R-bloggers http://www.r-bloggers.com R news and tutorials contributed by (365) R bloggers Sun, 27 May 2012 21:41:07 +0000 en hourly 1 http://wordpress.org/?v=3.3.2 RBloggershttp://feedburner.google.com The aesthetics of error bars http://feedproxy.google.com/~r/RBloggers/~3/jFYS43tBZnw/ http://www.r-bloggers.com/the-aesthetics-of-error-bars/#comments Sun, 27 May 2012 20:28:00 +0000 Thom http://www.r-bloggers.com/?guid=389ab9ff73c011c001d51d86bf682c7a
(This article was first published on Psychological Statistics, and kindly contributed to R-bloggers)

This blog and my other main blog (the companion blog for my book) are now syndicated via R-bloggers (posts tagged R only) and statsblogs.com. The latter is a relatively new blog aggregator but looks to have some interesting content. R-bloggers it quite well established and I was already an occasional reader.

Looking at some recent content I noticed an interesting piece by Ben Bolker (author, among other things, of the excellent bbmle package in R) on dynamite plots. Until a few years ago (possibly in the early research for my book) I had not heard the term 'dynamite plot' or the negative press the attract in some research fields. In my own discipline (psychology) and in experimental psychology in particular bar plots with error bars (looking like sticks of dynamite stacked in a row) are rather popular. In fact, I was taught to use them in preference to dot plots when plotting interactions in ANOVA (their main application in experimental psychology). The main arguments against dot plots are that it is easy to manipulate them to make effects look large large by adjusting the scale (and sometimes software does this automatically). The advantage of switching to a bar plot is that these are supposed to be zero-referenced and thus effects are likely to more appropriately scaled.

Here is an example of a dynamite plot adapted from chapter 3 of my book:

(Colleagues of mine will note that the quantity displayed by the error bars is not labeled. This should always be clear from plot or figure caption - here they are 95% CIs).

Some of the material on dynamite plots on the web is somewhat one-sided (e.g., see here, here, here or the comments here). Ben Bolker bravely presents a more balanced picture. He also gets to the heart of the issue by noting that most criticisms of dynamite plots suggest box plots or plots of raw data as alternatives. This doesn't seem appropriate if your goal is inference rather than description. As Bolker notes, if you've decided to something like ANOVA you are already implicitly assuming approximate normality of the errors and so forth. Thus if the main purpose of the plot is inferential or to display key patterns among the data, box plots or raw data plots are not so useful. (Don't get me wrong I think think that plotting raw data is a good idea - but exploratory work and model checking are different from inference). So for a plot of means with error bars, the choice of dot plot or bar plot is one of aesthetics. These days my preference is for dot plots (which are more versatile and have a better information to ink ratio), but I think a well constructed dynamite plot can be appropriate in some situations. I would usually save these for a situation in which the pattern was quite simple (e.g., a 2 by 2 interaction), there was a meaningful zero or other reference point and when my audience are familiar with this style of plot and may prefer them.

A further aesthetic point here is how to plot the error bars themselves. I am persuaded by Andrew Gelman's argument that the crossbars on conventional error bar plots are ugly and counterproductive. They draw your attention to the extremes of the error bar - when values closer to the statistic being estimated are more plausible. Here is the earlier dyamite plot redrawn as a conventional error bar plot and in cleaner Gelman-approved style:

I find the version on the right to be much prettier. Furthermore it makes it easier to adapt them into two-tiered error bar plots. I like to use two-tier plots to convey 95% CIs for individual means (outer tier) and inferential (difference-adjusted) 95% CIs (inner tier). The inner tier approximates to a 95% CI for the difference - so that the means can be considered different by conventional criteria if the inner tier error bars don't overlap:



In my paper on within-subject CIs I used the style on the left. However, with hindsight I wish I'd included the style on the right. Varying the width of the bars avoids the ugly crossbars but may make detecting a 'statistically significant' difference trickier. I think that aesthetics win here because graphical methods aim to support informal inference - they are not supposed to be there for fine-grain, formal inference (which can be supported by formal hypothesis tests of various kinds - not just null hypothesis significance tests).





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]]> http://www.r-bloggers.com/the-aesthetics-of-error-bars/feed/ 0 http://www.r-bloggers.com/the-aesthetics-of-error-bars/ Tweets Analysis about Himpuan Jutaan Belia PutraJaya (Malaysia Youth Day 2012) http://feedproxy.google.com/~r/RBloggers/~3/4btJ5tmSmmA/ http://www.r-bloggers.com/tweets-analysis-about-himpuan-jutaan-belia-putrajaya-malaysia-youth-day-2012/#comments Sun, 27 May 2012 09:06:24 +0000 CloudStat http://blog.cloudstat.org/post/23853039512
(This article was first published on CloudStat, and kindly contributed to R-bloggers)

I’m using the Twitter Listening Robot to know what people is talking Najib Razak, Malaysia Prime Minister. Apparently,  23-27 are the Malaysia Youth Day 2012.  There were many funny retweets (more than 50 times) by the public:

