Re: [R] more boa plots questions

2011-03-03 Thread emj83
Can anyone help?
Thanks in advance Emma

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Re: [R] boa library and plots

2011-03-01 Thread emj83
Many thanks for your response, and I am sorry I did not post correctly.

I have found dev.copy2eps() useful.

Emma

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[R] more boa plots questions

2011-03-01 Thread emj83
I have MCMC output chains A and B for example, I want to produce trace plots
for them using the boa command line...

#loads boa
boa.init()
#reads in chains
boa.chain.add(boa.importMatrix('A'), 'A')
boa.chain.add(boa.importMatrix('B'), 'B')
#plot trace plot
problems arise here!

I know I can get trace plots using boa.plot('trace') but this plots the
parameter chains on the same plot- I want separate plots using
boa.plot.trace()

#from the manual..
boa.plot.trace(lnames, pname, annotate = boa.par(legend))
lnames: Character vector giving the name of the desired MCMC sequence
   in the working session list of sequences.
pname: Character string giving the name of the parameters to be
  plotted.
annotate: Logical value indicating that a legend be included in the
  plot.

I tried boa.plot.trace(B) and boa.plot.trace(B,B) but both do not give me
a trace plot for chain B and print FALSE. I am obviously misinterpreting
lnames and pnames.

Can anyone help please?
Thanks in advance Emma





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[R] boa library and plots

2011-02-24 Thread emj83

Hi,

I would like to save the plots produced by boa into postscript files in R.

I am struggling- can anyone advise?

Thanks Emma
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[R] intervals command

2011-02-22 Thread emj83

Hi,

I am fitting a random effects model and I am interested in the 95%
confidence interval of the variance components.

When I use the intervals() command it gives me the 95% confidence interval
of the standard deviation. Is there anyway of getting the 95% confidence
interval of the variance?

Thanks Emma
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[R] Changing a logical matrix into a numeric matrix

2011-01-10 Thread emj83

Hi,

I would like to turn my TRUE/FALSE matrix into a 1/0 matrix (i.e. True=1 and
False=0)

  [,1]  [,2]  [,3]  
[1,]  TRUE FALSE FALSE 
[2,]  TRUE  TRUE FALSE 
[3,]  TRUE  TRUE  TRUE 

  [,1]  [,2]  [,3]  
[1,]10 0
[2,]11 0
[3,]11 1

Is there a quick way of doing this without a loop?

Thanks Emma
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Re: [R] Changing a logical matrix into a numeric matrix

2011-01-10 Thread emj83

Thanks for everyone's suggestionsI didn't realise it was so
straightforward- thanks for teaching me new tricks!

Emma
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[R] Summing over specific columns in a matrix

2011-01-07 Thread emj83

Hi,

I would like to sum some specific columns in my matrix- for example, my
matrix looks like this:
 [,1]  [,2]  [,3] [,4]  [,5]
[1,]1   NA   NA   NA   NA
[2,]21   NA1   NA
[3,]321 21
[4,]432 32
[5,]   NA   NA   NA43
[6,]   NA   NA   NA5   NA

I would like to find the sum of the first two columns, the second two
columns and the last column:
i.e I am left with a vector of c(16, 18, 6).

I know about colSums and sum overall- I just wondered if this type of
grouping can be included somehow in a vector such as c(2,2,1)? I don't
really want to have to use a loop for this.

Many thanks Emma
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[R] How to join matrices of different row length from a list

2011-01-06 Thread emj83

Hi,

I have several matrix in a list, for example:
e
[[1]]
 [,1] [,2]
[1,]13
[2,]24

[[2]]
 [,1] [,2]
[1,]14
[2,]25
[3,]36

[[3]]
 [,1] [,2]
[1,]21

I would like to join them by column i.e.
 [,1] [,2]   [,3] [,4][,5] [,6]
[1,]13   1421
[2,]24   25   NA  NA
[3,]   NA  NA  36   NA   NA

I have tried  do.call(cbind,e) but I get this error message as the rows are
of different length-
Error in function (..., deparse.level = 1)  :
  number of rows of matrices must match (see arg 2)

Can anyone advise me please?

