Re: [R] na.action in stats::factanal()

2012-02-07 Thread Timothy Bates
Thanks for the clear explanation Terry! It gets ugly for many factanal applications, where you are dealing with 300 variables… One question: what would be wrong with auto generating the formula from a matrix call? That way the matrix call gets the benefit of returning scores. Also: you say a

[R] na.action in stats::factanal() must be using formula interface and dataframe input to specify na.action?

2012-02-06 Thread Timothy Bates
hi, Does factanal() force the user to use the formula interface if they wish to specify an na.action? v1 <- c(1,1,1,1,1,1,1,1,NA,1,3,3,3,3,3,4,5,6) v2 <- c(1,2,1,1,1,1,2,1,2,1,3,NA,3,3,3,4,6,5) v3 <- c(3,3,3,3,3,1,1,1,1,1,1,1,1,1,1,5,4,6) v4 <- c(3,3,4,NA,3,1,1,2,1,1,1,1,2,NA,1,5,6,4) v5 <- c(1,1

Re: [R] help in fitted values in lm function

2011-11-14 Thread Timothy Bates
This caught me learning R, and no doubt thousands of others. When would one ever want the results of fitted() or residuals() to NOT match the data frame rows which went into the model? Certainly making shrinking the results the default is not what 99% of user will want if they need to access

Re: [R] Have write.csv write csv without observation number

2011-11-11 Thread Timothy Bates
If you find yourself asking "is there a way..?", put that question mark in front of the function you are wondering about and push return ?write.csv In this case, you will see that the write function has a parameter to say whether to write out row names ornot, which defaults to TRUE... row.nam

Re: [R] merging two dataframes

2011-10-26 Thread Timothy Bates
So when I do the merge on your example frames, I get the expected result. But the example component dataframes you sent are already full of NAs, and there are no rows which are present in both data sets. So I think perhaps, that merge is just highlighting a problem that has its roots in your com

Re: [R] merging two dataframes

2011-10-26 Thread Timothy Bates
I think you want something like this (I like to be explicit about what you are merging) df3 = merge(df1, df2, by = "date", all=T) You can be explicit about what you are merging on in each file: df3 = merge(df1,df2, by.x = "date”, by.y="date", all=T) You were trying to merge on “date1” but it l

Re: [R] constrain min and max of output

2011-10-25 Thread Timothy Bates
this works x=1; y=-100; z = min(5, max(1, x+y)); z On 25 Oct 2011, at 1:46 PM, Jim Maas wrote: > Hello, > > Is there a simple way/function to constrain the minimum and maximum value of > an output from an assignment? > > if I have > > z <- x +y > > but I want z to always be between 1 and 5

Re: [R] Length of string?

2011-10-24 Thread Timothy Bates
Dear Kevin, # this works nchar("read the help for length”) [1] 24 On 24 Oct 2011, at 4:14 PM, Kevin Burton wrote: > This is very basic but I have not been able to find an answer. Basically I > want to find the length of a string. > > length("Text") > > returns 1 so I know that is not right. >

Re: [R] Creating the mean using algebra matrix

2011-10-12 Thread Timothy Bates
On Oct 12, 2011, at 12:04 AM, Rolf Turner wrote: > On 12/10/11 08:31, Timothy Bates wrote: >> To do matrix multiplication: m x n, the Rows and columns of m must be equal >> to the columns and rows of n, respectively. > No. The number of columns of m must equal the number of r

Re: [R] Creating the mean using algebra matrix

2011-10-11 Thread Timothy Bates
To do matrix multiplication: m x n, the Rows and columns of m must be equal to the columns and rows of n, respectively. Sent from my iPhone On 11 Oct 2011, at 06:45 PM, flokke wrote: > Dear all, > I wanted to create the mean using a algebra matrix. > so I tried this one: > >> meanAnimal

Re: [R] get("a[1]") : object 'a[1]' not found

2011-10-11 Thread Timothy Bates
so… cleared out, and now it’s working: Must have been an obscure workspace conflict. Thanks for quick helpful replies a <- 1:4 assign("a[1]", 2) > a[1] == 2 [1] FALSE > get("a[1]") == 2 [1] TRUE On 11 Oct 2011, at 5:45 PM, Duncan Murdoch wrote: > On 11/10/20

[R] get("a[1]") : object 'a[1]' not found

2011-10-11 Thread Timothy Bates
In the help for get(), the following example is given: a <- 1:4 assign("a[1]", 2) a[1] == 2 #FALSE get("a[1]") == 2 #TRUE However, executing that last line for me gives Error in get("a[1]") : object 'a[1]' not found __ R-help@r-project.org

Re: [R] Plotting Lines Through multiple groups

2011-09-28 Thread Timothy Bates
if it was me, i'd do library("ggplot2") df <- read.table(pipe("pbpaste"), header=T, sep='\t') df$Animus=factor(df$Animal, labels=c("Tom", "Dick", "Harry")) qplot(Day, Cort, data = df, geom="line", colour=Animus) On Sep 28, 2011, at 8:03 AM, clara_eco wrote: > Hi I have data in the following forma

