[R] ANOVA with replicate measures
Hi, I have the following dataset (shown only part of it): WFPSsampling dayslurry depth replicates N2O (mg/m2/h) 1 1 1 3 1 0.007 1 1 1 3 2 0.022 1 1 1 3 3 0.015 1 1 2 3 1 0.033 1 1 2 3 2 0.010 1 1 2 3 3 0.022 1 1 2 6 1 0.038 1 1 2 6 2 0.048 1 1 2 6 3 0.043 1 1 3 0 1 0.024 1 2 1 3 1 0.017 1 2 1 3 2 0.016 1 2 1 3 3 0.015 1 2 2 3 1 0.047 1 2 2 3 2 0.083 1 2 2 3 3 0.042 1 2 2 6 1 0.036 1 2 2 6 2 0.048 1 2 2 6 3 0.030 1 2 3 0 1 0.020 1 3 1 3 1 0.006 1 3 1 3 2 0.007 1 3 1 3 3 0.019 1 3 2 3 1 0.055 1 3 2 3 2 0.004 1 3 2 3 3 0.025 1 3 2 6 1 0.030 1 3 2 6 2 0.024 1 3 2 6 3 0.042 1 3 3 0 1 0.017 What it is: daily N2O emission rate after the injection of 2 different types of slurry into the soil moistened at 2 different levels. So I want to test all the factors on the N2O emissions: 1) injection depth 2) slurry type 3) water content into the soil (=WFPS) Bu I want to take into account the replicates. How can I write the R syntax in this case? Something like: model2-aov(N2O.mg.m2.h. ~ WFPS*sampling_day*slurry*depth + Error(replicates/(WFPS + sampling_day + slurry + depth))) Thanks in advance, Joao [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] permutation test assumption?
Dear all, Can I do a permutation test if the number of individuals in one group is much bigger than in the other group? I searched the literature but I didin´t find any assumption that refers to this subject for permutation tests. Best regards João Fadista Ph.d. student UNIVERSITY OF AARHUS Faculty of Agricultural Sciences Dept. of Genetics and Biotechnology Blichers Allé 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 1900 E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Web: www.agrsci.org http://www.agrsci.org/ DJF now offers new degree programmes http://www.agrsci.org/content/view/full/34133 . News and news media http://www.agrsci.org/navigation/nyheder_og_presse . This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] permutation test assumption?
Dear Thierry, Thanks for the reply. But as you may read in the paper http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/18/2244 when the sample sizes are not the same there may be an increase in the Type I error rate. Comments will be appreciated. Best regards, João Fadista De: ONKELINX, Thierry [mailto:[EMAIL PROTECTED] Enviada: ter 08-04-2008 15:27 Para: João Fadista; r-help@r-project.org Assunto: RE: [R] permutation test assumption? Dear João, You can do permutation tests on an unbalanced design. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens João Fadista Verzonden: dinsdag 8 april 2008 15:18 Aan: r-help@r-project.org Onderwerp: [R] permutation test assumption? Dear all, Can I do a permutation test if the number of individuals in one group is much bigger than in the other group? I searched the literature but I didin´t find any assumption that refers to this subject for permutation tests. Best regards João Fadista Ph.d. student UNIVERSITY OF AARHUS Faculty of Agricultural Sciences Dept. of Genetics and Biotechnology Blichers Allé 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 1900 E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Web: www.agrsci.org http://www.agrsci.org/ DJF now offers new degree programmes http://www.agrsci.org/content/view/full/34133 . News and news media http://www.agrsci.org/navigation/nyheder_og_presse . This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] permutation test assumption?
