similar to: Question about correlation

Displaying 20 results from an estimated 334 matches similar to: "Question about correlation"

2017 Jul 05
Question about correlation
Hi Chin Yi, If you are trying to correlate "Health" with "Disease", i.e. cydf<-read.table(text="OTU ID Health Disease Bacterial 1 0.29 0.34 Bacterial 2 0.25 0.07 Bacterial 3 0.06 0.06 Bacterial 4 0.07 0.09 Bacterial 5 0.02 0.05", header=TRUE) print(cor(cydf$Health,cydf$Disease)) [1] 0.7103517 If you are getting that error, it probably means that
2017 Jul 05
Question about correlation
On 2017-07-05 11:56, Jim Lemon wrote: > Hi Chin Yi, > If you are trying to correlate "Health" with "Disease", i.e. > > cydf<-read.table(text="OTU ID Health Disease > Bacterial 1 0.29 0.34 > Bacterial 2 0.25 0.07 > Bacterial 3 0.06 0.06 > Bacterial 4 0.07 0.09 > Bacterial 5 0.02 0.05", > header=TRUE) >
2017 Jul 14
Conduct Network Analysis
Greeting. Dear Mr/Mrs/Miss, I want to create a network by using R but I only have a table that contain OTU ID and the abundance value of two samples ONLY. Isn't possible? If can, which package can be used? Greatly appreciated to any suggestions and helps. Thank you. Best regards, Kang Chin Yi [[alternative HTML version deleted]]
2017 Jul 06
Question about correlation
Please keep the conversation on the list: Others may be able to help you better than I can. On 2017-07-06 10:38, SEB140004 Student wrote: > Ya. I had successfully got the result. Thank you very much. :) > > Isn't possible for me to obtain the network from the correlation matrix? I know nothing about correlation networks, but by googling I found two R packages, ggraph and corrr,
2017 Jul 05
Question about correlation
I think that Goran is right, I didn't take "cor(data)" literally. Jim On Thu, Jul 6, 2017 at 3:38 AM, G?ran Brostr?m <goran.brostrom at> wrote: > On 2017-07-05 11:56, Jim Lemon wrote: >> >> Hi Chin Yi, >> If you are trying to correlate "Health" with "Disease", i.e. >> >> cydf<-read.table(text="OTU ID Health
2013 Apr 30
vegan -varpart is bigger than 100% in total?
I am trying to find the percentage of the parameters explaining the bacterial community composition. I have one data matrix with relative abundance of OTUs and one with environmental parameters. I used varpart in vegan package but the values in the venn diagram is bigger than 100% in total.How is it possible? What might be the reason? Thank you library(vegan) gotud <-
2013 Apr 03
Ask help
Hello! I am eager to learn if I only have a data about the relationship between otu and sample, could I use the function capscale, and final make a point plot that x-axis is CAP1 and y-axis is CAP2? Besides, what function could I use to make the different rarefaction curve with different color in the a plot in R? Appreciate very much.