Re: [R] help in interpreting paired t-test

2011-09-20 Thread Timothy Bates
Yes, in over 3/4s of the data points A is > B… which suggests the A measure is reading higher than the B measuring system. length(A[A>B])/length(A) On 20 Sep 2011, at 6:46 PM, Pedro Mardones wrote: > Dear all; > > A very basic question. I have the following data: > >

Re: [R] Referring to an object by a variable containing its name: 6 failures

2011-09-16 Thread Timothy Bates
On 16 Sep 2011, at 1:49 AM, andrewH wrote: >> I'm trying to make a function that takes column names then >> using the variable colName, containing the name of >> the column, to refer to the column itself rmail...@justemail.net said > What am I missing about your inquiry: It seems like x[ , colNam

Re: [R] x %>% y as an alternative to which( x > y)

2011-09-14 Thread Timothy Bates
>> %<% would extend the vocabulary established by %in%, and work in the same >> situations. >> e.g. >> # only set “flynnEffect" for people known to be under 12, not for people >> where age is NA >> twinData[twinData$Age %<% 12, "flynnEffect"] = FALSE >> Addressing Duncan's point about returni

Re: [R] x %>% y as an alternative to which( x > y)

2011-09-13 Thread Timothy Bates
Dear Duncan and Hadley, I stumbled across the NA behavior of subset a little while ago and thought it might do the trick. But my common usage case is not getting a subsetting sans NAs, but setting values in the whole dataframe. So I need T/F at each row, not just the list of rows that match th

[R] x %>% y as an alternative to which( x > y)

2011-09-13 Thread Timothy Bates
Dear R cognoscenti, While having NA as a native type is nifty, it is annoying when making binary choices. Question: Is there anything bad about writing comparison functions that behavior like %in% (which I love) and ignore NAs? "%>%" <- function(table, x) { return(which(table > x)) }

Re: [R] Comparing skewness of two distributions

2011-08-28 Thread Timothy Bates
> On Fri, Aug 26, 2011 at 10:20 AM, Benjamin Polidore > wrote: >> I have two distributions. Is there a statistical approach to determine >> if the skew of distribution 1 is similar to the skew of distribution 2? On Aug 26, 2011, at 10:07 PM, Joshua Wiley wrote: > par(mfrow = c(2, 1)) > plot(de

Re: [R] More efficient option to append()?

2011-08-18 Thread Timothy Bates
This takes a few seconds to do 1 million lines, and remains explicit/for loop form numberofSalaryBands = 100 # 200 x= sample(1:15,numberofSalaryBands, replace=T) y= sample((1:10)*1000, numberofSalaryBands, replace=T) df = data.frame(x,y) finalN = sum(df$x) myVar

Re: [R] How do I subset a dataframe

2011-08-14 Thread Timothy Bates
Perhaps this: matches = grep("^ibm|sears|exxon", zeespan$customer, value=F) zee = zeespan[matches,] t On Aug 14, 2011, at 12:44 AM, eric wrote: > I have a dataframe zeespan. One of the columns has the name "customer". The > data in the customer column is text. I would like to return a subset of

Re: [R] Adjacency Matrix help

2011-08-13 Thread Timothy Bates
diag(adjMatrix) <-0 On Aug 13, 2011, at 7:34 AM, collegegurl69 wrote: > I have created an adjacency matrix but have not been able to figure something > out. I need to put zeros on the diagonal of the adjacency matrix. For > instance, location (i,i) to equal 0. Please help. Thanks _

Re: [R] significance of differences in skew and kurtosis between two groups

2011-08-07 Thread Timothy Bates
7:24 PM, peter dalgaard wrote: > > On Aug 7, 2011, at 20:05 , David Winsemius wrote: > >> >> On Aug 6, 2011, at 1:19 PM, Timothy Bates wrote: >> >>> Dear R-users, >>> I am comparing differences in variance, skew, and kurtosis between two >>>

[R] significance of differences in skew and kurtosis between two groups

2011-08-06 Thread Timothy Bates
Dear R-users, I am comparing differences in variance, skew, and kurtosis between two groups. For variance the comparison is easy: just var.test(group1, group2) I am using agostino.test() for skew, and anscombe.test() for kurtosis. However, I can't find an equivalent of the F.test or Mood.test

Re: [R] Plotting just a portion of a smoother graph in ggplot2

2011-08-04 Thread Timothy Bates
It's not immediately obvious You need to look at coord_cartesian() and its ylim argument. Best, t Sent from my iPhone On 4 Aug 2011, at 02:38 PM, Christopher Desjardins wrote: > Hi, > I am using ggplot2 to with the following code: > > gmathk2 <- > qplot(time,math,colour=Kids,data=kids.ach.

