Novembro 2012 - R-br

[Dúvida] Upload de um pacote para o CRAN
by Pedro Rafael 19 Nov '12

19 Nov '12

Pessoal qual softwares vocês utilizam para fazer upload de um pacote para o CRAN? [ ], Pedro Rafael Diniz Marinho.

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Zelig vs RevolutionR
by Leonard Mendonça de Assis 19 Nov '12

19 Nov '12

Alguém já instalou a biblioteca Zelig no RevolutionR? Instalei o revolutionR acadêmico em uma vm windows e quando fui instalar o Zelig, deu um erro estranho na ide (que nada mais é que o visual studio 2008) e forçou a saída. Existe problema de incompatibilidade entre Zelig e o Revolution R? -- []s Leonard de Assis http://about.me/ldeassis

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pacotes do R para trabalhar com correlação
by alanarocha＠sapo.pt 19 Nov '12

19 Nov '12

Olá a todos, eu ando as voltas para instalar pacotes para trabalhar com correlação. install.packages("ppcor", lib="~/Rpacks") library" library(ppcor, lib="~/Rpacks") install.packages("ppcor", lib="~/Rpacks") library" library(ppcor, lib="~/Rpacks") no library trees found in 'lib.loc' > > help.search(“correlaction”) > > help.search(“correlation”) Error: unexpected input in "help.search(“" > > help.search(“correlation”) Error: unexpected input in "help.search(“" > > > help.search(“correlaction”) Error: unexpected input in "help.search(“" > > help.search(“cor”) Error: unexpected input in "help.search(“" > > help(package=ppcor) starting httpd help server ... done > help(package=ppcor) help(package=cor) install.packages("ppcor") Installing package(s) into ‘C:/Documents and Settings/ARua/My Documents/R/win-library/2.15’ (as ‘lib’ is unspecified) Warning: unable to access index for repository http://cran.fiocruz.br/bin/windows/contrib/2.15 Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.15 Warning message: package ‘ppcor’ is not available (for R version 2.15.1) > library(ppcor) Error in library(ppcor) : there is no package called ‘ppcor’ > e tambem com "cor" pscor etc se eu tenho um pdf do pacote por isso acho ainda mai estranho... que estou eu a fazer mal? tenho R2.15 Package ‘ppcor’ February 15, 2012 Type Package Title Partial and Semi-partial (Part) correlation Version 1.0 Date 2011-06-14 Author Seongho Kim Maintainer Seongho Kim <biostatistician.kim(a)gmail.com> Description The R package ppcor can calculate parital and semi-partial (part) correlations along with p-value. License GPL-2 Repository CRAN Date/Publication 2011-06-15 18:04:26 R topics documented: ppcor-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 pcor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 pcor.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 spcor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 spcor.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Index 9 ppcor-package Partial and Semi-partial (Part) correlation Description The R package ppcor can calculate parital and semi-partial (part) correlations along with p value. Details 1 2 ppcor-package Package: ppcor Type: Package Version: 1.0 Date: 2011-06-14 License: GPL-2 Author(s) Seongho Kim <biostatistician.kim(a)gmail.com> References Kim, S.H. and Yi, S. (2007) Understanding relationship between sequence and functional evolution in yeast proteins . Genetica, 131: 151. Kim, S.H. and Yi, S. (2006) Correlated asymmetry between sequence and functional divergence of duplicate proteins in Saccharomyces cerevisiae . Molecular Biology and Evolution, 23: 1068. Johnson, Richard A. and Dean W. Wichern (2002) Applied multivariate statistical analysis. Prentice Hall. Whittaker, Joe (1990) Graphical models in applied multivariate statistics. John Wiley & Sons. Examples # data y.data <- data.frame( hl=c(7,15,19,15,21,22,57,15,20,18), disp=c(0.000,0.964,0.000,0.000,0.921,0.000,0.000,1.006,0.000,1.011), deg=c(9,2,3,4,1,3,1,3,6,1), BC=c(1.78e-02,1.05e-06,1.37e-05,7.18e-03,0.00e+00,0.00e+00,0.00e+00,4.48e-03,2.10e-06,0.00e+00) ) # partial correlation pcor(y.data) # partial correlation between "hl" and "disp" given "deg" and "BC" pcor.test(y.data$hl,y.data$disp,y.data[,c("deg","BC")]) pcor.test(y.data[,1],y.data[,2],y.data[,c(3:4)]) pcor.test(y.data[,1],y.data[,2],y.data[,-c(1:2)]) # semi-partial (part) correlation spcor(y.data) # semi-partial (part) correlation between "hl" and "disp" given "deg" and "BC" spcor.test(y.data$hl,y.data$disp,y.data[,c("deg","BC")]) spcor.test(y.data[,1],y.data[,2],y.data[,c(3:4)]) spcor.test(y.data[,1],y.data[,2],y.data[,-c(1:2)]) pcor 3 pcor Partial correlation Description The function pcor can calculate the pairwise partial correlations for each pair of variables given others. In addition, it gives us the p value as well as statistic for each pair of variables. Usage pcor(x, method = c("pearson", "kendall", "spearman")) Arguments x a matrix or data fram. method a character string indicating which partial correlation coefficient is to be computed. One of "pearson" (default), "kendall", or "spearman" can be abbreviated. Details Partial correlation is the correlation of two variables while controlling for a third or more other variables. Value estimate a matrix of the partial correlation coefficient between two variables p.value a matrix of the p value of the test statistic a matrix of the value of the test statistic n the number of samples gn the number of given variables method the correlation method used Note Missing values are not allowed. Author(s) Seongho Kim <<biostatistician.kim(a)gmail.com>> References Kim, S.H. and Yi, S. (2007) Understanding relationship between sequence and functional evolution in yeast proteins . Genetica, 131: 151. Kim, S.H. and Yi, S. (2006) Correlated asymmetry between sequence and functional divergence of duplicate proteins in Saccharomyces cerevisiae . Molecular Biology and Evolution, 23: 1068. Johnson, Richard A. and Dean W. Wichern (2002) Applied multivariate statistical analysis. Prentice Hall. Whittaker, Joe (1990) Graphical models in applied multivariate statistics. John Wiley & Sons. 4 pcor.test See Also pcor.test, spcor, spcor.test Examples # data y.data <- data.frame( hl=c(7,15,19,15,21,22,57,15,20,18), disp=c(0.000,0.964,0.000,0.000,0.921,0.000,0.000,1.006,0.000,1.011), deg=c(9,2,3,4,1,3,1,3,6,1), BC=c(1.78e-02,1.05e-06,1.37e-05,7.18e-03,0.00e+00,0.00e+00,0.00e+00,4.48e-03,2.10e-06,0.00e+00) ) # partial correlation pcor(y.data) pcor.test Partial correlation for two variables given a third variable. Description The function pcor.test can calculate the pairwise partial correlations between two variables. In addition, it gives us the p value as well as statistic. Usage pcor.test(x, y, z, method = c("pearson", "kendall", "spearman")) Arguments x a numeric vector. y a numeric vector. z a numeric vector. method a character string indicating which partial correlation coefficient is to be computed. One of "pearson" (default), "kendall", or "spearman" can be abbreviated. Details Partial correlation is the correlation of two variables while controlling for a third variable. Value estimate the partial correlation coefficient between two variables p.value the p value of the test statistic the value of the test statistic n the number of samples gn the number of given variables method the correlation method used spcor 5 Note Missing values are not allowed Author(s) Seongho Kim <<biostatistician.kim(a)gmail.com>> References Kim, S.H. and Yi, S. (2007) Understanding relationship between sequence and functional evolution in yeast proteins . Genetica, 131: 151. Kim, S.H. and Yi, S. (2006) Correlated asymmetry between sequence and functional divergence of duplicate proteins in Saccharomyces cerevisiae . Molecular Biology and Evolution, 23: 1068. Johnson, Richard A. and Dean W. Wichern (2002) Applied multivariate statistical analysis. Prentice Hall. Whittaker, Joe (1990) Graphical models in applied multivariate statistics. John Wiley & Sons. See Also pcor, spcor, spcor.test Examples # data y.data <- data.frame( hl=c(7,15,19,15,21,22,57,15,20,18), disp=c(0.000,0.964,0.000,0.000,0.921,0.000,0.000,1.006,0.000,1.011), deg=c(9,2,3,4,1,3,1,3,6,1), BC=c(1.78e-02,1.05e-06,1.37e-05,7.18e-03,0.00e+00,0.00e+00,0.00e+00,4.48e-03,2.10e-06,0.00e+00) ) # partial correlation between "hl" and "disp" given "deg" and "BC" pcor.test(y.data$hl,y.data$disp,y.data[,c("deg","BC")]) pcor.test(y.data[,1],y.data[,2],y.data[,c(3:4)]) pcor.test(y.data[,1],y.data[,2],y.data[,-c(1:2)]) spcor Semi-partial (part) correlation Description The function spcor can calculate the pairwise semi-partial (part) correlations