2005 Sep 27
Locomotive 0.2.4 for Mac OS X 10.3+
I am pleased to announce the newest release of Locomotive! Mostly a bug fix release. If you are using Locomotive on 10.4 you should definitely upgrade. New in 0.2.4 ============ * Rename application entries in status window * Run/Restart/Stop buttons now immediately update * Bundle choosing is fixed for Mac OS X 10.4 * Missing gem dependencies
2013 Feb 05
plot significant spearman correlation
Hello, I calculate the correlation between two matrices cor(x,y, method="spearman") and I am wondering if it possible to see only the significant correlations. I can do that for single OTUs with cor.test() command but I would like to have an output for whole matrix. Besides,I would like to plot the relative abundance of each OTU, against the number of significant pair-wise correlations
2005 Dec 30
Locomotive 1.0.0 for Mac OS 10.3+
Hi All, I''m very happy to announce the release of Locomotive 1.0.0. Locomotive is a one-click development solution for Rails on Mac OS X. See more details at Get it at: What''s New? =========== * Server bundle updated to lighttpd 1.4.8 *
2011 Sep 09
NMDS plot and Adonis (PerMANOVA) of community composition with presence absence and relative intensity
Hi! Thanks for providing great help in R-related statistics. Now, however I''m stuck. I''m not a statistics person but I was recommended to use R to perform a nmds plot and PerMANOVA of my dataset. Sample(treatment) in the columns and species (OTU) in the rows. I have 4 treatments (Ambient Temperature, Ambient temperature+Low pH, High temperature, High temperature+low pH), and I
2014 Sep 04
gplot heatmaps: clustering according to rowsidecolors + key.xtickfun
Hi there, I have two questions about heatmap.2 in gplot. My input is a simple square matrix with numeric values between 75 and 100 (it is a similarity matrix based on bacterial DNA sequences). 1. I can sort my input matrix into categories with rowsidecolors (in this case, very conveniently by bacterial taxa). I do a clustering and reordering of my matrix by Rowv=TRUE (and
2006 Jan 02
How can one use GRUFF with locomotive ( I guess there is a wider question here, also)
Hi: I love Locomotive and use it exclusively for my rails projects. I''d like to install GRUFF and give it a try (a graph image creation package). I know I can do sudo gem install gruff from the command line for normal ruby and rails. How do I make gems available to Locomotive? bruce
2011 Feb 18
Confidence Intervals on Standard Curve
Hi, I wonder if anyone could advise me with this: I''ve been trying to make a standard curve in R with lm() of some standards from a spectrophotometer, so as I can express the curve as a formula, and so obtain values from my treated samples by plugging in readings into the formula, instead of trying to judge things by eye, with a curve drawn by hand. It is a curve and so I used the
2012 Feb 10
a) t-tests on loess splines; b) linear models, type II SS for unbalanced ANOVA
Dear all, I have some questions regarding the validity an implementation of statistical tests based on linear models and loess. I''ve searched the R-help arhives and found several informative threads that related to my questions, but there are still a few issues I''m not clear about. I''d be grateful for guidance. Background and data set: I wish to compare the growth
2005 Dec 31
What does this error mean when using scaffold?
Last login: Fri Dec 30 15:34:43 on ttyp1 source /private/var/tmp/folders.501/TemporaryItems/Locomotive. 1135999534.992790-16807 Welcome to Darwin! frank-roccos-powerbook58:~ farocco$ source /private/var/tmp/folders. 501/TemporaryItems/Locomotive.1135999534.992790-16807 frank-roccos-powerbook58:~/Documents/receipts farocco$ script/
2005 Oct 10
Under-dispersion - a stats question?
Hello all: I frequently have glm models in which the residual variance is much lower than the residual degrees of freedom (e.g. Res.Dev=30.5, Res.DF = 82). Is it appropriate for me to use a quasipoisson error distribution and test it with an F distribution? It seems to me that I could stand to gain a much-reduced standard error if I let the procedure estimate my dispersion factor (which
2005 Dec 15
Locomotive for Mac OS X 10.3+. Now with Rails 1.0
Hi All, The base Locomotive download now comes with Rails 1.0. If you already have a current version of Locomotive (0.4.1), all you need is a new bundle. Rails 1.0 Min: Rails 1.0 Max:
2013 Jun 22
Re: R-help Digest, Vol 124, Issue 22
"Vallejo, Roger" <Roger.Vallejo@ARS.USDA.GOV> asked: > I would like to know if we can estimate Rg between two binary traits > (disease status: alive vs. dead) with the R package. > > My data: we have 100 full-sib (FS) families, > and two random samples (each with n= 200 FS fish) from each FS family > were evaluated for disease resistance to two different
2006 Feb 09
Setting up Ruby + RubyOnRails on the new intel mac (any feedback?)
Hi I''m about to attempt to setup RoR on an iMac powered by an Intel core duo. Before I start, is there anyone who would have some feedback about a similar setup (and likely, the caveats hidden down there) ? thanks! Thibaut -------------- next part -------------- An HTML attachment was scrubbed... URL: