abikoushi

##
p_stat_t <- function(v, df = 1, 
                     alternative = "two.sided"){
    if (!alternative %in% c("two.sided", "less", "greater")) {
        stop("alternative must be either \"two.sided\", \"less\", or \"greater\".")
    }
    if(alternative == "two.sided"){
        p0 <- 2*pt(abs(v), df, lower.tail = FALSE)
    }else if(alternative == "less"){
        p0 <- pt(v, df)

abikoushi

library(reshape2)
library(ggplot2)

theme_dotdiagram <- function(...){
  theme_minimal(...)%+%
    theme(axis.text.y = element_text(colour="black"),
          axis.ticks = element_blank(),
          axis.text.x = element_blank(),
          axis.title.x = element_blank(),
          panel.grid.minor = element_blank(),

abikoushi

library(dplyr)
library(ggplot2)
x <- c("ward.D","ward.D2", "single","complete",
       "average","mcquitty","median","centroid")

X <- log(as.matrix(iris[,1:2]))

df <- data.frame(X)

d <- dist(X)

abikoushi

library(dplyr)
library(ggplot2)
x <- c("ward.D","ward.D2", "single","complete",
  "average","mcquitty","median","centroid")

X <- log(as.matrix(iris[,1:4]))

d <- dist(X)

dm <- as.matrix(d)

abikoushi

\documentclass[tikz,border=14pt]{standalone}
\usepackage{tikz}
\usetikzlibrary{matrix,shapes,decorations.pathreplacing, backgrounds, positioning}

\begin{document}
    \begin{tikzpicture}[
        %Styles
        Matrix/.style={
            matrix of nodes,
            text height=2.5ex,

abikoushi

library(pheatmap)
library(grid)

mid0scale <- function(test, paletteLength=120){
  myColor <- colorRampPalette(c("orange", "white", "royalblue"))(paletteLength)
  myBreaks <- c(seq(min(test), 0, length.out=ceiling(paletteLength/2) + 1), 
                seq(max(test)/paletteLength, max(test), length.out=floor(paletteLength/2)))
  return(list(color=myColor, breaks=myBreaks))
}
set.seed(123)

abikoushi

library(pheatmap)

# length(breaks) == length(paletteLength) + 1
# use floor and ceiling to deal with even/odd length pallettelengths
mid0scale <- function(test, paletteLength=120){
  myColor <- colorRampPalette(c("orange", "white", "royalblue"))(paletteLength)
  myBreaks <- c(seq(min(test), 0, length.out=ceiling(paletteLength/2) + 1), 
                seq(max(test)/paletteLength, max(test), length.out=floor(paletteLength/2)))
  return(list(color=myColor, breaks=myBreaks))
}

abikoushi

\documentclass[tikz,border=14pt]{standalone}
\usepackage{tikz}
\usetikzlibrary{shapes,positioning}
%\usepackage{xcolor}
\begin{document}
 \begin{tikzpicture}
\node[draw, rounded corners, fill=gray!10](dna) at (0,0){DNA};
\node[draw, rounded corners, fill=gray!10, right = of dna, xshift = +15pt](rna){RNA};
\node[draw, rounded corners, fill=gray!10, right = of rna, xshift = +15pt](protein) {protein};
\node[draw, rounded corners, fill=gray!10, right = of protein](phenotype) {phenotype};

abikoushi

# 須山『ベイズ推論による機械学習入門』（講談社）の実装例です

softmax <- function(x){
  maxx <- max(x)
  exp(x-maxx)/sum(exp(x-maxx))
}
logp_x <-function(x,lambda,loglambda){
  x*loglambda-lambda
}
logsumexp <- function(x){

abikoushi

library(ggplot2)
library(dplyr)

Andrews <- function(t,
                    Sepal.Length, Sepal.Width,
                    Petal.Length, Petal.Width,...){
  root2 <- sqrt(2)
  sapply(t, function(t){Sepal.Length/root2 +
                               Sepal.Width*sin(t) +
                               Petal.Length*cos(t) +