Thanks Emma


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Re: [R] How to join matrices of different row length from a list

2011-01-06 Thread emj83

Excellent- that is just what I need. Thank you so much for your prompt help,

Emma
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[R] Matrix Manipulation

2010-11-04 Thread emj83

Hi,

Is there a quick way to go from this matrix:
 A
 [,1] [,2] [,3]
[1,]111
[2,]222
[3,]333
[4,]444
[5,]5   NA5
[6,]   NA   NA6
[7,]   NA   NA   NA

to this matrix:
 B
 [,1] [,2] [,3]
[1,]1   NA   NA
[2,]2   NA1
[3,]312
[4,]423
[5,]534
[6,]   NA45
[7,]   NA   NA6

without using a loop? 
For example using a vector which describes how many NA's are required from
the top of the matrix- so in this case it would be c(0,2,1).

Many thanks Emma


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Re: [R] Matrix Manipulation

2010-11-04 Thread emj83

Many thanks-its worked a treat :-)

Emma
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[R] Sample in R

2010-10-19 Thread emj83

Hi,

Please can someone tell me if using sample() in R is actually a quick way of
doing the Inverse Transform Sampling Method? 

Many thanks Emma
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Re: [R] Between-group variance from ANOVA

2009-08-25 Thread emj83

can anyone advise me please?


emj83 wrote:
 
 I have done some ANOVA tables for some data that I have, from this I can
 read the within-group variance. can anyone tell me how i may find out the
 between-group variance?
 
 Thanks Emma
 

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Re: [R] Between-group variance from ANOVA

2009-08-25 Thread emj83

I have done this in R and this is the following ANOVA table I get:

 summary(aov(response ~ group, data=TDat))
 Df  Sum Sq Mean Sq F valuePr(F)
group 1 11203.5 11203.5  2505.0  2.2e-16 ***
Residuals   198   885.5 4.5

The model is response(i,j)= group(i)+ error(i,j),

we assume that group~N(0,P^2) and error~N(0,sigma^2)

I know that sigma^2 is equal to 4.5, how do I find out P^2? 

In the problem that I am trying to apply this to, I have more than 2 groups.
I was hoping there would be a function that helps you do this that I don't
know about.


Thanks for your help Emma




Mark Difford wrote:
 
 Hi Emma,
 
 
 
 R gives you the tools to work this out.
 
 ## Example
 set.seed(7)
 TDat - data.frame(response = c(rnorm(100, 5, 2), rnorm(100, 20, 2)))
 TDat$group - gl(2, 100, labels=c(A,B))
 with(TDat, boxplot(split(response, group)))
 summary(aov(response ~ group, data=TDat))
 
 Regards, Mark.
 
 
 emj83 wrote:
 
 can anyone advise me please?
 
 
 emj83 wrote:
 
 I have done some ANOVA tables for some data that I have, from this I can
 read the within-group variance. can anyone tell me how i may find out
 the between-group variance?
 
 Thanks Emma
 
 
 
 
 

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[R] Between-group variance from ANOVA

2009-08-13 Thread emj83

I have done some ANOVA tables for some data that I have, from this I can read
the within-group variance. can anyone tell me how i may find out the
between-group variance?

Thanks Emma
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[R] numbers loop in R

2009-04-17 Thread emj83

I would like to create a matrix in R that looks similar to this:

 [,1] [,2] [,3] [,4]
[1,]  NaN  1  2  3
[2,]  NaN  1  2  4
[3,]  NaN   1  2  5
[4,]  NaN  2  3  4
[5,]  NaN  2  3  5
[6,]  NaN345

I have the loop below:

where A for example is 5

matrixx-function(A){
B=matrix(NaN,nrow=(A+1),ncol=4)
for(k in 1:(A+1)){
for(i in 1:(A-2)){
 for(j in (i+2):A){ 
 }  
}   
   }
B[k,]=c(NaN,i,(i+1),j)
print(B)
}

But it only prints the final line in:

 matrixx(5)
 [,1] [,2] [,3] [,4]
[1,]  NaN  NaN  NaN  NaN
[2,]  NaN  NaN  NaN  NaN
[3,]  NaN  NaN  NaN  NaN
[4,]  NaN  NaN  NaN  NaN
[5,]  NaN  NaN  NaN  NaN
[6,]  NaN345

Could anyone give me a hand? Would be much appreciated.

