -8.8217241872956e-21, -7.84828807007467e-146, -7.48864562038427e+21, -1.00905374512e-187,... | /dcurver/inst/testfiles/ddc/AFL_ddc/ddc_valgrind_files/1609866546-test.R | no_license | akhikolla/updated-only-Issues | R | false | false | 632 | r | testlist <- list(phi = numeric(0), x = c(1.36656528938164e-311, -1.65791256519293e+82, 1.29418168595419e-228, -1.85353502606261e+293, 8.08855267383463e-84, -4.03929894096111e-178, 6.04817943207006e-103, -1.66738461804717e-220, -8.8217241872956e-21, -7.84828807007467e-146, -7.48864562038427e+21, -1.00905374512e-187,... |
#'Function to build a feature panel based on specific genomic regions.
#'
#'\code{buildFeaturePanel} builds panel slots of a TargetExperiment object.
#'Input can be a bam file or a pileup matrix. If the bed file contains a high
#'number of amplicons, the bam file as input is recommended in order to
#'diminish memory re... | /R/TargetExperiment-buildFeaturePanel.R | no_license | gamerino/TarSeqQC | R | false | false | 4,719 | r | #'Function to build a feature panel based on specific genomic regions.
#'
#'\code{buildFeaturePanel} builds panel slots of a TargetExperiment object.
#'Input can be a bam file or a pileup matrix. If the bed file contains a high
#'number of amplicons, the bam file as input is recommended in order to
#'diminish memory re... |
######################################################################################
# CRG
# Hana SUSAK
######################################################################################
# Function to calculate ploidy
# @param VAF - Variant allele frequency observed in reads;
# @param ploidy - ploidy in positi... | /R/ccf.R | permissive | yulab41/cDriver | R | false | false | 13,702 | r | ######################################################################################
# CRG
# Hana SUSAK
######################################################################################
# Function to calculate ploidy
# @param VAF - Variant allele frequency observed in reads;
# @param ploidy - ploidy in positi... |
context('All datasets')
test_that("The correct DropOutRates data is included", {
data(DropOutRates)
expect_that(digest(DropOutRates), equals("ca2667c6176daa1c21a05eb66d23dbaa"))
})
test_that("The correct AbuseRates data is included", {
data(AbuseRates)
expect_that(digest(AbuseRates), equals("1eda094dcea5de1fe... | /inst/tests/test-datasets.R | no_license | philliplab/mochModelData | R | false | false | 1,086 | r | context('All datasets')
test_that("The correct DropOutRates data is included", {
data(DropOutRates)
expect_that(digest(DropOutRates), equals("ca2667c6176daa1c21a05eb66d23dbaa"))
})
test_that("The correct AbuseRates data is included", {
data(AbuseRates)
expect_that(digest(AbuseRates), equals("1eda094dcea5de1fe... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ParallelUnix.R
\name{ParallelUnix}
\alias{ParallelUnix}
\title{Parallelize posterior draws for unix machine}
\usage{
ParallelUnix(TrainX, Times, Event, TestX, NumCores)
}
\arguments{
\item{TrainX}{Explanatory variables for training (in sample... | /man/ParallelUnix.Rd | no_license | nillen0/SurvBART | R | false | true | 843 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ParallelUnix.R
\name{ParallelUnix}
\alias{ParallelUnix}
\title{Parallelize posterior draws for unix machine}
\usage{
ParallelUnix(TrainX, Times, Event, TestX, NumCores)
}
\arguments{
\item{TrainX}{Explanatory variables for training (in sample... |
# USCRN
library(magrittr)
# Variables
# 1 WBANNO XXXXX
# 2 UTC_DATE YYYYMMDD
# 3 UTC_TIME HHmm
# 4 LST_DATE YYYYMMDD
# 5 LST_TIME HHmm
# 6 CRX_VN XXXXXX
# 7 LONGI... | /R/USCRN.R | no_license | trenchproject/RShiny_Microclim | R | false | false | 5,613 | r | # USCRN
library(magrittr)
# Variables
# 1 WBANNO XXXXX
# 2 UTC_DATE YYYYMMDD
# 3 UTC_TIME HHmm
# 4 LST_DATE YYYYMMDD
# 5 LST_TIME HHmm
# 6 CRX_VN XXXXXX
# 7 LONGI... |
#################################################################################
