R 相关笔记¶

序列减去常数¶

for (i in c(1:n-1))
  print(i)
##0
##1
##2
for (i in c(1:(n-1)))
  print(i)
##1
##2

Rstudio 清空历史图象¶

Error in plot.new() : figure margins too large in R

linux 下更新 R¶

参考https://mirrors.tuna.tsinghua.edu.cn/CRAN/ 中的README.md文件

若已经通过源码安装，则可以通过找到源码文件夹，使用sudo make uninstall进行卸载。

然后通过配置source.list，进行安装。

终端执行R code¶

参考run-r-script-from-command-line

touch main.R
vi main.R
### in main.R
##!/usr/bin/env Rscript
... ## R command
### save main.R
### run this file
./main.R

shiny¶

init

删除当前工作区所有变量¶

rm(list = ls(all = TRUE))

interval¶

http://blog.sciencenet.cn/blog-54276-288414.html

window 安装包¶

切换到R的安装路径下，在etc文件夹中编辑文件Rprofile.site文件

## set a CRAN mirror
    local({r <- getOption("repos")
        r["CRAN"] <- "http://mirrors.ustc.edu.cn/CRAN/"
          options(repos=r)})

sort(), rank(), order()¶

http://blog.sina.com.cn/s/blog_6caea8bf0100spe9.html

sort(x)是对向量x进行排序，返回值排序后的数值向量。rank()是求秩的函数，它的返回值是这个向量中对应元素的“排名”。而order()的返回值是对应“排名”的元素所在向量中的位置。

Interpreting Residual and Null Deviance in GLM R¶

Refer to https://stats.stackexchange.com/questions/108995/interpreting-residual-and-null-deviance-in-glm-r

缺少libRblas.so和libRlapack.so的解决办法¶

虽然缺少libRblas.so和libRlapack.so，但却有libblas.so和liblapack.so，而它们应该是一样的，只是文件名不同而已，为此添加链接即可。

cd /usr/lib
ln -s libblas.so libRblas.so
ln -s /usr/lib/R/module/lapack.so libRlapack.so

参考： 1. https://bugs.launchpad.net/ubuntu/+source/rkward/+bug/264436 2. http://promberger.info/linux/2009/03/20/r-lme4-matrix-not-finding-librlapackso/

RSQLite¶

参考博文https://statr.me/2011/10/large-regression/

代码见sqlite_ex.R

Rcpp¶

手动设置

cd /usr/local lib
##cd /usr/lib
ln -s /home/weiya/R/x86_64-pc-linux-gnu-library/library/Rcpp/libs/Rcpp.so libRcpp.so

function ‘dataptr’ not provided by package ‘Rcpp’¶

原因是因为没有在

dyn.load()

前面添加

library(Rcpp)
## 或require(Rcpp)

R check package about description¶

check locale

par cheatsheet¶

r-graphical-parameters-cheatsheet

Mathematical Annotation in R plot¶

plot(..., main = expression(paste("...", mu[1])))

参考 1. Mathematical Annotation in R

Problems installing the devtools package¶

关于curl

function ‘dataptr’ not provided by package ‘Rcpp’¶

参考function ‘dataptr’ not provided by package ‘Rcpp’

Rcpp reference¶

Rcpp-quickref

remove outliers from the boxplot¶

How to remove outliers from a dataset

rmarkdown转化中文字符为PDF的设置¶

---
title: "test"
author: "weiya"
output:
    pdf_document:
        latex_engine: xelatex
        includes:
            in_header: header.tex
---

在grid排列图¶

Arranging plots in a grid

x11 font cannot be loaded¶

参考X11 font -adobe-helvetica-%s-%s---%d-------*, face 2 at size 11 could not be loaded