Thanks Emma

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[R] cbind

2009-04-14 Thread emj83

I have a list of numbers with NAs as below:

 A[,1]
  [1]  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
NA
 [19]  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
NA
 [37]  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
NA
 [55]  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
NA
 [73]  NA  NA  NA  62  78  98  73  57  63  56  88  77 151 165 129  78  83 
63
 [91]  72  68  61  89  95  74  53  77  90 106 114 113  84  59  60  77  46 
91
[109] 108 111  76  75  70  61  65  61  52  94  71  67  52  86  79  97  80
101
[127]  87  53  85  79  86 104 153 128 155 148  NA  NA  NA  NA  NA  NA  NA 
NA
[145]  NA  NA  NA  NA  NA  NA  NA

I would like to  bind a column to this list which begins at 0 when the first
number has occured, but provides negative numbers prior to this as below:

  [1,] -75  NA
  [2,] -74  NA
  [3,] -73  NA
  [4,] -72  NA
  [5,] -71  NA
  [6,] -70  NA
  [7,] -69  NA
  [8,] -68  NA
  [9,] -67  NA
 [10,] -66  NA
 [11,] -65  NA
 [12,] -64  NA
 [13,] -63  NA
 [14,] -62  NA
 [15,] -61  NA
 [16,] -60  NA
 [17,] -59  NA
 [18,] -58  NA
 [19,] -57  NA
 [20,] -56  NA
 [21,] -55  NA
 [22,] -54  NA
 [23,] -53  NA
 [24,] -52  NA
 [25,] -51  NA
 [26,] -50  NA
 [27,] -49  NA
 [28,] -48  NA
 [29,] -47  NA
 [30,] -46  NA
 [31,] -45  NA
 [32,] -44  NA
 [33,] -43  NA
 [34,] -42  NA
 [35,] -41  NA
 [36,] -40  NA
 [37,] -39  NA
 [38,] -38  NA
 [39,] -37  NA
 [40,] -36  NA
 [41,] -35  NA
 [42,] -34  NA
 [43,] -33  NA
 [44,] -32  NA
 [45,] -31  NA
 [46,] -30  NA
 [47,] -29  NA
 [48,] -28  NA
 [49,] -27  NA
 [50,] -26  NA
 [51,] -25  NA
 [52,] -24  NA
 [53,] -23  NA
 [54,] -22  NA
 [55,] -21  NA
 [56,] -20  NA
 [57,] -19  NA
 [58,] -18  NA
 [59,] -17  NA
 [60,] -16  NA
 [61,] -15  NA
 [62,] -14  NA
 [63,] -13  NA
 [64,] -12  NA
 [65,] -11  NA
 [66,] -10  NA
 [67,]  -9  NA
 [68,]  -8  NA
 [69,]  -7  NA
 [70,]  -6  NA
 [71,]  -5  NA
 [72,]  -4  NA
 [73,]  -3  NA
 [74,]  -2  NA
 [75,]  -1  NA
 [76,]   0  62
 [77,]   1  78
 [78,]   2  98
 [79,]   3  73
 [80,]   4  57
 [81,]   5  63
 [82,]   6  56
 [83,]   7  88
 [84,]   8  77
 [85,]   9 151
 [86,]  10 165
 [87,]  11 129
 [88,]  12  78
 [89,]  13  83
 [90,]  14  63
 [91,]  15  72
 [92,]  16  68
 [93,]  17  61
 [94,]  18  89
 [95,]  19  95
 [96,]  20  74
 [97,]  21  53
 [98,]  22  77
 [99,]  23  90
[100,]  24 106
[101,]  25 114
[102,]  26 113
[103,]  27  84
[104,]  28  59
[105,]  29  60
[106,]  30  77
[107,]  31  46
[108,]  32  91
[109,]  33 108
[110,]  34 111
[111,]  35  76
[112,]  36  75
[113,]  37  70
[114,]  38  61
[115,]  39  65
[116,]  40  61
[117,]  41  52
[118,]  42  94
[119,]  43  71
[120,]  44  67
[121,]  45  52
[122,]  46  86
[123,]  47  79
[124,]  48  97
[125,]  49  80
[126,]  50 101
[127,]  51  87
[128,]  52  53
[129,]  53  85
[130,]  54  79
[131,]  55  86
[132,]  56 104
[133,]  57 153
[134,]  58 128
[135,]  59 155
[136,]  60 148
[137,]  61  NA
[138,]  62  NA
[139,]  63  NA
[140,]  64  NA
[141,]  65  NA
[142,]  66  NA
[143,]  67  NA
[144,]  68  NA
[145,]  69  NA
[146,]  70  NA
[147,]  71  NA
[148,]  72  NA
[149,]  73  NA
[150,]  74  NA
[151,]  75  NA