##
## R package spd by Alexios Ghalanos Copyright (C) 2008-2013
## This file is part of the R package spd.
##
## The R package spd is free software: you can redistribute it and/or modify
## it under the terms of the GNU Gene... | /spd/R/methods-spdFit.R | no_license | ingted/R-Examples | R | false | false | 3,981 | r | #################################################################################
##
## R package spd by Alexios Ghalanos Copyright (C) 2008-2013
## This file is part of the R package spd.
##
## The R package spd is free software: you can redistribute it and/or modify
## it under the terms of the GNU Gene... |
############################################################
# #
# Level of education #
# #
############################################################
# Load package... | /supplement-plot-F-education.R | permissive | kamermanpr/za-pain-epidemiology | R | false | false | 2,305 | r | ############################################################
# #
# Level of education #
# #
############################################################
# Load package... |
\name{pacotestset}
\alias{pacotestset}
\title{Create and Alter a Pacotest Options List}
\description{ The function creates or updates a list object, which is required for applying the \code{\link{pacotest}} function.}
\arguments{
\item{pacotestOptions}{
A options list for the \code{\link{pacotest}} function generat... | /man/pacotestset.Rd | no_license | SwapanK/pacotest | R | false | false | 5,686 | rd | \name{pacotestset}
\alias{pacotestset}
\title{Create and Alter a Pacotest Options List}
\description{ The function creates or updates a list object, which is required for applying the \code{\link{pacotest}} function.}
\arguments{
\item{pacotestOptions}{
A options list for the \code{\link{pacotest}} function generat... |
#' Bird Function
#'
#' Multimodal single-objective test function. The implementation is based on the
#' mathematical formulation
#' \deqn{f(\mathbf{x}) = (\mathbf{x}_1 - \mathbf{x}_2)^2 + \exp((1 - \sin(\mathbf{x}_1))^2)\cos(\mathbf{x}_2) + \exp((1 - \cos(\mathbf{x}_2))^2)\sin(\mathbf{x}_1).}
#' The function is restric... | /R/sof.bird.R | no_license | fmumbi/smoof | R | false | false | 1,534 | r | #' Bird Function
#'
#' Multimodal single-objective test function. The implementation is based on the
#' mathematical formulation
#' \deqn{f(\mathbf{x}) = (\mathbf{x}_1 - \mathbf{x}_2)^2 + \exp((1 - \sin(\mathbf{x}_1))^2)\cos(\mathbf{x}_2) + \exp((1 - \cos(\mathbf{x}_2))^2)\sin(\mathbf{x}_1).}
#' The function is restric... |
# Climate indices - this gives MEI impact on overlap
library(knitr)
library(readr)
library(tidyverse)
library(R2jags)
library(abind)
library(boot)
library(MCMCvis)
library(reshape2)
library(truncnorm)
library(lattice)
library(knitr)
library(kableExtra)
mei.data <- read.csv("mei_overlap.csv", header=F, stringsAsFacto... | /lme_mei_analysis_beta.R | no_license | dallasjordan/bayesian_project | R | false | false | 3,234 | r | # Climate indices - this gives MEI impact on overlap
library(knitr)
library(readr)
library(tidyverse)
library(R2jags)
library(abind)
library(boot)
library(MCMCvis)
library(reshape2)
library(truncnorm)
library(lattice)
library(knitr)
library(kableExtra)
mei.data <- read.csv("mei_overlap.csv", header=F, stringsAsFacto... |
combine_animation_frames_video <- function(out_file, animation_cfg) {
#build video from pngs with ffmpeg
#note that this will use all frames in 6_visualize/tmp
#have to rename files since can't use globbing with ffmpeg on Windows :(
png_frames <- list.files('6_visualize/tmp', full.names = TRUE)
file_name_df <... | /6_visualize/src/combine_animation_frames.R | no_license | lindsayplatt/gage-conditions-gif | R | false | false | 2,212 | r | combine_animation_frames_video <- function(out_file, animation_cfg) {
#build video from pngs with ffmpeg
#note that this will use all frames in 6_visualize/tmp
#have to rename files since can't use globbing with ffmpeg on Windows :(
png_frames <- list.files('6_visualize/tmp', full.names = TRUE)
file_name_df <... |
c DCNF-Autarky [version 0.0.1].