[R] equivalent of var.test(x,y) for skew and kurtosis

2011-08-03 Thread Timothy Bates
Dear R-users, I am comparing differences in variance, skew, and kurtosis between two groups. For variance the comparison is easy: just var.test(group1, group2) I am using agostino.test() for skew, and anscombe.test() for kurtosis. However, I can't find an equivalent of the F.test or Mood.tes

Re: [R] ideas about how to reduce RAM & improve speed in trying to use lapply(strsplit())

2011-05-29 Thread Timothy Bates
Hi Matt, Though it's the last solution on your list, I would treat this as a text editing problem: just find and replace "\.[0-9]", then read in the result. perl -pi -e 's/x\.[0-9]//g' *test.txt likely done in seconds. But other R solutions seem to be coming in in a fairly timely manner too. t

Re: [R] dataframe - column value calculation in R

2011-05-26 Thread Timothy Bates
On 26 May 2011, at 08:02, Vijayan Padmanabhan wrote: > I have a requirement for which I am seeking help. Best to just ask, compactly. This is a very straightforward question: best to read on how to use R: You are just set 1 column of a dataframe to a value based on the others, applying this to

Re: [R] R as.numeric()

2011-05-24 Thread Timothy Bates
On 24 May 2011, at 10:20 PM, Lutz Fischer wrote: > n<-data.matrix(s); > > s[1,2] > [1] 30.94346629 # 3136 Levels: 0.026307482 > turned into: > > n[1,2] > [1] 3020 Dear Lutz, “3020” is the factor level associated with 30.94346629, in turn generated by importing with strings in the column Try pas

Re: [R] Remove duplicate elements in lists via recursive indexing

2011-05-23 Thread Timothy Bates
Dear Janko, I think requires a for loop. The approach I took here was mark the dups, then dump them all in one hit: testData = expand.grid(letters[1:4],c(1:3)) testData$keep=F uniqueIDS = unique(testData$Var1) for(thisID in uniqueIDS) { firstCaseOnly = match(thisID,testData$Var1)

Re: [R] Downloading a csv from Dropbox using the shareable link

2011-05-21 Thread Timothy Bates
> Person A is working on the file on their computer the path to the data would > be (Mac OSX) /Users/PersonA/Dropbox/Project/data.csv However, to Person B > the path would be /Users/PersonB/Dropbox/data.csv I'm looking for a way to > keep the path to data.csv universal and independent of who i

Re: [R] Downloading a csv from Dropbox using the shareable link

2011-05-20 Thread Timothy Bates
The problem is that dropbox sharable links unpack to https URIs, and R doesn't support secture http (at least not on Mac, not sure about other platforms). Would be great to compile the read.table etc. functions to use curl when it is installed, as curl supports a myriad of protocols. Rcurl pac

Re: [R] How to do covariate adjustment in R

2011-05-20 Thread Timothy Bates
Dear Karena, x = 1:100 y = rnorm(100) fit = lm(x~y) # what properties does a fit have? names(fit) # [1] "coefficients" "residuals" "effects" "rank" "fitted.values" "assign""qr" # [8] "df.residual" "xlevels" "call" "terms" "model"

[R] within()

2011-05-19 Thread Timothy Bates
The most interesting thing in this thread for me was "within()" - that is what I want 99% of the time, but I had only ever heard of with() A real boon! Thanks Bill V! The help for within gives this example for with(), which seems unnecessary, as glm supports data= with(anorexia, { anorex.1

Re: [R] R Style Guide -- Was Post-hoc tests in MASS using glm.nb

2011-05-18 Thread Timothy Bates
lol:-) is there a way to get a fortune on start up in R? On 19 May 2011, at 00:33, Rolf Turner wrote: > > On 19/05/11 10:26, bill.venab...@csiro.au wrote: > > >> Most of [the Google style guide's] advice is very good (meaning I agree with >> it!) but some is a bit too much (for example, the b

Re: [R] Integral Symbol

2011-05-18 Thread Timothy Bates
Can’t you just embed it in the html as a symbol? ∫ or ∫ I’d have thought you also just put it into straight into the document as a character – ∫– , as long as the html is stored as unicode U+222B http://en.wikipedia.org/wiki/Integral_symbol On 18 May 2011, at 4:04 PM, Javi Hidalgo wrote: >

Re: [R] Date_Time detected as Duplicated (but they are not!)

2011-05-18 Thread Timothy Bates
Dear Augustin: What are the duplicated times? Looks they really do occur twice or more in your original data: perhaps two stamps less time apart than the resolution of your clock? delme[duplicated(delme)] aur2009[[duplicated(delme),1] On 18 May 2011, at 8:49 AM, Agustin Lobo wrote: > and is it

Re: [R] Box Plot under GUI (R Commander/RKward)

2011-05-17 Thread Timothy Bates
something like this will get you going, assuming your data are in a dataframe called “qual” # qual <- read.table(pipe("pbpaste"), header=T, sep='\t') boxplot(formula=Time~Distance+Season, data=qual) Followup question from me: i can’t see why boxplot(formula=Time, data=qual) should return the

Re: [R] Post-hoc tests in MASS using glm.nb

2011-05-17 Thread Timothy Bates
Dear Bryony: the suggestion was not to change the name of the data object, but to explicitly tell glm.nb what dataset it should look in to find the variables you mention in the formula. so the salient difference is: m1 <- glm.nb(Cells ~ Cryogel*Day, data = side) instead of attach(side) m1 <-