could anyone help me to with a function that would be able to calculate the
sequence I require to bind to the initial sequence?

thanks emma
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[R] naming vectors/ matrices in R

2009-03-31 Thread emj83

I would like to create a series of vectors in a loop and name them with
letters.

I know the command letters gives me the 26 letters of the alphabet.

For example, I have a dataframe, called A, with 6 columns.

B-length(A)
C-letters(1:B)
[1] a b c d e f

I would like to extract the first letter a, and put the first column of
dataframe A in a vector called a

C-e[1] 
[1] a

but when I type

e[1]=A[,1]

Warning message:
In e[1] =A[, 1] :
  number of items to replace is not a multiple of replacement length

It thinks I am trying to replace the first element of e with the first
column of A.

is there any other way in which I can achieve this?

Thanks in advance



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[R] matching vectors

2009-03-17 Thread emj83

I have two numerical vectors; hun2 is a subset of hun1:

 hun1
  [1] 147 198 141 170 184 136 150 134 144 161 124 103 107 110 121  79 106 
51
 [19] 102 109  52  71  52  80  95  78  75  96 101 107 107  80  71  49  71 
64
 [37]  58  68  75  85  55  52  70  90  98  90 100  98  74  78  60  69 106
103
 [55] 106 124 111  97  66  83  54  58  74  76  73 101  68  50  45  69  69 
75
 [73]  80  55  79  58  61  72  90  91  99  58  63  57  72  36  58  44  63 
54
 [91]  39  41  48  65  86  73  74  69  66  59  52  68  91 100 151 112 119 
93
[109]  66  73  87  99  79 109  94  80  63  51  46  39  28  34  49  45  36 
32
[127]  36  39  52  63  59  47  57  52  46  39  54  53  80  43  48  37  42 
43
[145]  47  34  42  45  50  48  49  55  62  46  61  60  42  48  58  49  60

hun2
 [1] 151 112 119  93  66  73  87  99  79 109  94  80  63  51  46  39  28  34 
49
[20]  45  36  32  36  39  52  63  59  47  57  52  46  39  54  53  80  43  48 
37
[39]  42  43  47  34  42  45  50  48  49  55  62  46  61  60  42  48  58  49 
60

i want to cbind hun1 to hun2 at the position where they match.

i have attempted to start this by using pmatch() to identify where it is
they match- i get the following results. 

 pmatch(hun1,hun2,duplicates.ok=TRUE)
  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA  9 NA 14 NA 10 25 NA 25
12 NA
 [26] NA NA NA NA NA NA 12 NA 19 NA NA 55 NA NA NA 48 25 NA NA NA NA NA NA
NA NA
 [51] 52 NA NA NA NA NA NA NA  5 NA 33 55 NA NA  6 NA NA 45 20 NA NA NA 12
48  9
 [76] 55 51 NA NA NA  8 55 13 29 NA 21 55 NA 13 33 16 NA 37 NA NA  6 NA NA 
5 27
[101] 25 NA NA NA  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19
20 21
[126] 22 21 16 25 13 27 28 29 25 15 16 33 34 12 36 37 38 39 36 28 18 39 20
45 37
[151] 19 48 49 15 51 52 39 37 55 19 52

is there anyway that i can specify pmatch() to work if and only if it
identifies all of hun2: something like this???
  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA
 [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA
 [51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA
 [76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA
[101] NA NA NA NA NA NA NA NA NA  1  2  3  4  5  6  7  8  9 10 11 12 13 14
15 16
[126] 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
40 41
[151] 42 43 44 45 46 47 48 49 50 51 52 



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[R] pairs of numbers

2009-03-13 Thread emj83

Hi,

I have two lists of numbers which are both 1,2,3,4.
I would like to combine pairs so that I have:
1,2
1,3
1,4
2,3
2,4
3,4.