c Copyright (c) 2018-2019 Swansea University.
c
c Input Clause Count: 827
c Performing E1-Autarky iteration.
c Remaining clauses count after E-Reduction: 827
c
c Input Parameter (command line, file):
c input filename QBFLIB/Letombe/Abduction/aim-50-3_4-yes1-1-00.qdimacs
c output fi... | /code/dcnf-ankit-optimized/Results/QBFLIB-2018/E1/Experiments/Letombe/Abduction/aim-50-3_4-yes1-1-00/aim-50-3_4-yes1-1-00.R | no_license | arey0pushpa/dcnf-autarky | R | false | false | 628 | r | c DCNF-Autarky [version 0.0.1].
c Copyright (c) 2018-2019 Swansea University.
c
c Input Clause Count: 827
c Performing E1-Autarky iteration.
c Remaining clauses count after E-Reduction: 827
c
c Input Parameter (command line, file):
c input filename QBFLIB/Letombe/Abduction/aim-50-3_4-yes1-1-00.qdimacs
c output fi... |
## SANDRA COBO OLLERO --- 9 MARCH 2021
##that's an example with the aim of looking if I can connect github with Rstudio
plot(iris$Sepal.Length)
summary(iris$Sepal.Length)
##https://www.r-bloggers.com/2015/07/rstudio-and-github/ | /test2.R | no_license | sandritachinita/test2 | R | false | false | 234 | r |
## SANDRA COBO OLLERO --- 9 MARCH 2021
##that's an example with the aim of looking if I can connect github with Rstudio
plot(iris$Sepal.Length)
summary(iris$Sepal.Length)
##https://www.r-bloggers.com/2015/07/rstudio-and-github/ |
testlist <- list(x = structure(c(2.31584307393098e+77, 9.53818252170339e+295, 1.22810536108214e+146, 4.12396251261199e-221, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), .Dim = c(5L, 7L)))
result <- do.call(multivariance:::doubleCenterBiasCorrected,testlist)
str(result... | /multivariance/inst/testfiles/doubleCenterBiasCorrected/AFL_doubleCenterBiasCorrected/doubleCenterBiasCorrected_valgrind_files/1613139770-test.R | no_license | akhikolla/updatedatatype-list3 | R | false | false | 321 | r | testlist <- list(x = structure(c(2.31584307393098e+77, 9.53818252170339e+295, 1.22810536108214e+146, 4.12396251261199e-221, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), .Dim = c(5L, 7L)))
result <- do.call(multivariance:::doubleCenterBiasCorrected,testlist)
str(result... |
#' lookup_users
#'
#' @description Returns Twitter user data_frame object for
#' specified user_ids or screen_names.
#'
#' @param users User id or screen name of target user.
#' @param token OAuth token (1.0 or 2.0). By default
#' \code{token = NULL} fetches a non-exhausted token from
#' an environment variable @... | /R/users.R | no_license | hucara/rtweet | R | false | false | 2,336 | r | #' lookup_users
#'
#' @description Returns Twitter user data_frame object for
#' specified user_ids or screen_names.
#'
#' @param users User id or screen name of target user.