for each pair of variables given others. In addition, it gives us the p value as well as statistic for each pair of variables. Usage spcor(x, method = c("pearson", "kendall", "spearman")) 6 spcor Arguments x a matrix or data fram. method a character string indicating which semi-partial (part) correlation coefficient is to be computed. One of "pearson" (default), "kendall", or "spearman" can be abbreviated. Details Semi-partial correlation is the correlation of two variables with variation from a third or more other variables removed only from the second variable. Value estimate a matrix of the semi-partial (part) correlation coefficient between two variables p.value a matrix of the p value of the test statistic a matrix of the value of the test statistic n the number of samples gn the number of given variables method the correlation method used Note Missing values are not allowed. Author(s) Seongho Kim <<biostatistician.kim(a)gmail.com>> References Kim, S.H. and Yi, S. (2007) Understanding relationship between sequence and functional evolution in yeast proteins . Genetica, 131: 151. Kim, S.H. and Yi, S. (2006) Correlated asymmetry between sequence and functional divergence of duplicate proteins in Saccharomyces cerevisiae . Molecular Biology and Evolution, 23: 1068. Johnson, Richard A. and Dean W. Wichern (2002) Applied multivariate statistical analysis. Prentice Hall. Whittaker, Joe (1990) Graphical models in applied multivariate statistics. John Wiley & Sons. See Also spcor.test, pcor, pcor.test Examples # data y.data <- data.frame( hl=c(7,15,19,15,21,22,57,15,20,18), disp=c(0.000,0.964,0.000,0.000,0.921,0.000,0.000,1.006,0.000,1.011), deg=c(9,2,3,4,1,3,1,3,6,1), spcor.test 7 BC=c(1.78e-02,1.05e-06,1.37e-05,7.18e-03,0.00e+00,0.00e+00,0.00e+00,4.48e-03,2.10e-06,0.00e+00) ) # semi-partial (part) correlation spcor(y.data) spcor.test Semi-partial (part) correlation for two variables given a third variable. Description The function spcor.test can calculate the pairwise semi-partial (part) correlations between two variables. In addition, it gives us the p value as well as statistic. Usage spcor.test(x, y, z, method = c("pearson", "kendall", "spearman")) Arguments x a numeric vector. y a numeric vector. z a numeric vector. method a character string indicating which partial correlation coefficient is to be computed. One of "pearson" (default), "kendall", or "spearman" can be abbreviated. Details Semi-partial correlation is the correlation of two variables with variation from a third variable removed only from the second variable. Value estimate the semi-partial (part) correlation coefficient between two variables p.value the p value of the test statistic the value of the test statistic n the number of samples gn the number of given variables method the correlation method used Note Missing values are not allowed 8 spcor.test Author(s) Seongho Kim <<biostatistician.kim(a)gmail.com>> References Kim, S.H. and Yi, S. (2007) Understanding relationship between sequence and functional evolution in yeast proteins . Genetica, 131: 151. Kim, S.H. and Yi, S. (2006) Correlated asymmetry between sequence and functional divergence of duplicate proteins in Saccharomyces cerevisiae . Molecular Biology and Evolution, 23: 1068. Johnson, Richard A. and Dean W. Wichern (2002) Applied multivariate statistical analysis. Prentice Hall. Whittaker, Joe (1990) Graphical models in applied multivariate statistics. John Wiley & Sons. See Also spcor, pcor, pcor.test Examples # data y.data <- data.frame( hl=c(7,15,19,15,21,22,57,15,20,18), disp=c(0.000,0.964,0.000,0.000,0.921,0.000,0.000,1.006,0.000,1.011), deg=c(9,2,3,4,1,3,1,3,6,1), BC=c(1.78e-02,1.05e-06,1.37e-05,7.18e-03,0.00e+00,0.00e+00,0.00e+00,4.48e-03,2.10e-06,0.00e+00) ) # semi-partial (part) correlation between "hl" and "disp" given "deg" and "BC" spcor.test(y.data$hl,y.data$disp,y.data[,c("deg","BC")]) spcor.test(y.data[,1],y.data[,2],y.data[,c(3:4)]) spcor.test(y.data[,1],y.data[,2],y.data[,-c(1:2)]) Index _Topic htest pcor, 3 pcor.test, 4 ppcor-package, 1 spcor, 5 spcor.test, 7 pcor, 3, 5, 6, 8 pcor.test, 4, 4, 6, 8 ppcor (ppcor-package), 1 ppcor-package, 1 spcor, 4, 5, 5, 8 spcor.test, 4–6, 7 u9no meu caso qero trabalhar com matrizes de celação obrigada Ana Rocha