安装多版本R¶

Installing multiple versions of R

semi-transparency is not supported on this device¶

semi-transparency is not supported on this device

MC, MCMC, Gibbs采样原理¶

MC, MCMC, Gibbs采样原理&实现（in R）

贝叶斯集锦（3）：从MC、MC到MCMC

随机采样方法整理与讲解（MCMC、Gibbs Sampling等）

简单易学的机器学习算法——马尔可夫链蒙特卡罗方法MCMC

DP: Collapsed Gibbs Sampling

Metropolis Hasting算法

Running R in batch mode on Linux¶

Running R in batch mode on Linux

RStudio: Warning message: Setting LC_CTYPE failed, using “C” 浅析¶

RStudio: Warning message: Setting LC_CTYPE failed, using “C” 浅析

“Kernel density estimation” is a convolution of what?¶

“Kernel density estimation” is a convolution of what?

unable to start rstudio in centos getting error “unable to connect to service”¶

unable to start rstudio in centos getting error “unable to connect to service”

发布R包¶

Releasing a package

Presentations with Slidy¶

Presentations with Slidy

Estimation of the expected prediction error¶

Estimation of the expected prediction error

协方差矩阵的几何解释¶

参考协方差矩阵的几何解释

ROCR包中prediction函数¶

prediction定义如下

prediction(predictions, labels, label.ordering = NULL)

在绘制ROC曲线时，必要时需要指定label.ordering中negative和positive，否则结果会完全相反。举个例子

## generate some data with a non-linar class boundary
set.seed(123)
x = matrix(rnorm(200*2), ncol = 2)
x[1:100, ] = x[1:100, ] + 2
x[101:150, ] = x[101:150, ] - 2
y = c(rep(1, 150), rep(2, 50))
dat = data.frame(x = x, y = as.factor(y))
plot(x, col = y)

## randomly split into training and testing groups
train = sample(200, 100)

## training data using radial kernel
svmfit = svm(y~., data = dat[train, ], kernel = "radial", cost = 1)
plot(svmfit, dat[train, ])

## cross-validation 
set.seed(123)
tune.out = tune(svm, y~., data = dat[train, ], kernel = "radial",
                ranges = list(cost = c(0.1, 1, 10, 100, 1000),
                              gamma = c(0.5, 1, 2, 3, 4)))
summary(tune.out)

## prediction
table(true = dat[-train, "y"], pred = predict(tune.out$best.model, newdata = dat[-train, ]))

## ROC curves
library(ROCR)
rocplot = function ( pred , truth , ...) {
  predob = prediction ( pred, truth , label.ordering = c("2", "1"))
  perf = performance ( predob , "tpr" , "fpr")
  plot ( perf,...) 
}
svmfit.opt = svm(y~., data = dat[train, ], kernel = "radial",
                 gamma = 3, cost = 10, decision.values = T)
fitted = attributes(predict(svmfit.opt, dat[train, ], decision.values = T))$decision.values

rocplot ( fitted , dat [ train ,"y"] , main ="Training Data")

对于上述代码，如果不指定label.ordering = c("2", "1")，则得到的ROC曲线如下图

原因是因为fitted与y大小关系相反，即前者大时后者小，而前者小时后者大。

pairs中自定义panel函数¶

问题来自R语言绘图？ - 知乎

my.lower <- function(x,y,...){
  points(x, y)
  lines(lowess(x, y), col = "red", lwd=2)
}

my.upper <- function(x, y, ...){
  cor.val = round(cor(x,y), digits = 3)
  if (abs(cor.val) > 0.5){
    text(mean(x), mean(y), cor.val, cex = 3)
    text(sort(x)[length(x)*0.8], max(y), '***', cex = 4, col = "red")
  } else
  {
    text(mean(x), mean(y), cor.val, cex = 1)
  }
}

pairs(iris[1:4], lower.panel =my.lower, upper.panel = my.upper)

参考网址： 1. Different data in upper and lower panel of scatterplot matrix

神奇的`[`¶

来自R语言中以矩阵引用多维数组的元素

比如

A = array(sample(0:255, 100*100*3, replace = T), dim = c(100,100,3))
B = array(sample(1:100, 2*5), dim = c(2,5))
apply(A, 3, `[`, t(B))

proxy 代理¶

参考

`lm()` 中有无 `I()` 的差异¶

注意

lm(Y ~ X + X^2)

和

lm(Y ~ X + I(X^2))

是不一样的。若要表示多项式回归，则应该用 I(X^2)。

多项式作图¶

参考Plot polynomial regression curve in R

custom print¶

class(obj) = "example"
print.example <- function(x)
{

}

refer to Example Needed: Change the default print method of an object

write lines to file¶

fileConn<-file("output.txt")
writeLines(c("Hello","World"), fileConn)
close(fileConn)

refer to Write lines of text to a file in R

combine base and ggplot graphics in R figure¶

refer to Combine base and ggplot graphics in R figure window

specify CRAN mirror in `install.package`¶

r <- getOption("repos")
       r["CRAN"] <- "https://cran.r-project.org" 
       options(repos=r)

we also can wrap it with local({...}) and save in ~/.Rprofile.