#' @param token OAuth token (1.0 or 2.0). By default
#' \code{token = NULL} fetches a non-exhausted token from
#' an environment variable @... |
setwd("~/GettingandCleaningData")
if (!file.exists("data")){dir.create("data")}
##read test data
data<-scan("./data/UCI HAR Dataset/test/X_test.txt",strip.white=TRUE)
n=length(data)/561
data<-matrix(data,nrow=n,ncol=561,byrow=T)
subjid<-read.table("./data/UCI HAR Dataset/test/subject_test.txt")
activity<-read.table("./... | /run_analysis.R | no_license | RongSu/GettingCleaningDataProject | R | false | false | 2,133 | r | setwd("~/GettingandCleaningData")
if (!file.exists("data")){dir.create("data")}
##read test data
data<-scan("./data/UCI HAR Dataset/test/X_test.txt",strip.white=TRUE)
n=length(data)/561
data<-matrix(data,nrow=n,ncol=561,byrow=T)
subjid<-read.table("./data/UCI HAR Dataset/test/subject_test.txt")
activity<-read.table("./... |
library(openxlsx)
library(lubridate)
wb<-read.csv("Book1.csv", header = T)
# Sina fix rates and acquired
wbco<-read.csv("wilshire charge offs cleaned.csv", header=T)
colnames(wbco)<-c("Note.Number","first_co_date","co_amt")
wb<-merge(wb,wbco, by="Note.Number", all.x=T)
rm(wbco)
wb$Y<-0
wb$Y[which... | /PD/Wilshire.R | no_license | hyunyouchoi/R-Studio | R | false | false | 4,088 | r | library(openxlsx)
library(lubridate)
wb<-read.csv("Book1.csv", header = T)
# Sina fix rates and acquired
wbco<-read.csv("wilshire charge offs cleaned.csv", header=T)
colnames(wbco)<-c("Note.Number","first_co_date","co_amt")
wb<-merge(wb,wbco, by="Note.Number", all.x=T)
rm(wbco)
wb$Y<-0
wb$Y[which... |
#'
#' Read Compact Optical Profiling System (COPS) files in both CSV and TSV formats
#'
#'@param file is the file name without the full path
#'@param number.of.fields.before.date is the number of fields begore the date in the file name.
#' For example the file COPS_IML4_150626_1546_C_data_001.csv contains 2 fields... | /R/read_cops.R | no_license | raphidoc/Cops | R | false | false | 4,960 | r | #'
#' Read Compact Optical Profiling System (COPS) files in both CSV and TSV formats
#'
#'@param file is the file name without the full path
#'@param number.of.fields.before.date is the number of fields begore the date in the file name.
#' For example the file COPS_IML4_150626_1546_C_data_001.csv contains 2 fields... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/index.annual.cycle.R
\name{index.annual.cycle}
\alias{index.annual.cycle}
\title{Annual cycle statistics}
\usage{
index.annual.cycle(ts, dates, type = c("min", "max", "amp", "relamp"))
}
\arguments{
\item{ts}{A vector containing the data}
\i... | /man/index.annual.cycle.Rd | no_license | Predictia/R_VALUE | R | false | true | 944 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/index.annual.cycle.R
\name{index.annual.cycle}
\alias{index.annual.cycle}
\title{Annual cycle statistics}
\usage{
index.annual.cycle(ts, dates, type = c("min", "max", "amp", "relamp"))
}
\arguments{
\item{ts}{A vector containing the data}
\i... |
# Install and load packages
package_names <- c("survey","dplyr","foreign","devtools")
lapply(package_names, function(x) if(!x %in% installed.packages()) install.packages(x))
lapply(package_names, require, character.only=T)
install_github("e-mitchell/meps_r_pkg/MEPS")
library(MEPS)
options(survey.lonely.ps... | /_check/test_code/pmed/r_codes/totPOP_RXDRGNAM_ind_2014.R | permissive | HHS-AHRQ/MEPS-summary-tables | R | false | false | 909 | r | # Install and load packages
package_names <- c("survey","dplyr","foreign","devtools")
lapply(package_names, function(x) if(!x %in% installed.packages()) install.packages(x))
lapply(package_names, require, character.only=T)
install_github("e-mitchell/meps_r_pkg/MEPS")
library(MEPS)
options(survey.lonely.ps... |
testlist <- list(A = structure(c(3.21991735724713e-193, 1.17980782037495e-16, 4.14310534109414e-235, 6.76251072361731e-281, 4.76852914066932e+305, 2.87579039425864e+227, 8.44453472300785e-14, 7.03605297312039e-119, 1.23014208619275e+199, 135758725862.383, 1.90368023855323e-163, 3.22669675848698e-206, 9.845235313145... | /issuestests/hetGP/inst/testfiles/fast_trace/fast_trace_output/log_457439da60840556f569447e766c0854dd9066bc/fast_trace-test.R | no_license | akhikolla/RcppDeepStateTest | R | false | false | 3,100 | r | testlist <- list(A = structure(c(3.21991735724713e-193, 1.17980782037495e-16, 4.14310534109414e-235, 6.76251072361731e-281, 4.76852914066932e+305, 2.87579039425864e+227, 8.44453472300785e-14, 7.03605297312039e-119, 1.23014208619275e+199, 135758725862.383, 1.90368023855323e-163, 3.22669675848698e-206, 9.845235313145... |
###################################################################
### Memory-based Collaborative Filtering Algorithm Starter Code ###
###################################################################
### Authors: CIndy Rush
### Project 3
### ADS Spring 2018
######################################################... | /Project_Starter_Codes/Project3-Algorithms/doc/memory_based_model.R | no_license | GU4243-ADS/Spring2018 | R | false | false | 6,559 | r |
###################################################################
### Memory-based Collaborative Filtering Algorithm Starter Code ###
###################################################################
### Authors: CIndy Rush
### Project 3
### ADS Spring 2018
######################################################... |
#__________________________________________________
# DATA GENERATORS
#__________________________________________________
#' Generates matrix of mixing probabilities.
#'
#' \code{genunifp} returns a matrix whose rows are independent
#' random vectors uniformly distributed over the M-simplex.
#'
#' @param n number of s... | /R/start2.R | no_license | RostyslavMaiboroda/mixvconc | R | false | false | 39,161 | r | #__________________________________________________
# DATA GENERATORS
#__________________________________________________
#' Generates matrix of mixing probabilities.
#'
#' \code{genunifp} returns a matrix whose rows are independent
#' random vectors uniformly distributed over the M-simplex.
#'
#' @param n number of s... |
#' Ensure Space After Comma
#'
#' Adds a space after a comma as strip and many other functions may consider a
#' comma separated string as one word (i.e., \code{"one,two,three"} becomes
#' \code{"onetwothree"} rather than \code{"one two three"}).
#'
#' @param text.var The text variable.
#' @return Returns a vector... | /R/comma_spacer.R | no_license | cran/qdap | R | false | false | 623 | r | #' Ensure Space After Comma
#'
#' Adds a space after a comma as strip and many other functions may consider a
#' comma separated string as one word (i.e., \code{"one,two,three"} becomes
#' \code{"onetwothree"} rather than \code{"one two three"}).
#'
#' @param text.var The text variable.
#' @return Returns a vector... |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/IPDFilecheck.R
\name{get_contents_cols}
\alias{get_contents_cols}
\title{Function to return the unique contents of the column given the column name}
\usage{
get_contents_cols(data, colname)
}
\arguments{
\item{data}{a data frame}
\item{colna... | /man/get_contents_cols.Rd | no_license | sheejamk/IPDFileCheck | R | false | true | 639 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/IPDFilecheck.R
\name{get_contents_cols}
\alias{get_contents_cols}
\title{Function to return the unique contents of the column given the column name}
\usage{
get_contents_cols(data, colname)
}
\arguments{
\item{data}{a data frame}
\item{colna... |
library(readr)
library(ggplot2)
library(ggrepel)
# S&P data from https://github.com/CNuge/kaggle-code/tree/master/stock_data
all_stocks_5yr <- read_csv("all_stocks_5yr.csv")
# remover duplicate:
all_stocks_5yr <- filter(all_stocks_5yr, Name != "GOOGL")
# convert dates to standard format:
all_stocks_5yr$date <- as.Da... | /Week3_StockPrices.R | no_license | robjohnnoble/MathProcFin_R_code | R | false | false | 7,349 | r | library(readr)
library(ggplot2)
library(ggrepel)
# S&P data from https://github.com/CNuge/kaggle-code/tree/master/stock_data
all_stocks_5yr <- read_csv("all_stocks_5yr.csv")
# remover duplicate:
all_stocks_5yr <- filter(all_stocks_5yr, Name != "GOOGL")
# convert dates to standard format:
all_stocks_5yr$date <- as.Da... |
#' @title Read the reference gene file
#' @name read_master_gene_file
#'
#' @return a data.frame
#'
#' @export
#'
#' @examples
read_master_gene_file <- function() {
master_gene_file <- system.file("extdata", "master_gene_file.tsv", package = "EcoliGenes")
master_gene_table <- read.delim(master_gene_file, comment.char... | /R/master_gene_file.R | no_license | PGC-CCG/EcoliGenes | R | false | false | 1,289 | r | #' @title Read the reference gene file
#' @name read_master_gene_file
#'
#' @return a data.frame
#'
#' @export
#'
#' @examples
read_master_gene_file <- function() {
master_gene_file <- system.file("extdata", "master_gene_file.tsv", package = "EcoliGenes")
master_gene_table <- read.delim(master_gene_file, comment.char... |
#drastically simplified, March 14, 2009 from two loops to 1 matrix operation
