[R] extracting the t-statistic: just the numbers, please

2004-07-29 Thread Michael Rennie 

Hi, there

I am quite sure there is an easy answer to this, but I am unsure how to gather 
a bunch of t-statistics in an organized format.

I am trying to generate a list of t-statistics for a randomization routine. If 
I try to collect a bunch of t-statistics from a run, this is what happens:


 M - 10 ; simt - NULL
 for(i in 1:M)
+ {
+perm-sample(site,replace=F)
+ 
+ permute-cbind(perm, site, a, b, c)
+ 
+ m- order(perm)
+ 
+ m1-cbind(perm[m], site[m], a[m], b[m], c[m])
+ 
+ black-c((m1[1:5,5]),(m1[11:15,5]))
+ #black
+ 
+ white-c((m1[6:10,5]),(m1[16:20,5]))
+ #white
+ 
+ sims - t.test(black,white,var.equal=FALSE,mu=0)$statistic
+ simt-c(simt,sims)
+ #simt
+ } # Next i (next simulation)
 
 simt
 t  t  t  t  t  t  t 
 0.3474150  0.1542973 -0.4044992  1.243 -0.2933944 -0.5809257  0.7799080 
 t  t  t 
-1.4132713  1.2048335 -0.6596936

Which gives me a list, but not in a form that I can do anything with. This is 
in stark contrast to what happens when requesting p-values, which gives output 
like this:



 M - 10 ; simt - NULL
 for(i in 1:M)
+ {
+perm-sample(site,replace=F)
+ 
+ permute-cbind(perm, site, a, b, c)
+ 
+ m- order(perm)
+ 
+ m1-cbind(perm[m], site[m], a[m], b[m], c[m])
+ 
+ black-c((m1[1:5,5]),(m1[11:15,5]))
+ #black
+ 
+ white-c((m1[6:10,29]),(m1[16:20,5]))
+ #white
+ 
+ sims - t.test(black,white,var.equal=FALSE,mu=0)$p.value
+ simt-c(simt,sims)
+ #simt
+ } # Next i (next simulation)
 
 simt
 [1] 0.6763749 0.7480091 0.9447851 0.3342029 0.7852635 0.3199006 0.5272153
 [8] 0.3863616 0.7333693 0.7268907

Now THAT'S what I'd like to get for my t-statistics- a nice vector (simt) that 
I can deal with later, rather than the output I am currently getting (the first 
output above).

Does anyone know a way to extract JUST the t-statistics from the t.test, 
without the t character header, so I can generate a nice little vector? 
Alternatively, can I manipulate the output I am currently getting for the t-
statistics so that I can isolate just the numbers? 

-- 
Michael Rennie
Ph.D. Candidate
University of Toronto at Mississauga
3359 Mississauga Rd. N.
Mississauga ON  L5L 1C6
Ph: 905-828-5452  Fax: 905-828-3792

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Re: [R] extracting the t-statistic: just the numbers, please

2004-07-29 Thread Christian Schulz 
   data(sleep)
  t.test(extra ~ group, data = sleep)$statistic[1]
t
-1.860813
  t.test(extra ~ group, data = sleep)$statistic[[1]]
[1] -1.860813

hope this helps,
christian


Am Donnerstag, 29. Juli 2004 07:57 schrieb Michael Rennie:
 Hi, there

 I am quite sure there is an easy answer to this, but I am unsure how to
 gather a bunch of t-statistics in an organized format.

 I am trying to generate a list of t-statistics for a randomization routine.
 If

 I try to collect a bunch of t-statistics from a run, this is what happens:
  M - 10 ; simt - NULL
  for(i in 1:M)

 + {
 +perm-sample(site,replace=F)
 +
 + permute-cbind(perm, site, a, b, c)
 +
 + m- order(perm)
 +
 + m1-cbind(perm[m], site[m], a[m], b[m], c[m])
 +
 + black-c((m1[1:5,5]),(m1[11:15,5]))
 + #black
 +
 + white-c((m1[6:10,5]),(m1[16:20,5]))
 + #white
 +
 + sims - t.test(black,white,var.equal=FALSE,mu=0)$statistic
 + simt-c(simt,sims)
 + #simt
 + } # Next i (next simulation)

  simt

  t  t  t  t  t  t 
 t 0.3474150  0.1542973 -0.4044992  1.243 -0.2933944 -0.5809257 
 0.7799080 t  t  t
 -1.4132713  1.2048335 -0.6596936

 Which gives me a list, but not in a form that I can do anything with. This
 is in stark contrast to what happens when requesting p-values, which gives
 output like this:



  M - 10 ; simt - NULL

  for(i in 1:M)

 + {
 +perm-sample(site,replace=F)
 +
 + permute-cbind(perm, site, a, b, c)
 +
 + m- order(perm)
 +
 + m1-cbind(perm[m], site[m], a[m], b[m], c[m])
 +
 + black-c((m1[1:5,5]),(m1[11:15,5]))
 + #black
 +
 + white-c((m1[6:10,29]),(m1[16:20,5]))
 + #white
 +
 + sims - t.test(black,white,var.equal=FALSE,mu=0)$p.value
 + simt-c(simt,sims)
 + #simt
 + } # Next i (next simulation)

  simt

  [1] 0.6763749 0.7480091 0.9447851 0.3342029 0.7852635 0.3199006 0.5272153
  [8] 0.3863616 0.7333693 0.7268907

 Now THAT'S what I'd like to get for my t-statistics- a nice vector (simt)
 that I can deal with later, rather than the output I am currently getting
 (the first output above).