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[off topic] Adobe!
by FHRB Toledo 19 Nov '12

19 Nov '12

Senhores, Esse é um thread totalmente OFF TOPIC, peço a compreensão de vocês quanto a isso! Um colega da lista brasileira do DEBIAN ( debian-user-portuguese(a)lists.debian.org) encabeça essa iniciativa. Acho extremamente válida, quem for da mesma opinião, por favor assine. Leiam o email abaixo! att, FH ---------- Forwarded message ---------- From: Juliano Cesar <cetapsao883(a)yahoo.com.br> Date: 2012/11/18 Subject: Assinem a petição para a Adobe sempre fazer a versão mais recente do Adobe Reader para Linux. To: "debian-user-portuguese(a)lists.debian.org" < debian-user-portuguese(a)lists.debian.org> Vamos divulgar e assinar http://www.change.org/pt-BR/peti%C3%A7%C3%B5es/adobe-systems-incorporated-w… Se alguém tiver uma ideia de uma melhor descrição em inglês e portarmos a descrição em vários idiomas, pode ser que isso dê certo. A meta é de 2 milhões de assinaturas, sabemos que existem alternativas de leitores de PDF, mas nenhum se compara ao Adobe Reader, é uma pena que a Adobe parou de atualizar a sua versão para Linux.