#modified July 2, 2013 to allow not counting the diagonal
"count.pairwise" <-
function (x, y=NULL,diagonal=TRUE)
{
if(is.null(y)) {n <- t(!is.na(x)) %*% (!is.na(x)) } else { n <- t(!is.na(x)) %*% (!is.na(y)) }
if(!diagonal) diag(n) <-... | /R/count.pairwise.R | no_license | frenchja/psych | R | false | false | 504 | r | #drastically simplified, March 14, 2009 from two loops to 1 matrix operation
#modified July 2, 2013 to allow not counting the diagonal
"count.pairwise" <-
function (x, y=NULL,diagonal=TRUE)
{
if(is.null(y)) {n <- t(!is.na(x)) %*% (!is.na(x)) } else { n <- t(!is.na(x)) %*% (!is.na(y)) }
if(!diagonal) diag(n) <-... |
## Step 1. Data preperation
#(i) loading
#load IO data
IOT_b=read.csv(file="IOT_b.csv",header=T, as.is=T)
#load index mapping
sector_ind=read.csv(file="indcode_20161202.csv",header=T, as.is=T)
#(ii)preparing index
row_ind=sector_ind[,1:2]
col_ind=sector_ind[,3:4]
sec_group=sector_ind[,5:8]
va_ind=sector_ind[,9:10]
fd_... | /SAM/agg_1202.r | no_license | katto2/GIRprep | R | false | false | 10,442 | r | ## Step 1. Data preperation
#(i) loading
#load IO data
IOT_b=read.csv(file="IOT_b.csv",header=T, as.is=T)
#load index mapping
sector_ind=read.csv(file="indcode_20161202.csv",header=T, as.is=T)
#(ii)preparing index
row_ind=sector_ind[,1:2]
col_ind=sector_ind[,3:4]
sec_group=sector_ind[,5:8]
va_ind=sector_ind[,9:10]
fd_... |
#' PCA-based outlier detection
#'
#' Takes a matrix of samples x measurements and looks for outliers in the two
#' first principal components of the data as defined by mahalanobis distance
#' to the center of the data in number of standard deviations
#'
#' @param x a numerical matrix with samples by row, measurements b... | /R/prcout.R | permissive | zouw2/nowaclean | R | false | false | 4,013 | r | #' PCA-based outlier detection
#'
#' Takes a matrix of samples x measurements and looks for outliers in the two
#' first principal components of the data as defined by mahalanobis distance
#' to the center of the data in number of standard deviations
#'
#' @param x a numerical matrix with samples by row, measurements b... |
library(ggmap)
### Name: qmplot
### Title: Quick map plot
### Aliases: qmplot
### ** Examples
## Not run:
##D # these are skipped to conserve R check time
##D
##D qmplot(lon, lat, data = crime)
##D
##D
##D # only violent crimes
##D violent_crimes <- subset(crime,
##D offense != "auto theft" &
##D offense ... | /data/genthat_extracted_code/ggmap/examples/qmplot.Rd.R | no_license | surayaaramli/typeRrh | R | false | false | 6,535 | r | library(ggmap)
### Name: qmplot
### Title: Quick map plot
### Aliases: qmplot
### ** Examples
## Not run:
##D # these are skipped to conserve R check time
##D
##D qmplot(lon, lat, data = crime)
##D
##D
##D # only violent crimes
##D violent_crimes <- subset(crime,
##D offense != "auto theft" &
##D offense ... |
leftZones = function()
{
zones=matrix(c(0,2,3,1), ncol=2, byrow=TRUE)
layout(zones, widths=c(1/5,4/5), heights=c(1/5,4/5))
}
# Not implemented; or won't work right. The problem is limits and such for the
# shifted barplot
rightZones = function()
{
zones=matrix(c(0,2,3,1), ncol=2, byrow=TRUE)
layout(zones, widths=... | /funhist.R | no_license | parksw3/Generation_distributions | R | false | false | 1,691 | r | leftZones = function()
{
zones=matrix(c(0,2,3,1), ncol=2, byrow=TRUE)
layout(zones, widths=c(1/5,4/5), heights=c(1/5,4/5))
}
# Not implemented; or won't work right. The problem is limits and such for the
# shifted barplot
rightZones = function()
{
zones=matrix(c(0,2,3,1), ncol=2, byrow=TRUE)
layout(zones, widths=... |
###############
# Create a simple scatter plot of cars speed and stopping distances
# Christopher Gandrud
# 6 January 2012
###############
plot(x = cars$speed, y = cars$dist,
xlab = "Speed (mph)",
ylab = "Stopping Distance (ft)",
cex.lab = 1.5) | /B_analysts_sources_github/christophergandrud/Rep-Res-Examples/SimpleScatter.R | no_license | Irbis3/crantasticScrapper | R | false | false | 260 | r | ###############
# Create a simple scatter plot of cars speed and stopping distances
# Christopher Gandrud
# 6 January 2012
###############
plot(x = cars$speed, y = cars$dist,
xlab = "Speed (mph)",
ylab = "Stopping Distance (ft)",
cex.lab = 1.5) |
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/phylo.R
\name{node_labels}
\alias{node_labels}
\alias{named_edges}
\alias{ape_layout_unrooted}
\title{Utilities for phylo class of ape package}
\usage{
node_labels(x)
named_edges(x)
ape_layout_unrooted(phy, centering = TRUE, rotate = 0)
}
\... | /man/phylo.Rd | permissive | heavywatal/rwtl | R | false | true | 498 | rd | % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/phylo.R
\name{node_labels}
\alias{node_labels}
\alias{named_edges}
\alias{ape_layout_unrooted}
\title{Utilities for phylo class of ape package}
\usage{
node_labels(x)
named_edges(x)
ape_layout_unrooted(phy, centering = TRUE, rotate = 0)
}
\... |
\name{dccFit}
\alias{dccFit}
\title{Dynamic Cross-Correlation Model Fitting
}
\description{Fits a DCC model using either multivariate Gaussian or
multivariate Student-t innovations. Two types of DCC models are available. The first type is proposed by Engle
and the other is by Tse and Tsui. Both models appear in the J... | /man/dccFit.Rd | no_license | chenlu-hung/MTS | R | false | false | 1,698 | rd | \name{dccFit}
\alias{dccFit}
\title{Dynamic Cross-Correlation Model Fitting
}
\description{Fits a DCC model using either multivariate Gaussian or
multivariate Student-t innovations. Two types of DCC models are available. The first type is proposed by Engle
and the other is by Tse and Tsui. Both models appear in the J... |
#------------------------
# Combine network datasets
#------------------------
library(tidyverse)
#-----------------
# Total Invasives
#-----------------
#---NETN Total Invasives
netn_totinv<-read.csv("./data/NETN/NETN_invasive_total_data.csv")
netn_totinv<-netn_totinv %>% mutate(network='NETN') %>%
select(network,U... | /scripts/01b_Combine_Network_Data.R | permissive | KateMMiller/invasive_trend_analysis | R | false | false | 12,737 | r | #------------------------
# Combine network datasets
#------------------------
library(tidyverse)
#-----------------
# Total Invasives
#-----------------
#---NETN Total Invasives
netn_totinv<-read.csv("./data/NETN/NETN_invasive_total_data.csv")
netn_totinv<-netn_totinv %>% mutate(network='NETN') %>%
select(network,U... |
# convert a plink .frq to files suitable to garfield maftssd
library(here)
library(readr)
library(dplyr)
library(magrittr)
library(biomaRt)
library(GenomicRanges)
# OUTPUT FILES #########################################################################################################
output.dir <- here("data/garfield-... | /src/garfield/make_maftssd/hg38-mirQTL-MIXED/02_format_maftssd.R | no_license | mikelaff/mirna-eqtl-manuscript | R | false | false | 3,343 | r | # convert a plink .frq to files suitable to garfield maftssd
library(here)
library(readr)
library(dplyr)
library(magrittr)
library(biomaRt)
library(GenomicRanges)
# OUTPUT FILES #########################################################################################################
output.dir <- here("data/garfield-... |