I know that expand.grid() can give me all combinations of pairs. 

Any suggestions would be much appreciated.

Emma
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Re: [R] pairs of numbers

2009-03-13 Thread emj83

I have solved my problem using:
 x-1:4
 x
[1] 1 2 3 4
 combn(x,2)
 [,1] [,2] [,3] [,4] [,5] [,6]
[1,]111223
[2,]234344

Thanks Emma


emj83 wrote:
 
 Hi,
 
 I have two lists of numbers which are both 1,2,3,4.
 I would like to combine pairs so that I have:
 1,2
 1,3
 1,4
 2,3
 2,4
 3,4.
 
 I know that expand.grid() can give me all combinations of pairs. 
 
 Any suggestions would be much appreciated.
 
 Emma
 

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[R] auto.arima in forecasting package

2009-02-18 Thread emj83

I am using auto.arima to find the best arima model but am a little confused
by the output. I want to choose the best model using the BIC criteria.
This is my code (straightforward where a is the data)
auto.arima(a,d=0,D=0,max.p=5,max.q=5,max.P=0,max.Q=0,max.order=5,start.p=0,start.q=0,start.P=0,start.Q=0,ic=c(aic),
stationary=FALSE,stepwise=FALSE,trace=TRUE)

Part of the results I get back are:
 ARIMA(1,0,1) with zero mean : 1e+20
 ARIMA(1,0,1) with non-zero mean : -92.117
 ARIMA(1,0,2) with zero mean : 1e+20
 ARIMA(1,0,2) with non-zero mean : -101.8145
 ARIMA(1,0,3) with zero mean : 1e+20
 ARIMA(1,0,3) with non-zero mean : -110.5995

I am unsure what the values are after the colon. I thought it was the BIC
but it is found that the best model for the data is ARIMA(1,0,3) with
non-zero-mean and BIC= -91.42.

Could anyone tell me what the values are after the colon? I have tried
looking at the help page to no avail.

Thanks in advance Emma

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[R] ARIMA models

2009-02-17 Thread emj83

is there some sort of R function which can advise me of the best ARIMA(p,q,r)
model to use based on the Schwarz criterion e.g for e.g p=0-5, q =0, r=0-5
or for example p+r 5???

or is this something I will have to write my own code for?

Thanks Emma
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[R] selecting parts of a table

2009-01-14 Thread emj83

I have a dataframe called Match with two columns: position and tvalue.

I would like to select the parts of the dataframe that have a position 10
but 50 and tvalues 3.5 as a new stand alone dataframe.

Could anyone help me with how to do this?

Thanks Emma
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[R] systematically matching the numbers in two sequences

2008-12-05 Thread emj83

I am having trouble writing a code for matching two pairs of sequences with
differing lengths:

for example sequence1= 1,2,3,4,5,6,7 sequence2=1,2,3,4,5,6,7,8,9,10

I want to create several new pairs of sequences in several dataframes such
that:
1st dataframe is 1,10 (start of sequence1, end of sequence 2)
2nd dataframe is 1, 9
 2, 10

3rd dataframe is 1, 8
2, 9
3, 10

etc etc.

I realise this may involve a complicated loop and am really struggling to
make a start on it.
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[R] systematically matching the numbers in two sequences

2008-12-05 Thread emj83

I am having trouble writing a code for matching two pairs of sequences with
differing lengths:

for example sequence1= 1,2,3,4,5,6,7 sequence2=1,2,3,4,5,6,7,8,9,10

I want to create several new pairs of sequences in several dataframes such
that:
1st dataframe is 1,10 (start of sequence1, end of sequence 2)
2nd dataframe is 1, 9
 2, 10

3rd dataframe is 1, 8
2, 9
3, 10

etc etc.

I realise this may involve a complicated loop and am really struggling to
make a start on it. 
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[R] Function output difficulties

2008-12-03 Thread emj83

is there anyway for some parts of the function output to not be returned,
even if the output has been used to calculate a further part of the
function? i have tried invisible() to no avail.

Thanks Emma
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