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Re: [R-br] Cluster para r
by Diogo Ferrari 18 Nov '12

18 Nov '12

Fabio, vc usou esses pacotes que o Benilton mencionou? abs 2012/11/18 Fabio Mathias Corrêa <fabio.ufla(a)yahoo.com.br> > Eu já li arquivos .txt de 50Gb em meu laptop com 4 Gb de RAM e processador > dual core. > > Faça um teste. > > Valeu! > > Fábio Mathias Corrêa > > Universidade Estadual de Santa Cruz > Departamento de Ciências Exatas e da Terra - DCET > > > Campus Soane Nazaré de Andrade, km 16 Rodovia Ilhéus-Itabuna > CEP 45662-900. Ilhéus-Bahia > > > Tel.: 73-3680-5076 > ------------------------------ > *De:* Diogo Ferrari <diogoferrari(a)gmail.com> > *Para:* r-br(a)listas.c3sl.ufpr.br; Fabio Mathias Corrêa < > fabio.ufla(a)yahoo.com.br> > *Enviadas:* Domingo, 18 de Novembro de 2012 13:20 > > *Assunto:* Re: [R-br] Cluster para r > > Legal, não conhecia esse pacote. Mas no caso de bancos de 20 GB, a memória > não basta.... > > > 2012/11/18 Fabio Mathias Corrêa <fabio.ufla(a)yahoo.com.br> > > O pacote bigmemory permite trabalhar com grandes bancos de dados sem > sobrecarregar a memória. > > > > Fábio Mathias Corrêa > > Universidade Estadual de Santa Cruz > Departamento de Ciências Exatas e da Terra - DCET > > > Campus Soane Nazaré de Andrade, km 16 Rodovia Ilhéus-Itabuna > CEP 45662-900. Ilhéus-Bahia > > > Tel.: 73-3680-5076 > ------------------------------ > *De:* Diogo Ferrari <diogoferrari(a)gmail.com> > *Para:* r-br(a)listas.c3sl.ufpr.br; regis barros <regisgbarros(a)yahoo.com.br> > > *Enviadas:* Domingo, 18 de Novembro de 2012 12:07 > *Assunto:* Re: [R-br] Cluster para r > > Ola Regis, > > Já trabalhei, ou melhor, tentei trabalhar, com R operando em servidor > linux. O principal problema é a divisão do processamento. Não é possível > dividir o processamento entre os nós. é possível apenas dividir dentro do > próprio núcleo do processador. Eu trabalhei com bases na casa de 20x10^9. A > melhor solução que encontrei foi o RevolutionR, fazer proc. paralelo local > e converter os arquivos para .xdf (usado pelo revolution). Se o seu > problema é computar sobre os dados, e não fazer simulações por exemplo, vc > tem que encontrar uma solução que permita isso. É mais um problema de > geranciamento e acesso aos dados do que capaciadade de processamento. O R > tradicional carrega tudo na memória e, portanto, limita o uso de big data. > O .xdf e o RevolutionR solucionam isso permitindo trabalhar com os dados > sem carregá-los, além de dividir e indexar o banco, como se faz em SQL, por > exemplo. Mas isso vai depender do que vc precisa fazer com os dados. As > funções disponível para o RevolutionR são as mais simples.estão no pacote > RevoscaleR. > > abs > > > 2012/11/18 regis barros <regisgbarros(a)yahoo.com.br> > > Bom dia Pessoal > Gostaria de saber de pessoas que trabalham com cluster para linux e usam o > r para executar os cálculos e modelos que venho trabalhando. Li nos e-mails > anteriores que pessoas que estavam usando uma base de dados de 1*10^9, > todavia gostaria de trabalhar com mais do que isto alguém trabalha? > Grato > Regis Godoy Barros > > _______________________________________________ > R-br mailing list > R-br(a)listas.c3sl.ufpr.br > https://listas.inf.ufpr.br/cgi-bin/mailman/listinfo/r-br > Leia o guia de postagem (http://www.leg.ufpr.br/r-br-guia) e forneça > código mínimo reproduzível. > > > > > -- > Diogo Ferrari > University of San Paulo (USP) > Faculty of Philosophy, Languages, Literature and Human Sciences (FFLCH) > Department of Political Science (DCP) > San Paulo/SP - Brazil > E-mail: diogo.ferrari(a)usp.br > > Open Source! Use R! Use Linux! > > "A vida é a arte de tirar conclusões suficientes de dados insuficientes" > > > _______________________________________________ > R-br mailing list > R-br(a)listas.c3sl.ufpr.br > https://listas.inf.ufpr.br/cgi-bin/mailman/listinfo/r-br > Leia o guia de postagem (http://www.leg.ufpr.br/r-br-guia) e forneça > código mínimo reproduzível. > > > _______________________________________________ > R-br mailing list > R-br(a)listas.c3sl.ufpr.br > https://listas.inf.ufpr.br/cgi-bin/mailman/listinfo/r-br > Leia o guia de postagem (http://www.leg.ufpr.br/r-br-guia) e forneça > código mínimo reproduzível. > > > > > -- > Diogo Ferrari > University of San Paulo (USP) > Faculty of Philosophy, Languages, Literature and Human Sciences (FFLCH) > Department of Political Science (DCP) > San Paulo/SP - Brazil > E-mail: diogo.ferrari(a)usp.br > > Open Source! Use R! Use Linux! > > "A vida é a arte de tirar conclusões suficientes de dados insuficientes" > > > > -- Diogo Ferrari University of San Paulo (USP) Faculty of Philosophy, Languages, Literature and Human Sciences (FFLCH) Department of Political Science (DCP) San Paulo/SP - Brazil E-mail: diogo.ferrari(a)usp.br Open Source! Use R! Use Linux! "A vida é a arte de tirar conclusões suficientes de dados insuficientes"