  • RT @Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan letak aircond 1Malaysia di semua kelas sekolah di Malaysia “ 
  • RT @Faizrawrr: Best Words To Hear from Najib Razak ” Buku teks akan digantikan dengan iPad “ 
  • RT @Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia “ 
  • RT @FahmeeMacos: Best Words To Hear from Najib Razak “Semua dapat RM100 lagi “  
  • RT @Faizrawrr: Best Words To Hear from Najib Razak ” Isteri saya dah bertudung “ 
  • RT @Hanisnees: Best Words To Hear from Najib Razak .. “Pada minggu hadapan, iPad akan diagihkan kepada setiap pelajar sekolah di Malaysia dgn percuma” 
  • RT @Hanisnees: Best Words To Hear from Najib Razak “Bermula pada minggu hadapan, pelajar sekolah dikehendaki belajar menggunakan iPad sahaja” 
  • RT @alenmeri: Malaysia ade seorang Perdana Menteri , Datuk Seri Rosmah Mansor & Isterinya , Datin Seri Najib Razak . 
  • RT @501Awani: “Belia yg bertindak liar dgn menyerang polis serta melompat di atas kereta peronda bukan contoh belia di Malaysia”- PM Najib Razak 
Just in case you don’t know Malays, I used Google Translation:
  • RT @ Faizrawrr: Best Words To Hear from Najib Razak “I will put the aircond 1Malaysia in all classes of schools in Malaysia”
  • RT @ Faizrawrr: Best Words To Hear from Najib Razak “Textbooks will be replaced with iPad”
  • RT @ Faizrawrr: Best Words To Hear from Najib Razak “I will build Disneyland in Malaysia”
  • RT @ FahmeeMacos: Best Words To Hear from Najib Razak “All can be RM100 again”
  • RT @ Faizrawrr: Best Words To Hear from Najib Razak “I covered my wife”
  • RT @ Hanisnees: Best Words To Hear from Najib Razak .. “In the weeks ahead, the iPad will be distributed to every school student in Malaysia with free”
  • RT @ Hanisnees: Best Words To Hear from Najib Razak “Starting next week, students are required to learn to use iPad only”
  • RT @ alenmeri: ade a Prime Minister of Malaysia, Datuk Seri Rosmah Mansor & wife, Datin Seri Najib Razak.
  • RT @ 501Awani: “Youth I act wild and jump with the police attack on the patrol car is not an example of youth in Malaysia” - PM Najib Razak

Warning messages:
1: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, :
duplicated levels will not be allowed in factors anymore
2: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, :
duplicated levels will not be allowed in factors anymore