But in that paper they refer to another (http://www.bepress.com/cgi/viewcontent.cgi?article=1053context=ucbbiostat) where they say that permutation distribution produces an asymptotically correct null distribution if (i) the sample sizes are equal Best regards, João De: Achim Zeileis [mailto:[EMAIL PROTECTED] Enviada: qua 09-04-2008 0:26 Para: João Fadista Cc: ONKELINX, Thierry; r-help@r-project.org Assunto: Re: [R] permutation test assumption? On Wed, 9 Apr 2008, João Fadista wrote: Dear Thierry, Thanks for the reply. But as you may read in the paper http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/18/2244 when the sample sizes are not the same there may be an increase in the Type I error rate. No, this is false and not what the reference above says. Please read more carefully. Comments will be appreciated. The basic assumption for permutation tests is exchangeability of the observations (regardless of sample sizes). The reference above describes a situation when this assumption is violated. Z Best regards, João Fadista De: ONKELINX, Thierry [mailto:[EMAIL PROTECTED] Enviada: ter 08-04-2008 15:27 Para: João Fadista; r-help@r-project.org Assunto: RE: [R] permutation test assumption? Dear João, You can do permutation tests on an unbalanced design. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens João Fadista Verzonden: dinsdag 8 april 2008 15:18 Aan: r-help@r-project.org Onderwerp: [R] permutation test assumption? Dear all, Can I do a permutation test if the number of individuals in one group is much bigger than in the other group? I searched the literature but I didin´t find any assumption that refers to this subject for permutation tests. Best regards João Fadista Ph.d. student UNIVERSITY OF AARHUS Faculty of Agricultural Sciences Dept. of Genetics and Biotechnology Blichers Allé 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 1900 E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Web: www.agrsci.org http://www.agrsci.org/ DJF now offers new degree programmes http://www.agrsci.org/content/view/full/34133 . News and news media http://www.agrsci.org/navigation/nyheder_og_presse . This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] wilcox.test test statistic
Dear all, When we perform a Wilcoxon rank sum test (on two samples with different sizes) we get a test statistic. My question is, as the value of test statistic increases the difference between the distributions of the two samples also increase, right? Thanks in advance, João Fadista [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] chisq.test in batch
Dear all, I would like to compute hundreds of chisq.test ´s, and for each test output I would like to extract only the p-values. So my question is: how can I make this without making it manually? Example: # Test nº1 chisq.test(c(220,240)) Chi-squared test for given probabilities data: c(220, 240) X-squared = 0.8696, df = 1, p-value = 0.3511 # Test nº2 chisq.test(c(301,258)) Chi-squared test for given probabilities data: c(301, 258) X-squared = 3.3077, df = 1, p-value = 0.06896 ... # Test nº200 chisq.test(c(242,281)) Chi-squared test for given probabilities data: c(242, 281) X-squared = 2.9082, df = 1, p-value = 0.08813 Desired output: Test 1 2 ... 200 p-value 0.3511 0.06896 ... 0.08813 Thanks in advance. Best regards, João Fadista __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] subsetting a data.frame
Dear all, I would like to be able to subset a data.frame in a special way. I will put here an example: Score Name 88 19_0070 88 19_0070 87 19_0070 79 002127_0658 79 002127_0658 77 002127_0658 So, for the above example I would like to have a new data.frame that has only the best Score for each Name: Score Name 88 19_0070 88 19_0070 79 002127_0658 79 002127_0658 Thanks in advance. Best regards, João Fadista [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] read only certain parts of a file
Dear all, I would like to know how can I read a text file and create a data frame of only certain parts of the file. For instance, from this text file: === Matches For Query 0 (108 bases): 19_0070 === Score Q_Name S_Name Q_Start Q_End S_Start S_End Direction Bases identity 89 19_0070 Chr15 3 108 43251883 43251778 C 106 95.28 88 19_0070 Chr1 4 108 85826948 85826844 C 105 95.24 === Matches For Query 1 (124 bases): 24_1262 === Score Q_Name S_Name Q_Start Q_End S_Start S_End Direction Bases identity 99 24_1262 Chr6 16 124 35738256 35738364 F 109 100.00 I would like to have a data frame that has only: Score Q_Name S_Name Q_Start Q_End S_Start S_End Direction Bases identity 89 19_0070 Chr15 3 108 43251883 43251778 C 106 95.28 88 19_0070 Chr1 4 108 85826948 85826844 C 105 95.24 99 24_1262 Chr6 16 124 35738256 35738364 F 109 100.00 Best regards, João Fadista [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Barnard's exact test
Dear all, I would like to know if there is any R package that has the Barnard´s exact test. I also like to have any opinions about which test is more powerful: Fisher´s exact test or Barnard´s exact test. Best regards João Fadista Ph.d. student UNIVERSITY OF AARHUS Faculty of Agricultural Sciences Dept. of Genetics and Biotechnology Blichers Allé 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 1900 E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Web: www.agrsci.org http://www.agrsci.org/ News and news media http://www.agrsci.org/navigation/nyheder_og_presse . This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
