## ----setup, include=FALSE, message=FALSE--------------------------------------
knitr::opts_chunk$set(echo = TRUE)
library(NNS)
library(data.table)
data.table::setDTthreads(2L)
options(mc.cores = 1)
Sys.setenv("OMP_THREAD_LIMIT" = 1)
RcppParallel::setThreadOptions(numThreads = 1)

## ----setup2,message=FALSE,warning = FALSE-------------------------------------
library(NNS)
library(data.table)
require(knitr)
require(rgl)

## ----cars, fig.width=10, fig.align='center'-----------------------------------
mpg_auto_trans = mtcars[mtcars$am==1, "mpg"]
mpg_man_trans = mtcars[mtcars$am==0, "mpg"]

NNS.ANOVA(control = mpg_man_trans, treatment = mpg_auto_trans, robust = TRUE)

## ----cars2, warning=FALSE-----------------------------------------------------
wilcox.test(mpg ~ am, data=mtcars) 

## ----equalmeans, echo=TRUE, fig.width=10, fig.align='center'------------------
set.seed(123)
x = rnorm(1000, mean = 0, sd = 1)
y = rnorm(1000, mean = 0, sd = 2)

NNS.ANOVA(control = x, treatment = y,
          means.only = TRUE, robust = TRUE, plot = TRUE)

t.test(x,y)

## ----unequalmeans, echo=TRUE, fig.width=10, fig.align='center'----------------
set.seed(123)
x = rnorm(1000, mean = 0, sd = 1)
y = rnorm(1000, mean = 1, sd = 1)

NNS.ANOVA(control = x, treatment = y,
          means.only = TRUE, robust = TRUE, plot = TRUE)

t.test(x,y)

## ----unequalmedians, echo=TRUE, fig.width=10, fig.align='center'--------------
NNS.ANOVA(control = x, treatment = y,
          means.only = TRUE, medians = TRUE, robust = TRUE, plot = TRUE)

## ----stochsuperiority, echo=TRUE, eval=TRUE-----------------------------------
set.seed(123)
x = rnorm(1000, mean = 0, sd = 1)
y = rnorm(1000, mean = 1, sd = 1)

NNS.SS(x, y)

## ----stochsuperiorityci, echo=TRUE, eval = FALSE------------------------------
# NNS.SS(x, y, confidence.interval = TRUE, reps = 999, ci = 0.95)[1:5]
# 
# $p_gt
# [1] 0.233915
# 
# $p_tie
# [1] 0
# 
# $p_star
# [1] 0.233915
# 
# $lower
# [1] 0.2105631
# 
# $upper
# [1] 0.2537789

## ----stochsuperioritydiscrete, echo=TRUE, eval=TRUE---------------------------
set.seed(123)
x = sample(1:5, 100, replace = TRUE)
y = sample(1:5, 100, replace = TRUE)

NNS.SS(x, y)

## ----stochdom, fig.width=7, fig.align='center'--------------------------------
set.seed(123)
x = rnorm(1000, mean = 0, sd = 1)
y = rnorm(1000, mean = 1, sd = 1)

NNS.FSD(x, y)

## ----stochdomset, eval=TRUE---------------------------------------------------
set.seed(123)
x1 = rnorm(1000)
x2 = x1 + 1
x3 = rnorm(1000)
x4 = x3 + 1
x5 = rnorm(1000)
x6 = x5 + 1
x7 = rnorm(1000)
x8 = x7 + 1

NNS.SD.efficient.set(cbind(x1, x2, x3, x4, x5, x6, x7, x8), degree = 1, status = FALSE)

## ----stochdomclust, eval=TRUE, fig.width=7, fig.align='center'----------------
NNS.SD.cluster(cbind(x1, x2, x3, x4, x5, x6, x7, x8), degree = 1, dendrogram = TRUE)