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RT T
408 92 

RT @Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan letak aircond 1Malaysia di semua kelas sekolah di Malaysia ”
RT @Faizrawrr: Best Words To Hear from Najib Razak ” Buku teks akan digantikan dengan iPad ”
89 
RT @Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia ”
66 
RT @FahmeeMacos: Best Words To Hear from Najib Razak “Semua dapat RM100 lagi ”
23 
RT @Faizrawrr: Best Words To Hear from Najib Razak ” Isteri saya dah bertudung ”
RT @Hanisnees: Best Words To Hear from Najib Razak .. “Pada minggu hadapan, iPad akan diagihkan kepada setiap pelajar sekolah di Malaysia dgn percuma”
RT @Hanisnees: Best Words To Hear from Najib Razak “Bermula pada minggu hadapan, pelajar sekolah dikehendaki belajar menggunakan iPad sahaja”
RT @alenmeri: Malaysia ade seorang Perdana Menteri , Datuk Seri Rosmah Mansor & Isterinya , Datin Seri Najib Razak .
RT @501Awani: “Belia yg bertindak liar dgn menyerang polis serta melompat di atas kereta peronda bukan contoh belia di Malaysia”- PM Najib Razak
7 
RT @Hanisnees: Best Words To Hear from Najib Razak.. “Peperiksaan akan dihapuskan. Ini adalah kerana kami nak ‘Save Trees!’ Selamatkan bumi” Yeah!
7 
RT @ameliameliy: Best Words To Hear from Najib Razak ”homework tidak dibenarkan sama sekali diberikan pada pelajar masa musim sekolah ” hohoho *loncat*
5 
RT @imNan4: Best Words To Hear from Najib Razak: “sorang satu iPad untuk setiap pelajar, no text book. save our planet”
4 
RT @Pwincessayu: Best Words To Hear from Najib Razak.. “Peperiksaan akan dihapuskan. Ini adalah kerana kami nak ‘Save Trees!’ Selamatkan bumi” Yeahman ^~^
3 
“Belia yg bertindak liar dgn menyerang polis serta melompat di atas kereta peronda bukan contoh belia di Malaysia”- PM Najib Razak
2 
Best Words To Hear from Najib Razak .. “Pada minggu hadapan, iPad akan diagihkan kepada setiap pelajar sekolah di Malaysia dgn percuma” ^~^
2 
RT @HasbullahAwang: Najib Razak vs Anwar Ibrahim? Jgn mimpi lah Dr Mazli, tentu saya menjadi moderatornya.
2 
RT @PapaGomo: Ucapan Najib Razak Sempena HBN 2012 - Belia Semakin Bijak Dan Matang http://t.co/kv54ahov
2 
RT @Qayyummmm: Best Words To Hear from Najib Razak ” semua sekolah ada locker dan hanya perlu bawak ipad yang dibagi free sahaja ”
2 
” @imNan4 : Best Words To Hear from Najib Razak: “sorang satu iPad untuk setiap pelajar, no text book. save our planet” ”
“@Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia “”
“@Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia “” dgn bayaran tiket 10 ringgit setiap org.
“@HasbullahAwang: Najib Razak vs Anwar Ibrahim? Jgn mimpi lah Dr Mazli, tentu saya menjadi moderatornya.”
#SRWKAMEK Cabaran Debat Bakal Perdana Menteri (Najib Razak VS Anwar Ibrahim). Moderator Dihentam di Twitter!!
@anwaribrahim dsai najib razak duk pki rantai pasai pa…???duk berasa betol la tu..haha
@farhanzulhusmi kena loh tukar screen meh. mintak aje kat Najib Razak, nak dekat PRU ni semua benda tak mustahil boleh dapat XD
@fatinbajang haha, tapi najib razak ada pengalaman luas :b okay, trimas :D nak yang cmne ? Cakap je :)
@fatinbajang memilih doe, najib razak ada pulau tau xD haha . Perli aku ke -,- takde ? Nak aku carikan :b haha
@fatinbajang najib razak takkan kau tak kenal :p aku comel ke ? Erk -,- haha
@jasunka_05 Kalau lu niat nak saiko wa sorry lah der! Gua pergi pada kenyataan. Najib Bin Razak bacul dengan Anwar Bin Ibrahim!!
@MuhaiminMzln haha,jgn risau hati ini tetap utk Najib Razak:)
AHHHHH HEAVEN NYA~~~~~~~ RT @Faizrawrr: Best Words To Hear from Najib Razak ” Buku teks akan digantikan dengan iPad ”
Belia di Malaysia bukan ‘demo crazy’, kata Najib: - Datuk Seri Najib Tun Razak hari ini menegaskan bahawa go… http://t.co/Xj0Bpuxf #fb
Belia Di Malaysia Bukan �Demo Crazy�, Kata Najib: PUTRAJAYA, 26 Mei � Datuk Seri Najib Tun Razak hari ini menega… http://t.co/3Q6ixv6W
Belia Di Malaysia Bukan �Demo Crazy�, Kata Najib: PUTRAJAYA, 26 Mei � Datuk Seri Najib Tun Razak hari ini menega… http://t.co/9LCilBhO
Belia Di Malaysia Bukan �Demo Crazy�, Kata Najib: PUTRAJAYA, 26 Mei � Datuk Seri Najib Tun Razak hari ini menega… http://t.co/fyQF8HKV
Belia Di Malaysia Bukan �Demo Crazy�, Kata Najib: PUTRAJAYA, 26 Mei � Datuk Seri Najib Tun Razak hari ini menega… http://t.co/x4lZD6dG
Belia Di Malaysia Bukan �Demo Crazy�, Kata Najib: PUTRAJAYA, 26 Mei � Datuk Seri Najib Tun Razak hari ini menegaskan… http://t.co/iPRCuP90
Belia Di Malaysia Bukan �Demo Crazy�: Datuk Seri Najib Tun Razak menegaskan bahawa golongan belia di negara ini… http://t.co/KBiXKcTo
BEST WORDS EVER! :D RT @Faizrawrr Best Words To Hear from Najib Razak ” Buku teks akan digantikan dengan iPad ”
Best Words To Hear from Najib Razak” pelajar x perlu guna buku teks , saya akan menukarkan buku teks kepada i pad..”
Best Words To Hear from Najib Razak” sekolah akan bermula pada pukul 8.00 pagi supaya tidak menyusahkan pelajar bangun awal2”
Best Words To Hear from Najib Razak ” Waktu persekolahan akan ditukar daripada lima hari seminggu kepada tiga hari seminggu ”