 Does anyone know a way to extract JUST the t-statistics from the t.test,
 without the t character header, so I can generate a nice little vector?
 Alternatively, can I manipulate the output I am currently getting for the
 t- statistics so that I can isolate just the numbers?

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Re: [R] extracting the t-statistic: just the numbers, please

2004-07-29 Thread Spencer Graves 
 The function as.vector will remove the names: 

 t.test(1:9)$statistic
  t
5.477226
 as.vector(t.test(1:9)$statistic)
[1] 5.477226
 Is this what you want?  spencer graves
Michael Rennie wrote:
Hi, there
I am quite sure there is an easy answer to this, but I am unsure how to gather 
a bunch of t-statistics in an organized format.

I am trying to generate a list of t-statistics for a randomization routine. If 
I try to collect a bunch of t-statistics from a run, this is what happens:

 

M - 10 ; simt - NULL
for(i in 1:M)
   

+ {
+perm-sample(site,replace=F)
+ 
+ permute-cbind(perm, site, a, b, c)
+ 
+ m- order(perm)
+ 
+ m1-cbind(perm[m], site[m], a[m], b[m], c[m])
+ 
+ black-c((m1[1:5,5]),(m1[11:15,5]))
+ #black
+ 
+ white-c((m1[6:10,5]),(m1[16:20,5]))
+ #white
+ 
+ sims - t.test(black,white,var.equal=FALSE,mu=0)$statistic
+ simt-c(simt,sims)
+ #simt
+ } # Next i (next simulation)
 

simt
   

t  t  t  t  t  t  t 
0.3474150  0.1542973 -0.4044992  1.243 -0.2933944 -0.5809257  0.7799080 
t  t  t 
-1.4132713  1.2048335 -0.6596936

Which gives me a list, but not in a form that I can do anything with. This is 
in stark contrast to what happens when requesting p-values, which gives output 
like this:


M - 10 ; simt - NULL
 

for(i in 1:M)
   

+ {
+perm-sample(site,replace=F)
+ 
+ permute-cbind(perm, site, a, b, c)
+ 
+ m- order(perm)
+ 
+ m1-cbind(perm[m], site[m], a[m], b[m], c[m])
+ 
+ black-c((m1[1:5,5]),(m1[11:15,5]))
+ #black
+ 
+ white-c((m1[6:10,29]),(m1[16:20,5]))
+ #white
+ 
+ sims - t.test(black,white,var.equal=FALSE,mu=0)$p.value
+ simt-c(simt,sims)
+ #simt
+ } # Next i (next simulation)
 

simt
   

[1] 0.6763749 0.7480091 0.9447851 0.3342029 0.7852635 0.3199006 0.5272153
[8] 0.3863616 0.7333693 0.7268907
Now THAT'S what I'd like to get for my t-statistics- a nice vector (simt) that 
I can deal with later, rather than the output I am currently getting (the first 
output above).

Does anyone know a way to extract JUST the t-statistics from the t.test, 
without the t character header, so I can generate a nice little vector? 
Alternatively, can I manipulate the output I am currently getting for the t-
statistics so that I can isolate just the numbers? 

 

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Re: [R] extracting the t-statistic: just the numbers, please

2004-07-29 Thread Peter Dalgaard 
Michael Rennie [EMAIL PROTECTED] writes:

  simt
  t  t  t  t  t  t  t 
  0.3474150  0.1542973 -0.4044992  1.243 -0.2933944 -0.5809257  0.7799080 
  t  t  t 
 -1.4132713  1.2048335 -0.6596936
 
 Which gives me a list, but not in a form that I can do anything with. This is 
 in stark contrast to what happens when requesting p-values, which gives output 
 like this:

..

  simt
  [1] 0.6763749 0.7480091 0.9447851 0.3342029 0.7852635 0.3199006 0.5272153
  [8] 0.3863616 0.7333693 0.7268907
 
 Now THAT'S what I'd like to get for my t-statistics- a nice vector (simt) that 
 I can deal with later, rather than the output I am currently getting (the first 
 output above).
 
 Does anyone know a way to extract JUST the t-statistics from the t.test, 
 without the t character header, so I can generate a nice little vector? 
 Alternatively, can I manipulate the output I am currently getting for the t-
 statistics so that I can isolate just the numbers? 

It *is* a nice little vector! It's just that it has names. 

names(simt) - NULL 

gets rid of them. 

BTW, simt - c(simt, sims) is going to kill performance with large repeat
counts since it copies all previous results every time around.
Preallocate the result, or consider using replicate() or sapply().

-- 
   O__   Peter Dalgaard Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics 2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark  Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907

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