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Duvidas de amostras.
by edmar Caldas 18 Nov '12

18 Nov '12

Pessoal, uma ajuda. 1) Tenho 10.000 observações. DP = 10 Média = 70 Distribuição normal. 2) Imagina dividir essas 10.000 observações em 1.000 (Mil) amostras de 10 (dez) observações. DP = 3 Média = 70 3) Agora dividimos essa mesma 10.000 observações em 100 amostras de 100 observações. DP = 1 Média = 70. Portanto: No item 2 cada amostra tem sua própria média, sabendo que são observações diferentes. Essa diferença da média da amostra de uma para a outra é chamada de variação amostral correto? Se eu fizer uma distribuição com todas as médias das mil amostras eu tenho uma distribuição amostral? Se a média das médias dessas 1000 amostras for igual a média da população do item 1. Podemos dizer que qualquer amostra do item 2 representa a população? Está certo essa minha conclusão? Só para ter certeza, Toda vez que aumentar minha amostra meu DP diminui? Porquê?

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Re: [R-br] AKAIKE
by Helio Gallo Rocha 18 Nov '12

18 Nov '12

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Dados com tendência em geoestatística
by Fernando Zuchello 18 Nov '12

18 Nov '12

Olá a todos, estou trabalhando com distribuição espacial de dados de solo, principalmente dados físicos e da emissão de gases como (CH4 e N2O). Quando trabalho com variogramas grande parte destes valores apresentam tendencia! porém quando uso os argumentos trend só consigo usar funções para retirar a tendencia de 1 ordem e 2 ordem, como faço para utilizar outra função neste argumento? Utilizando o pacote geoR. Obj.geo.vt<-variog(Obj.geo,coords=Obj.geo$coords,log(data=Obj.geo$data[,1]),uvec=seq(,100,by=5),trend="1st"); Outra dúvida é como faço o jackknifing do modelo ajustado, uma vez que o utilizo como critério para seleção do melhor ajuste? agradeço! -- Fernando Zuchello Engenheiro Agrônomo (UFRRJ) Mestre em Agronomia - Ciência do Solo (UFRRJ) Doutorando em agronomia - Ciência do Solo (UFRRJ)

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Re: [R-br] AKAIKE
by Helio Gallo Rocha 18 Nov '12

18 Nov '12

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AKAIKE
by Helio Gallo Rocha 17 Nov '12

17 Nov '12

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