Best Words To Hear from Najib Razak ”homework tidak dibenarkan sama sekali diberikan pada pelajar masa musim sekolah ” hohoho *loncat*
Best Words To Hear from Najib Razak - “Mulai hari ni, hukuman hudud dan qisas akan dilaksanakan” Automatik , kadar jenayah turun (Y)
Best Words To Hear From Najib Razak ” Bermula minggu depan , sekolah tidak di perlukan lagi ” ORHH !!
Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia ”
Best Words To Hear from Najib Razak ” Saya akan letak aircond 1Malaysia di semua kelas sekolah di Malaysia ”
Best Words To Hear from Najib Razak ” semua sekolah ada locker dan hanya perlu bawak ipad yang dibagi free sahaja ”
Best Words To Hear from Najib Razak “Bermula pada minggu hadapan, pelajar sekolah dikehendaki belajar menggunakan iPad sahaja”
Best Words To Hear from Najib Razak “Bermula pada minggu hadapan, pelajar sekolah dikehendaki belajar menggunakan iPad sahaja” :’D
Best Words To Hear from Najib Razak “Buku Teks akan ditukarkan kepada iPad” :)
Best Words To Hear from Najib Razak “Rosmah akan mula berhijab”
Best Words To Hear from Najib Razak “Saya dah pasang lif kat semua sekolah”
Best Words To Hear from Najib Razak “Tahun ni semua pelajar sekolah akan dapat duit raya”
Best Words To Hear from Najib Razak .. “Pada minggu hadapan, iPad akan diagihkan kepada setiap pelajar sekolah di Malaysia dgn percuma”
Best Words To Hear from Najib Razak.. “Peperiksaan akan dihapuskan. Ini adalah kerana kami nak ‘Save Trees!’ Selamatkan bumi” Yeah!
Best Words To Hear from Najib Razak.. “Peperiksaan akan dihapuskan. Ini adalah kerana kami nak ‘Save Trees!’ Selamatkan bumi” Yeahman ^~^
Best Words To Hear from Najib Razak: “sorang satu iPad untuk setiap pelajar, no text book. save our planet”
Bumi akan panas T.T RT @tikaaaaahhhhh: RT @Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan letak aircond 1Malaysia di semua k …
Cc Najib Razak ,Anwar Ibrahim RT @_LoveShak: Sape je la yang dok sibuk tweet berkualiti ni oi.. aku nak gak tgk.
Dan ipad adalah hak milik kekal semua pelajar :) “@Faizrawrr: Best Words To Hear from Najib Razak ” Buku teks akan digantikan dengan iPad “”
Dear najib razak, tolong dengar luahan kami. kami tuntut hak kami kami nak belajar guna iPad *campak buku teks dalam laut*
Debat Dato’ Seri Anwar Ibrahim vs Dato’ Seri Najib Razak. hahaha~ - Alang http://t.co/EHJP2Sra
Dia kata dalam forum mana? RT @Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia ”
gua steady sebab najib razak akan bekap gua. gua kan belia
Hidup DS Najib! RT @LokmanAdam: Himpunan 2 Juta Belia Capai Sasaran - Najib Razak http://t.co/YAt6WxN4
http://t.co/KiIT5lHv blog najib tun razak\nhttp://t.co/Zl3kLWwI pharmacists without borders canada
Huduh betol aku tgk najib razak ni duk pki rantai..bajet 3 line la tu..aku kutip jgk kang…
Macam2 hal negara Najib Razak ni, heran gua.
Malaysia ade seorang Perdana Menteri , Datuk Seri Rosmah Mansor & Isterinya , Datin Seri Najib Razak .
Malaysian Youths Are Not ‘Demo Crazy’, Says PM: \n\tPUTRAJAYA, May 26 2012 (Bernama) — Datuk Seri Najib Tun Razak… http://t.co/ErSbJeyc
Malaysian Youths Are Not ‘Demo Crazy’, Says PM: \n\tPUTRAJAYA, May 26 2012 (Bernama) — Datuk Seri Najib Tun Razak… http://t.co/uAYc19Xp
Memang cuti pun ~ RT @Faizrawrr: Best Words To Hear from Najib Razak ” Semua akan cuti esok ”
Najib janji negara yang lebih baik untuk semua belia ..: Datuk Seri Najib Tun Razak berkata kerajaan berjanji ak… http://t.co/PM7NxsMB
Najib janji negara yang lebih baik untuk semua belia ..: Datuk Seri Najib Tun Razak berkata kerajaan berjanji ak… http://t.co/YyQv0TLy
Najib Razak is the new Opposition Leader of Malaysia #BestWordsToHear
najib razak tu kulit putih gebu x heran la dia ok je pakai pink. tengok la muhyidin yasin pakai pink. hamagaddd
NST NEWS: Najib will launch FGVH prospectus on Thursday: Dungun: Prime Minister Datuk Seri Najib Tun Razak will … http://t.co/TTo5epse
owh, AMIN ! RT @Faizrawrr Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia ”
Penat bru blek Hari Belia , balik pukul 7 pm . lps Najib Tun Razak buat perasmian .
PENDEDAHAN!! BUKAN ROSMAH SAJA YANG CINTA PM RUPENYER ADA LAGI?: Najib Razak, Sebut saja sudah kenal.. semua rak… http://t.co/7ZbHyR9e
PENDEDAHAN!! BUKAN ROSMAH SAJA YANG CINTA PM RUPENYER ADA LAGI?: Najib Razak, Sebut saja sudah kenal.. semua rak… http://t.co/uazrCn9c
PM lancar prospektus FGVH Khamis: DUNGUN: Perdana Menteri, Datuk Seri Najib Razak akan melancarkan prospektus… http://t.co/LAsfgc8I
PM Najib Razak telah di masukkan ke hospital hari ini kerana serangan jantung akibat daripada himpunan sejuta… http://t.co/5bflZBMm
PM urges country�s youth to ensure future by voting for BN: � PUTRAJAYA: Prime Minister Datuk Seri Najib Tun Razak… http://t.co/CO4sQPED
PM urges country�s youth to ensure future by voting for BN: PUTRAJAYA:�Prime Minister Datuk Seri Najib Tun Razak… http://t.co/4nZaMgxZ
PM urges country�s youth to ensure future by voting for BN: PUTRAJAYA:�Prime Minister Datuk Seri Najib Tun Razak… http://t.co/daX5fUSS
PM urges country�s youth to ensure future by voting for BN: PUTRAJAYA:�Prime Minister Datuk Seri Najib Tun Razak… http://t.co/egnVuy66
