R
!!!R.package Rで便利なパッケージ
{{outline}}
!!パッケージのインストール
*たとえば、gplots を使いたい場合
{{pre
> install.packages("gplots", dependencies = T)
> library(gplots)
}}

!どんなライブラリーを、読み込むことができるか <<library()>>
!どんなライブラリーが、すでに使えるようになっているか <<search()>>

!パッケージの概要を知る <<library(help="パッケージ名")>>


!!!よく使うパッケージ

{{pre

library(openxlsx)

library(tidyverse)

}}

* tidyverseには、以下のものが含まれる
{{pre
&#10004; ggplot2 3.3.6     &#10004; purrr   0.3.4
&#10004; tibble  3.1.7     &#10004; dplyr   1.0.9
&#10004; tidyr   1.2.0     &#10004; stringr 1.4.0
&#10004; readr   2.1.2     &#10004; forcats 0.5.1
}}
!!!A-G

!!corpus

!!dagitty

!!easystats
!!eyetrackingR

!!ggplot2

!!ggstatsplot
!!!H-P
!!ngram

!!!O-U
!!quanteda
!!tidyverse
!!tm

!!!V-Z

----


!!!List of Packages


!!retimes
https://cran.r-project.org/web/packages/retimes/index.html

!!stringi
!!stringr

!!psych
心理学系のパッケージ
基本的な記述統計量は <<summary(x)>>で出るが、
もう少し詳しく見るには、このパッケージをインストールして <<describe(x)>>を使う。
{{pre
> describe(x)
   vars   n mean   sd median trimmed  mad  min  max range  skew kurtosis   se
X1    1 100 0.06 1.06   0.04    0.07 0.87 -2.9 2.51  5.41 -0.04    -0.32 0.11
}}
*標準偏差、歪度、尖度、標準誤差なども出る。
!!sjmisc
!find_var 該当するデータ列を検索・選択
 find_var(data, pattern="パターン", out=出力形式)
 find_var(data, pattern="score", out="df")
*列名に score を含むものを選んで、データフレーム形式で出力



!!tm
https://www.rdocumentation.org/packages/tm/versions/0.7-3

*Boost_tokenizer(x)
*MC_tokenizer(x)
*removePunctuation(tmp)
*removeNumbers(x)
----
{{pre
tmp.v <- Vectorsource(tmp)
tmp.c <- Corpus(tmp.v)
tmpc.td <- TermDocumentMatrix(tmp.c)
findFreqTerms(tmpc.td)
 findMostFreqTerms(tmpc.td)
$`1`
     the     said      and computer      its terminal 
      15        7        6        6        5        5 
}}
----

!!koRpus
https://reaktanz.de/R/pckg/koRpus/koRpus_vignette.html
!tokenize()

 install.packages("koRpus.lang.en")
 library(koRpus.lang.en)
 temp <- tokenize(choose.files(), lang="en")

これで、例えば、Project Gutenbergから、グリム童話のGolden Birdのテキストファイルを読み込む
{{pre
A certain king had a beautiful garden, and in the garden stood a tree
which bore golden apples. These apples were always counted, and about
the time when they began to grow ripe it was found that every night one
of them was gone. The king became very angry at this, and ordered the
gardener to keep watch all night under the tree. The gardener set his
eldest son to watch; but about twelve o’clock he fell asleep, and in
}}

{{pre
> temp
     doc_id     token      tag lemma lttr   wclass desc stop stem  idx sntc
1      <NA>         A word.kRp          1     word <NA> <NA> <NA>    1    1
2      <NA>   certain word.kRp          7     word <NA> <NA> <NA>    2    1
3      <NA>      king word.kRp          4     word <NA> <NA> <NA>    3    1
4      <NA>       had word.kRp          3     word <NA> <NA> <NA>    4    1
5      <NA>         a word.kRp          1     word <NA> <NA> <NA>    5    1
6      <NA> beautiful word.kRp          9     word <NA> <NA> <NA>    6    1
                                             [...]                         
2948   <NA>         a word.kRp          1     word <NA> <NA> <NA> 2948  140
2949   <NA>     great word.kRp          5     word <NA> <NA> <NA> 2949  140
2950   <NA>      many word.kRp          4     word <NA> <NA> <NA> 2950  140
2951   <NA>      many word.kRp          4     word <NA> <NA> <NA> 2951  140
2952   <NA>     years word.kRp          5     word <NA> <NA> <NA> 2952  140
2953   <NA>         .     .kRp          1 fullstop <NA> <NA> <NA> 2953  140

}}
!lex.div()
*各種の語彙多様性指標の算出
 lex.div(temp)
!MTLD()
 > library(koRpus)
 
 > ns002 <- tokenize(choose.files(), lang="en")
で、たとえば、NS002のテキストだけのファイルを読み込んで、

 > MTLD(ns002)
 Language: "en"
 
 Total number of tokens: 463
 Total number of types:  218
 
 Measure of Textual Lexical Diversity
                 MTLD: 87.62
    Number of factors: 5.28
          Factor size: 0.72
     SD tokens/factor: 36.8 (all factors)
                       30.05 (complete factors only)
 
 Note: Analysis was conducted case insensitive.

