[R] Q2/R2 ratio in PLSDA

Hello, I would like to perform a Partial least square discriminate analysis (PLSDA) in R. To do this I use the package mixOmics. I could perform the PLSDA in R. however I would also like to perform a leave-one-out cross validation in order to assess the performance of my model. My supervisor

[R] Data arrangement for PLSDA using the ropls package

Hello, I would like to do a partial least square discriminant analysis (PLSDA) in R using the package "ropls" Which is in R available via the R command : source("https://bioconductor.org/biocLite.R";) I try to do a PLSDA to illustrate the impact of two genders (AP,C) on 5 compounds measured in

[R] Data arrangement for PLSDA using the ropls package

Hello, I would like to do a partial least square discriminant analysis (PLSDA) in R using the package "ropls" Which is in R available via the R command : source("https://bioconductor.org/biocLite.R";) When I try to do a PLSDA using my own data. The impact of two genders (AP,C) on 5 compounds mea

Re: [R] non-parametric manova with post-hoc test

Dear Brian, Thank you for your answer. Another thing that came to my mind: Would it be possible just to separately rank-transform my 3 dependent variables and then to conduct a normal MANOVA on this data? Thanks, Mike Eisenring Michael, Msc. PhD Student Federal Department of Economic Affairs,

[R] non-parametric manova with post-hoc test

Good day, I am looking for a way to perform a non parametric manova and to analyze the result using post-hoc tests (an equivalent of the kruskal wallis test for anova) In my book (discovering statistic using R) two tests are described Munzel and Brunners method (mulrank) and Choi and Mardens tes

[R] Change sum of squares type for ANOVA

Dear R-list members, I compared my statistics with my supervisor yesterday. He is using STATISTICA, I am using R. We both loaded the same data-file and did a two-way ANOVA with treatment and trial as factors; treatment means were then compared to the untreated control using Dunnett's test. Surp

[R] "Group" argument of kruskal function (agricolae package) does not coincide with p-values

Hello, I work with the kruskla function of the agricolae package to conduct Kurskal-Wallis tests. The kurskal function has the argument "group"=T/F. If group=T, the output of the kruskal test assigns a "significance letter" to each mean of each tested treatment (means with the same letter are not

Re: [R] How to conduct a PERMANOVA using a dissimilarity matrix

Dear Erica and Hazel, Thank you very much for your help. Based on Ericas feedback I use now a the raw data giving me information on abundance of bat species (I changed the data set) that were caught at 6 different sites (file named bats) Thanks to Hazels input I use now an additional file (named

[R] How to conduct a PERMANOVA using a dissimilarity matrix

Dear R-List members, I have to compare how similar two types of forest (old growth=O) and (young forest=Y) in terms of moth communities are. I sampled moths at 4 O and 4 Y sites. I need to analyse the data using a PERMANOVA approach. But I am having a really hard time to do this in R. I found o

[R] Black outlines for errorbar using geom_line

Hi there, I would like to create black outlines around my errorbars in order to get especially the white errorbar better visible. Is that even possible with ggplot2 and if yes how? I would be very grateful if anyone could help me. I added my code and a dput() of my data, Thank you very much, Mi

[R] modifications using “stat_summary” in ggplot

Dear R-list members I am using �stat_summary� in ggplot to plot a error bar graph comparing three treatmens (damage, see code below). I would like to change the shape of the three symbols displaying the mean values (e.g one symbol should be a point (default) one should be a triangle and one sho

[R] Order Bars in ggplot2 bar graph

Dear experts, I am trying to make a bar graph using ggplot2. I would like to define the order of my bars independently of alphabetical or numerical order. How can I do that. Here a simplified example of my code and comments(#) describing my problem: #Code start library(ggplot2) bar<-ggplot(da

[R] WG: horizontal bar plots for CI visualization

2.50% 97.50% intercept 29787966 glands 13143611 damage 169 6144 treatment L1778 6703 treatment L4-3899 5125 Length -1817 1828 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.

[R] horizontal bar plots for CI visualization

2.50% 97.50% intercept 29787966 glands 13143611 damage 169 6144 treatment L1778 6703 treatment L4-3899 5125 Length -1817 1828 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.