PM urges country�s youth to ensure future by voting for BN: PUTRAJAYA:�Prime Minister Datuk Seri Najib Tun Razak… http://t.co/hes1FNCa
PM urges country�s youth to ensure future by voting for BN: PUTRAJAYA:�Prime Minister Datuk Seri Najib Tun Razak… http://t.co/kEboYCAa
PM urges country�s youth to ensure future by voting for BN: PUTRAJAYA:�Prime Minister Datuk Seri Najib Tun Razak… http://t.co/pEQpdnU3
PM urges country�s youth to ensure future by voting for BN: PUTRAJAYA:�Prime Minister Datuk Seri Najib Tun Razak… http://t.co/XTFERD4V
PM urges country�s youth to ensure future by voting for BN: PUTRAJAYA:�Prime Minister Datuk Seri Najib Tun Razak… http://t.co/zApsh8EM
PM will launch FGVH prospectus on Thursday: DUNGUN, May 26 � Prime Minister Datuk Seri Najib Tun Razak will laun… http://t.co/ciIFKTXk
PM will launch FGVH prospectus on Thursday: DUNGUN, May 26 � Prime Minister Datuk Seri Najib Tun Razak will laun… http://t.co/FCyA4U0M
Rosmah gila dengan tas tangan dan cincin berlian nya. Najib Razak pula dengan rantai emasnya.
RT “@Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia “”
RT @_RayScxha_: RT @Faizrawrr: Best Words To Hear from Najib Razak ” Buku teks akan digantikan dengan iPad ”
RT @AimieMalek: RT @FahmeeMacos: Best Words To Hear from Najib Razak “Semua dapat RM100 lagi ”
RT @alenmeri: soalan: kenapa najib razak botak ? jawapan: sebab rosmah cabut rambut najib n gam d kepala dia untuk buat sarang lebah .
RT @AnesHoran: This ;) RT @Faizrawrr : Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia ”
RT @apaijas: saya hot macam najib razak RT: @farishakim: saya hot seperti bieber
RT @apitrusdi: Best Words To Hear from Najib Razak: ”Disneyland akan dibina di Malaysia! Kamu semua tak payah susah-susah pergi luar negara.”
RT @FaezAzam: Dia kata dalam forum mana? RT @Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia ”
RT @HeyyPaish: #KamiRemaja yang masih bersekolah memohon supaya Najib Tun Razak menyediakan Ipad 1 Malaysia untuk kami belajar. Baru bersemangat :p
RT @LeanaKamal: “@Faizrawrr: Best Words To Hear from Najib Razak ” Isteri saya dah bertudung “” really? :o
RT @lullabygift: RT @_RayScxha_: RT @Faizrawrr: Best Words To Hear from Najib Razak ” Buku teks akan digantikan dengan iPad ”
RT @nadcydot: “@Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia “” dgn bayaran tiket 10 ringgit setiap org.
RT @NoraliaAshikin: RT @AimieMalek: RT @FahmeeMacos: Best Words To Hear from Najib Razak “Semua dapat RM100 lagi ”
RT @Npowerof2: RT @lullabygift: RT @_RayScxha_: RT @Faizrawrr: Best Words To Hear from Najib Razak ” Buku teks akan digantikan dengan iPad ”
RT @panglima_cyber: Berita Harian : Najib gariskan lima ciri belia masa depan: PUTRAJAYA: Perdana Menteri, Datuk Seri Najib Razak me… http://t.co/JDmbmonT
RT @PapaGomo: Himpunan 2 Juta Belia Capai Sasaran - Najib Razak http://t.co/OZk30NXW
RT @PapaGomo: Himpunan 2 Juta Belia Capai Sasaran - Najib Razak: YAB Dato Sri Najib Razak Perdana Menteri Malaysia”Belia akan … http://t.co/iV8jGiqD
RT @PapaGomo: Ucapan Najib Razak Sempena HBN 2012 - Belia Semakin Bijak Dan Matang: �Golongan belia yang … http://t.co/tdZiB774
RT @PapaGomo: Ucapan Najib Razak Sempena HBN 2012 - Belia Semakin Bijak Dan Matang: �Golongan belia yang mempunyai nilai kemas… http://t.co/rEftrjE2
RT @PasBeruk: Himpunan 2 Juta Belia Capai Sasaran - Najib Razak: YAB Dato Sri Najib Razak Perdana Menteri Malaysia”Belia akan … http://t.co/H0voA7nT
RT @PasBeruk: Ucapan Najib Razak Sempena HBN 2012 - Belia Semakin Bijak Dan Matang: �Golongan belia yang mempunyai nilai kemas… http://t.co/M1lhCnv8
RT @PelikHensem: BEST WORDS EVER! :D RT @Faizrawrr Best Words To Hear from Najib Razak ” Buku teks akan digantikan dengan iPad ”
RT @SrikandiMelayu: Ucapan Najib Razak Sempena HBN 2012 - Belia Semakin Bijak Dan Matang http://t.co/Pwp6UhF3
RT @tiewnama: PM Najib Razak telah di masukkan ke hospital hari ini kerana serangan jantung akibat daripada … http://t.co/RGnVZe9G
RT @TokGuru86: PM urges country�s youth to ensure future by voting for BN: PUTRAJAYA:�Prime Minister Datuk Seri Najib Tun Razak… http://t.co/zApsh8EM
RT tomorrowland better (Y) @Afiqalalala: RT @Faizrawrr: Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia ”
saya hot macam najib razak RT: @farishakim: saya hot seperti bieber
sinar : Belia di Malaysia bukan ‘demo crazy’, kata Najib: - Datuk Seri Najib Tun Razak hari ini menegaskan bahaw… http://t.co/zcugaNcc
soalan: kenapa najib razak botak ? jawapan: sebab rosmah cabut rambut najib n gam d kepala dia untuk buat sarang lebah .
This ;) RT @Faizrawrr : Best Words To Hear from Najib Razak ” Saya akan bina Disneyland di Malaysia ”
Tika… Najib Tun Razak tu tiap2 tahun baju raya dia warna pink ok.. Restu jer kak mah tengok… Kah kah kah
Ucapan Najib Razak Sempena HBN 2012 - Belia Semakin Bijak Dan Matang: �Golongan belia yang mempunyai nilai… http://t.co/sd7hOffI
Untung pelajar Singapore dah start pakai dah :( RT @Hanisnees Best Words To Hear from Najib Razak “Bermula pada minggu hadapan, pela…….”
Wahh, best feeling ever. RT @Faizrawrr: Best Words To Hear from Najib Razak ” Buku teks akan digantikan dengan iPad ”
>