# RDA
# Prepare data ----
rm(list=ls())
source("code/data_processing_code.R")
library(psych)
treats_to_plot <- as.character(unique(treats$treat))[c(3,4)]
treats_trimmed <- treats[(treats$treat %in% treats_to_plot), ]
treats_trimmed$codes <- as.character(treats_trimmed$codes)
treats_dummy <- dummy.code(as.character(t... | /code/pdi_diet_shift.R | no_license | szefer-piotr/garden_food_webs | R | false | false | 4,478 | r | # RDA
# Prepare data ----
rm(list=ls())
source("code/data_processing_code.R")
library(psych)
treats_to_plot <- as.character(unique(treats$treat))[c(3,4)]
treats_trimmed <- treats[(treats$treat %in% treats_to_plot), ]
treats_trimmed$codes <- as.character(treats_trimmed$codes)
treats_dummy <- dummy.code(as.character(t... |
context("ANOVAs: known bugs")
test_that("aov does not throw 'Error() model is singular' warning for missing values", {
data(md_12.1)
md_12.1b <- md_12.1[-1,]
expect_warning(aov_ez("id", "rt", md_12.1b, within = c("angle", "noise")), "Missing values", all = TRUE)
})
test_that("regex works correctly in aov_car w... | /tests/testthat/test-aov_car-bugs.R | no_license | minghao2016/afex | R | false | false | 13,926 | r |
context("ANOVAs: known bugs")
test_that("aov does not throw 'Error() model is singular' warning for missing values", {
data(md_12.1)
md_12.1b <- md_12.1[-1,]
expect_warning(aov_ez("id", "rt", md_12.1b, within = c("angle", "noise")), "Missing values", all = TRUE)
})
test_that("regex works correctly in aov_car w... |
#written by Santiago Velazco & Andre Andrade
# Function for summary of models performance
Validation_Table_TMLA<-function(Eval,
Eval_JS,
N){
#Creates model validation table
summres <- data.frame(matrix(0, N, 6))
for(i in 1:N){
#... | /R/ValidationTable_TMLA.R | no_license | neiljun/ENMTML | R | false | false | 1,228 | r | #written by Santiago Velazco & Andre Andrade
# Function for summary of models performance
Validation_Table_TMLA<-function(Eval,
Eval_JS,
N){
#Creates model validation table
summres <- data.frame(matrix(0, N, 6))
for(i in 1:N){
#... |
brkpt.accuracy=function(model.brkpts, true.brkpts, acc.tol, dup.tol, miss.tol) {
model.brkpts<- as.numeric(model.brkpts) %>% na.omit() %>% as.vector()
true.brkpts<- as.numeric(true.brkpts) %>% na.omit() %>% as.vector()
all.brkpts<- data.frame(brks = c(true.brkpts, model.brkpts),
type... | /helper functions.R | no_license | ValleLabUF/method_comparison | R | false | false | 8,998 | r |
brkpt.accuracy=function(model.brkpts, true.brkpts, acc.tol, dup.tol, miss.tol) {
model.brkpts<- as.numeric(model.brkpts) %>% na.omit() %>% as.vector()
true.brkpts<- as.numeric(true.brkpts) %>% na.omit() %>% as.vector()
all.brkpts<- data.frame(brks = c(true.brkpts, model.brkpts),
type... |
#######################################################################
# Auxiliary functions for the hyperPheno R package.
#
# The hyperPheno is developed and maintained by Bijan Seyednasrollah.
# The main initial development was done in November, 2017.
#
# Most recent release: https://github.com/bnasr/hyperPheno
##... | /harvardsoc/f.R | permissive | GRSEB9S/hyperPheno | R | false | false | 7,665 | r | #######################################################################
# Auxiliary functions for the hyperPheno R package.
#
# The hyperPheno is developed and maintained by Bijan Seyednasrollah.
# The main initial development was done in November, 2017.
#
# Most recent release: https://github.com/bnasr/hyperPheno
##... |
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