!MATTR()
{{pre
> MATTR(temp)
Language: "en"

Total number of tokens: 606
Total number of types:  261

Moving-Average Type-Token Ratio
               MATTR: 0.69
          SD of TTRs: 0.05
         Window size: 100 
}}
!!rpart

 >model1 = rpart(LMH ~ DD + SL + MDD, data = C3L2)
 
 > rpart.plot(model)

!!gplots
{{pre
install.packages("gplots", dependencies = T)
library(gplots)

> head(meanMHD)
  Group      MHD
1    C2 1.500000
2    C2 1.000000
3    C2 2.000000
4    C2 1.250000
5    C2 1.333333
6    C2 1.333333

attach(meanMHD)
plotmeans(MHD ~ Group)
detach(oneWayMHD)
}}
{{ref_image meanComparisonMHD.png}}

!!orddom　効果量を出してくれる
*psychパッケージがインストールしてあること
 orddom(x, y)
*これだけで各種効果量を出してくれて、お好きなのをどうぞ、って感じ。
{{pre
> orddom(dmu02shd$MDD, dmu03shd$MDD)
              ordinal                metric                
var1_X        "group 1 (x)"          "group 1 (x)"         
var2_Y        "group 2 (y)"          "group 2 (y)"         
type_title    "indep"                "indep"               
n in X        "592"                  "592"                 
n in Y        "547"                  "547"                 
N #Y>X        "176563"               "176563"              
N #Y=X        "13390"                "13390"               
N #Y<X        "133871"               "133871"              
PS X>Y        "0.413406665349078"    "0.432442005161643"   
PS Y>X        "0.545243712634023"    "0.567557994838357"   
A X>Y         "0.434081476357528"    "0.434081476357528"   
A Y>X         "0.565918523642472"    "0.565918523642472"   
delta         "0.131837047284944"    "0.128573222406733"   
1-alpha       "95"                   "95"                  
CI low        "0.0647643614128363"   "0.0665435144203836"  
CI high       "0.197723891470872"    "0.190602930393082"   
s delta       "0.0339578629779545"   "0.533045085206667"   
var delta     "0.00115313645802954"  "0.284137062862983"   
se delta      NA                     "0.0316134060048762"  
z/t score     "3.88237173141703"     "4.0670474540738"     
H1 tails p/CI "2"                    "2"                   
p             "0.000109396219747593" "5.52499619534335e-05"
Cohen's d     "0.177125083672158"    "0.241205155014015"   
d CI low      "0.0839111293425067"   "0.124543945177201"   
d CI high     "0.275869162430133"    "0.357866364850828"   
var d.i       "0.291361840460969"    "0.251891629550177"   
var dj.       "0.362041171144457"    "0.319040086833437"   
var dij       "0.941272277686609"    "0.569924729477023"   
df            "1137"                 "1094.88514066995"    
NNT           "7.58512133420789"     "5.70864949792907"    
}}

ノンパラメトリックの場合、Cliff's deltaをみると、以下の基準に基づき判断すればよい：
https://www.rdocumentation.org/packages/effsize/versions/0.7.4/topics/cliff.delta
 The magnitude is assessed using the thresholds provided in (Romano 2006), i.e. 
 |d|<0.147 "negligible", 
 |d|<0.33 "small", 
 |d|<0.474 "medium", 
 otherwise "large" 

!!effsize 効果量を出してくれる
*ノンパラメトリックのCliff's deltaを見てみる例
{{pre
install.packages("effsize")
library(effsize)
> cliff.delta(dmu02shd$MDD, dmu03shd$MDD)

Cliff's Delta

delta estimate: -0.131837 (negligible)
95 percent confidence interval:
      lower       upper 
-0.19765420 -0.06483658 
}}
*「(negligible)」と、評価もコメントしてつけてくれる。

!!lawstat
Brunner-Munzel Testが入っている。
{{pre
> brunner.munzel.test(dmu02shd$MDD, dmu03shd$MDD)

        Brunner-Munzel Test

data:  dmu02shd$MDD and dmu03shd$MDD
Brunner-Munzel Test Statistic = 3.8809, df = 1098.7, p-value = 0.0001103
95 percent confidence interval:
 0.5325908 0.5992463
sample estimates:
P(X<Y)+.5*P(X=Y) 
       0.5659185 
}}

!!brunnermunzel
 install.packages("brunnermunzel")
 library(brunnermunzel)

{{pre
> brunnermunzel.test(dmu02shd$MDD, dmu03shd$MDD)

        Brunner-Munzel Test

data:  dmu02shd$MDD and dmu03shd$MDD
Brunner-Munzel Test Statistic = 3.8809, df = 1098.7, p-value = 0.0001103
95 percent confidence interval:
 0.5325908 0.5992463
sample estimates:
P(X<Y)+.5*P(X=Y) 
       0.5659185 
}}

!!dplyr

!!ggplot2

!!quanteda
*quanteda2
https://github.com/koheiw/workshop-IJTA
!!lme4

!!effects

!!car
!!tabplot

!!GGally
!相関のグラフ

!!参考情報
*https://openbox-stat.net/entry/r-package
*http://www.okadajp.org/RWiki/?R%E3%83%91%E3%83%83%E3%82%B1%E3%83%BC%E3%82%B8%E3%82%AC%E3%82%A4%E3%83%89%E3%83%96%E3%83%83%E3%82%AF