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]]> http://www.r-bloggers.com/tweets-analysis-about-himpuan-jutaan-belia-putrajaya-malaysia-youth-day-2012/feed/ 0 http://www.r-bloggers.com/tweets-analysis-about-himpuan-jutaan-belia-putrajaya-malaysia-youth-day-2012/ Updating to R 2.15, warnings in R and an updated function list for Serious Stats http://feedproxy.google.com/~r/RBloggers/~3/IE5EPoNCpjk/ http://www.r-bloggers.com/updating-to-r-2-15-warnings-in-r-and-an-updated-function-list-for-serious-stats/#comments Sun, 27 May 2012 08:09:10 +0000 Thom http://seriousstats.wordpress.com/?p=176 Continue reading →]]>
(This article was first published on Serious Stats » R code, and kindly contributed to R-bloggers)

Whilst writing the book  the latest version of R changed several times. Although I started on an earlier version, the bulk of the book was written with 2.11 and it was finished under R 2.12. The final version of the R scripts were therefore run and checked using R 2.12 and, in the main, the most recent packages versions for R 2.12.

When it came to proof read R 2.13 was already out and therefore most of the examples were also checked with version, but I stuck with R 2.12 on my home and work machines until last week.

In general I don’t see the point of updating to a new version number if everything is working fine. One advantage of this approach is that the version I install will usually have bugs from the initial release already ironed out. That said, new versions of R have (in my experience) been very stable.

I tend to download the version only when I fall several versions behind or if it is a requirement for a new package or package version. On this occasion it turned out that the latest version of the ordinal package (for fitting ordered logistic regression and multilevel ordered logistic regression models). There are two main drawbacks with updating. The first is reinstalling all your favourite package libraries (and generally getting it set up how you like it). The second is dealing with changes in the way R behaves.

For re-installing all my packages I use a very crude system. For any given platform (Mac OS, Windows or Linux) there are cleverer solutions (that you can find via google). My solution works across cross-platform and is fairly robust, if inelegant. I simply keep an R script with a number of install.packages() commands such as:

install.packages(‘lme4′, ‘exactci’, ‘pwr’, ‘arm’)

I run these in batches after installing the new R version. I find this useful because I’m forever installing R on different machines (so far Mac OS or Windows) at work (e.g., for teaching or if working away from the office or on a borrowed machine). I can also comment the file (e.g., to note if there are issues with any of the packages under a particular version of R). This usually suffices for me as I usually run a ‘vanilla’ set-up without customization. It would be more efficient for me to customize my set-up, but for teaching purposes I find it helps not to do that. Likewise, I tend to work with a clean workspace (and use a script file to save R code that creates my workspaces). I should stress that this isn’t advice – and I would work differently myself if I didn’t use R so much for teaching.

One of the first things that happened after installing R 2.15 was that some of my own functions started producing warnings. R warnings can be pretty scary for new users but are generally benign. Some of them are there to detect behaviour associated with common R errors or common statistical errors (and thus give you a chance to check your work). Others alert you to non-standard behaviour from a function in R (e.g., changing the procedure it uses when sample sizes are small). Yet others offer tips on writing better R code. Only very rarely are they an indication that something has gone badly wrong.

Thus most R warnings are slightly annoying but potentially useful. In my case R 2.15 disliked a number of my functions of the form:

mean(data.frame)

The precise warning was:

Warning message:
mean() is deprecated.
Use colMeans() or sapply(*, mean) instead. 

All the functions worked just fine, but (after my initial irritation had receded) I realize that colMeans() is a much better function. It is more efficient but, even better, it is obvious that it calculates the means of the columns of a data frame or matrix. With the more general  mean() function it is not immediately obvious what will happen when called with a data frame as an argument. It is also trivial to infer that rowMeans() calculates the row means.

I have now re-written  a number of functions to deal with this problem and to make a few other minor changes. The latest version of my functions can be loaded with the call:

source('http://sites.google.com/site/seriousstats2012/home/SeriousStatsAllfunctions.txt')

I will try and keep this file up-to-date with recent versions of R and correct any bugs as they are detected.

The functions can be downloaded as a text file from:

http://sites.google.com/site/seriousstats2012/home/


Filed under: news, R code, serious stats Tagged: R, software

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]]> http://www.r-bloggers.com/updating-to-r-2-15-warnings-in-r-and-an-updated-function-list-for-serious-stats/feed/ 0 http://www.r-bloggers.com/updating-to-r-2-15-warnings-in-r-and-an-updated-function-list-for-serious-stats/ Cross-valitation variability example, part I http://feedproxy.google.com/~r/RBloggers/~3/fnqnuMv8vNM/ http://www.r-bloggers.com/cross-valitation-variability-example-part-i/#comments Sat, 26 May 2012 15:48:00 +0000 Bogumił Kamiński http://www.r-bloggers.com/?guid=9e535ea2b8317ba016574c7cb8f1f6ff
(This article was first published on R snippets, and kindly contributed to R-bloggers)

Recently I had a discussion with a student about variability of results obtained from cross-validation procedure. While the subject is well known there are not many examples on the web showing it, so I have written its simple presentation.
Results from cross-validation are reported as a standard by rpart procedure (printcp and plotcp) and optimal cp is selected for tree pruning. Many people I have talked to think that because each time rpart is run on the same data-set the same tree is obtained that also printcp and plotcp results do not change. However, it should be remembered that x-val relative error returned by them is based on random sampling and is not constant. Therefore two runs of rpart might indicate different values of optimal cp.

Here is the code that illustrates this situation using Participation data from Ecdat package:

library(Ecdat)
library(rpart)
data(Participation)

set.seed(1)
xerror <- t(replicate(8192,
    rpart(lfp ~ ., data = Participation)$cptable[,4]))
tree.size <- factor(
    rpart(lfp ~ ., data = Participation)$cptable[,2] + 1)
colnames(xerror) <- tree.size
par(mfrow = c(1, 2))
boxplot(xerror, xlab = "size of tree",
    ylab = "X-val Relative Error")
plot(tree.size[apply(xerror,1, which.min)], xlab = "size of tree",
    ylab = "# minimal")

The resulting plot is the following:


We can see that using x-val criterion tree of size 5 is selected in around 2/3 of cases and size 6 is found best otherwise.

The other issue is why there is no variability of x-val for tree size 1 and almost no variability at size 2. The answer is that for those tree sizes the split in every cross-validation fold is made on nominal variable (for example foreign for tree size 1) at the same cut-point and all resulting trees are identical (one outlier for tree size 2 is due single different split). For tree sizes 5 and 6 continuous variables enter the tree (age and lnnlinc) and cut-points start moving, so the resulting trees in different cross-validation runs are different.

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]]> http://www.r-bloggers.com/cross-valitation-variability-example-part-i/feed/ 0 http://www.r-bloggers.com/cross-valitation-variability-example-part-i/ MathJax Syntax Change http://feedproxy.google.com/~r/RBloggers/~3/ogW0xuiT_Hs/ http://www.r-bloggers.com/mathjax-syntax-change/#comments Fri, 25 May 2012 21:07:09 +0000 jjallaire http://blog.rstudio.org/?p=495 ]]>
(This article was first published on RStudio Blog, and kindly contributed to R-bloggers)

We’ve just a made a change to the syntax for embedding MathJax equations in R Markdown documents. The change was made to eliminate some parsing ambiguities and to support future extensibility to additional formats.

The revised syntax adds a “latex” qualifier to the $ or $$ equation begin delimiter. It looks like this:

This change was the result of a few considerations:

  1. Some users encountered situations where the $<equation>$ syntax recognized standard text as an equation. There was an escape sequence (\$) to avoid this but for users not explicitly aware of MathJax semantics this was too hard to discover.
  2. The requirement to have no space between equation delimiters ($) and the equation body (intended to reduce parsing ambiguity) was also confusing for users.
  3. We want to eventually support ASCIIMath and for this will require an additional qualifier to indicate the equation format.

RStudio v0.96.227 implements the new MathJax syntax and is available for download now.


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]]> http://www.r-bloggers.com/mathjax-syntax-change/feed/ 0 http://www.r-bloggers.com/mathjax-syntax-change/ Facebook-class social network analysis with R and Hadoop http://feedproxy.google.com/~r/RBloggers/~3/rW3vifH6asY/ http://www.r-bloggers.com/facebook-class-social-network-analysis-with-r-and-hadoop/#comments Fri, 25 May 2012 18:58:00 +0000 David Smith http://www.r-bloggers.com/?guid=652f955c7d487f0f97973464d7164eb8
(This article was first published on Revolutions, and kindly contributed to R-bloggers)

In computing, social networks are traditionally represented as graphs: a connection of nodes (people), pairs of which may be connected by edges (friend relationships). Visually, the social networks can then be represented like this:

Network-graph

Social network analysis often amounts to calculating the statistics on a graph like this: the number of edges (friends) connected to a particular node (person), and the distribution of the number of edges connected to nodes across the entire graph. When the graph consists of up to 10 billion elements (nodes and edges), such computations can be done on a single server with dedicated graph software like Neo4j. But bigger networks — like Facebook's social network, which is a graph with more than 60 billion elements — require a distributed solution.

Facebook-friendships

Marko A. Rodriguez, a graph consultant with Aurelius, shows in a blog post how to use R and Hadoop (integrated with Revolution Analytics' RHadoop packages) to analyze Facebook-scale social networks. He first simulates a social network (shown at the top of this post) using R's igraph package, and then distributed the network in the Hadoop cluster with to.dfs function (from the rhdfs package). He then used the mapreduce function (from the rmr package) to write a simple map-reduce algorithm in R to count the number of edges associated with each node:

degree.V <- mapreduce(edge.list, 
    map=function(k,v) keyval(v[2],1), 
    reduce=function(k,v) keyval(k,length(v)))
from.dfs(degree.V)[[1]]

From there, it's another simple map-reduce job to calculate the connectivity statistics for the entire network. For more details on how Marko used RHadoop to perform this analysis, see the entire blog post linked below.

Aurelius blog: 

To leave a comment for the author, please follow the link and comment on his blog: Revolutions.
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]]> http://www.r-bloggers.com/facebook-class-social-network-analysis-with-r-and-hadoop/feed/ 0 http://www.r-bloggers.com/facebook-class-social-network-analysis-with-r-and-hadoop/ Forecasting: Principles and Practice http://feedproxy.google.com/~r/RBloggers/~3/5-KwA9bWWTY/ http://www.r-bloggers.com/forecasting-principles-and-practice/#comments Fri, 25 May 2012 16:27:00 +0000 Dave Giles http://www.r-bloggers.com/?guid=ab79a8314d8892615d3b8cd3abc8b5af
(This article was first published on Econometrics Beat: Dave Giles' Blog, and kindly contributed to R-bloggers)

Forecasting: Principles and Practice is the title of a new book by Rob Hyndman and George Athanasopoulos.

As Rob says on his webpage:

"The book is dif­fer­ent from other fore­cast­ing text­books in sev­eral ways.
  • It is free and online, mak­ing it acces­si­ble to a wide audience.
  • It is based around the fore­cast pack­age for R.
  • It is con­tin­u­ously updated. You don’t have to wait until the next edi­tion for errors to be removed or new meth­ods to be dis­cussed. We will update the book frequently.
  • There are dozens of real data exam­ples taken from our own con­sult­ing prac­tice. We have worked with hun­dreds of busi­nesses and orga­ni­za­tions help­ing them with fore­cast­ing issues, and this expe­ri­ence has con­tributed directly to many of the exam­ples given here, as well as guid­ing our gen­eral phi­los­o­phy of forecasting.
  • We empha­sise graph­i­cal meth­ods more than most fore­cast­ers. We use graphs to explore the data, analyse the valid­ity of the mod­els fit­ted and present the fore­cast­ing results."
This looks really good!

    © 2012, David E. Giles

    To leave a comment for the author, please follow the link and comment on his blog: Econometrics Beat: Dave Giles' Blog.
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    ]]>     http://www.r-bloggers.com/forecasting-principles-and-practice/feed/ 0 http://www.r-bloggers.com/forecasting-principles-and-practice/     Monitor: Adding "RER" and "RPD" statistics http://feedproxy.google.com/~r/RBloggers/~3/0ZGIRNTKyjY/ http://www.r-bloggers.com/monitor-adding-rer-and-rpd-statistics/#comments Fri, 25 May 2012 15:46:00 +0000 jrcuesta http://www.r-bloggers.com/?guid=8fb0347684ee89b35d541d7170a191d0
    (This article was first published on NIR-Quimiometría, and kindly contributed to R-bloggers)

    I continue developing the Monitor function in R. The idea is to get statistics which help me to understand the performance of my model.
    Of course the validation set must be free of outliers (X or Y).
    I add this time two new statistics: RER and RPD.
    These statistics must be treated with caution, because depends of the range, standard deviation and number of samples for the validation set.
    See the new video for the calculation of these statistics in "R":
     Monitor: Adding "RER" and "RPD" statistics

    To leave a comment for the author, please follow the link and comment on his blog: NIR-Quimiometría.
    R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series,ecdf, trading) and more...