Refer to How to select a CRAN mirror in R

R 符号运算¶

参考 R 语言做符号计算。

NormDensity <- expression(1 / sqrt(2 * pi) * exp(-x^2 / 2))
D(NormDensity, "x")
DD <- function(expr, name, order = 1) {
 if (order < 1)
     stop("'order' must be >= 1")
 if (order == 1)
     D(expr, name) else DD(D(expr, name), name, order - 1)
 }
DD(NormDensity, "x", 3)

DFun <- deriv(NormDensity, "x", function.arg = TRUE)
DFun(1)

Show all R’s shortcuts¶

Alt-Shift-K.

Mistake with colon operator¶

vec <- c()
for (i in 1:length(vec)) print(vec[i])

would print two NULL because 1:length(vec) would be c(1,0). A method to avoid this

for (i in seq_along(vec)) print(vec[i])

refer to Two common mistakes with the colon operator in R

Conda 管理版本¶

Using R language with Anaconda
单独安装 rstudio conda install -c r rstudio

error in install `gRbase`¶

environment: Ubuntu 16.04 (gcc 5.4.0)

g++: error: unrecognized comma line option ‘-fno-plt’

the reason should be that the current gcc is too old.

In conda env R:

install latest gcc v7.3.0, but it still does not work
Sys.getenv() indeed switch to the latest gcc
remove ~/.R/Makevars, which would force the gcc to be the gcc declared in that file.
then it works well.

refer to

R Packages Fail to Compile with gcc

Note that some packages cannot be installed via CRAN, and you can check bioconductor.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("graph")

R 相关笔记¶

序列减去常数¶

Rstudio 清空历史图象¶

linux 下更新 R¶

终端执行R code¶

shiny¶

删除当前工作区所有变量¶

interval¶

window 安装包¶

sort(), rank(), order()¶

Interpreting Residual and Null Deviance in GLM R¶

缺少libRblas.so和libRlapack.so的解决办法¶

RSQLite¶

Rcpp¶

function ‘dataptr’ not provided by package ‘Rcpp’¶

R check package about description¶

par cheatsheet¶

Mathematical Annotation in R plot¶

Problems installing the devtools package¶

function ‘dataptr’ not provided by package ‘Rcpp’¶

Rcpp reference¶

remove outliers from the boxplot¶

rmarkdown转化中文字符为PDF的设置¶

在grid排列图¶

x11 font cannot be loaded¶

安装多版本R¶

semi-transparency is not supported on this device¶

MC, MCMC, Gibbs采样 原理¶

Running R in batch mode on Linux¶

RStudio: Warning message: Setting LC_CTYPE failed, using “C” 浅析¶

“Kernel density estimation” is a convolution of what?¶

unable to start rstudio in centos getting error “unable to connect to service”¶

发布R包¶

Presentations with Slidy¶

Estimation of the expected prediction error¶

协方差矩阵的几何解释¶

ROCR包中prediction函数¶

pairs中自定义panel函数¶

神奇的[¶

proxy 代理¶

lm() 中有无 I() 的差异¶

多项式作图¶

custom print¶

write lines to file¶

combine base and ggplot graphics in R figure¶

specify CRAN mirror in install.package¶

R 符号运算¶

Show all R’s shortcuts¶

Mistake with colon operator¶

Conda 管理版本¶

error in install gRbase¶

MC, MCMC, Gibbs采样原理¶

神奇的`[`¶

`lm()` 中有无 `I()` 的差异¶

specify CRAN mirror in `install.package`¶

error in install `gRbase`¶