    ]]>     http://www.r-bloggers.com/monitor-adding-rer-and-rpd-statistics/feed/ 0 http://www.r-bloggers.com/monitor-adding-rer-and-rpd-statistics/     A course in statistical programming http://feedproxy.google.com/~r/RBloggers/~3/PIMSQQb-3pg/ http://www.r-bloggers.com/a-course-in-statistical-programming/#comments Fri, 25 May 2012 14:14:23 +0000 Karl Broman http://kbroman.wordpress.com/?p=987 ]]>
    (This article was first published on The stupidest thing... » R, and kindly contributed to R-bloggers)

    Graduate students in statistics often take (or at least have the opportunity to take) a statistical computing course, but often such courses are focused on methods (like numerical linear algebra, the EM algorithm, and MCMC) and not on actual coding.

    For example, here’s a course in “advanced statistical computing” that I taught at Johns Hopkins back in 2001.

    Many (perhaps most) good programmers learned to code outside of formal courses. But many statisticians are terrible programmers and would benefit by a formal course.

    Moreover, applied statisticians spend the vast majority of their time interacting with a computer and would likely benefit from more formal presentations of how to do it well. And I think this sort of training is particularly important for ensuring that research is reproducible.

    One really learns to code in private, struggling over problems, but I benefited enormously from a statistical computing course I took from Phil Spector at Berkeley.

    Brian Caffo, Ingo Ruczinski, Roger Peng, Rafael Irizarry, and I developed a statistical programming course at Hopkins that (I think) really did the job.

    I would like to develop a similar such course at Wisconsin: on statistical programming, in the most general sense.

    I have in mind several basic principles:

    • be self-sufficient
    • get the right answer
    • document what you did (so that you will understand what you did 6 months later)
    • if primary data change, be able to re-run the analysis without a lot of work
    • are your simulation results reproducible?
    • reuse of code (others’ and your own) rather than starting from scratch every time
    • make methods accessible to (and used by) others

    Here are my current thoughts about the topics to include in such a course. The key aim would be to make students aware of the basic principles and issues: to give them a good base from which to learn on their own. Homework would include interesting and realistic programming assignments plus create a Sweave-type document and an R package.

    • Basic unix tools (find; df; top; ps ux; grep); unix on Mac and windows
    • Emacs/vim/other editors (rstudio/eclipse)
    • Latex (for papers; for presentations)
    • slides for talks; posters; figures/tables
    • Advanced R (fancy data structures; functions; object-oriented stuff)
    • Advanced R graphics
    • R packages
    • Sweave/asciidoc/knitr
    • minimal Perl (or Python or Ruby); example of data manipulation
    • Minimal C (or C++); examples of speed-up
    • version control (eg git or mercurial); backups
    • reproducible research ideas
    • data management
    • managing projects: data, analyses, results, papers
    • programming style (readable, modular); general but not too general
    • debugging/profiling/testing
    • high-throughput computing; parallel computing; managing big jobs
    • finding answers to questions: man pages; documentation; web
    • more on visualization; dynamic graphics
    • making a web page; html & css; simple cgi-type web forms?
    • writing and managing email
    • managing references to journal articles

    To leave a comment for the author, please follow the link and comment on his blog: The stupidest thing... » R.
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    ]]>     http://www.r-bloggers.com/a-course-in-statistical-programming/feed/ 0 http://www.r-bloggers.com/a-course-in-statistical-programming/     Trend Following Factors from Hsieh and Fung http://feedproxy.google.com/~r/RBloggers/~3/-tupFjdNrH8/ http://www.r-bloggers.com/trend-following-factors-from-hsieh-and-fung/#comments Fri, 25 May 2012 13:42:00 +0000 klr http://www.r-bloggers.com/?guid=64b301d0062784c2f98e264225fa3541
    (This article was first published on Timely Portfolio, and kindly contributed to R-bloggers)

    The beauty of R and academic replication is that on the Friday before Memorial Day weekend I can read an academic paper and do some analysis all before breakfast.  In this case, the paper is

    Hsieh, David A. and Fung, William, The Risk in Hedge Fund Strategies: Theory and Evidence from Trend Followers. The Review of Financial Studies, Vol. 14, No. 2, Summer 2001 .
    Available at author’s site at Duke University: PDF file.

    with data courtesy of the authors available at http://faculty.fuqua.duke.edu/~dah7/DataLibrary/TF-Fac.xls

    Let’s get the factors into R and run some very introductory analysis on the Edhec data from PerformanceAnalytics.  The factors as defined by the authors are:

    Trend Following Risk Factors from Fung and Hsieh, RFS (2001)
    PTFSBD: Return of PTFS Bond lookback straddle
    PTFSFX: Return of PTFS Currency Lookback Straddle
    PTFSCOM:Return of PTFS Commodity Lookback Straddle
    PTFSIR: Return of PTFS Short Term Interest Rate Lookback Straddle
    PTFSSTK:Return of PTFS Stock Index Lookback Straddle

    From TimelyPortfolio
    From TimelyPortfolio

    What a nice way to ease into the weekend. Now for the hard part--thinking about how I might use this.

    R code from GIST:

    To leave a comment for the author, please follow the link and comment on his blog: Timely Portfolio.
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