tapply and error bars

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tapply and error bars

Ogbos
Dear workers,
I have a data of length 1136. Below is the code I use to get the means B.
It worked fine and I had the mean calculated and plotted.

I wish to plot the error bars as well. I already plotted such means with
error bars before. Please see attached for example.

I tried to redo the same plot but unlikely could not get around it as I
lost my system containing the script.
Among many attempts, I tried:
library(gplots)

 plotmeans(errors~AB,xlab="Factor A",ylab="mean errors", p=.68, main="Main
  effect Plot",barcol="black")
Nothing worked.

I would really be thankful should somebody return me to the track.
Many, many thanks for your time.
Ogbos

A sample of the data is:
S/N      A        B
1    -5  64833
2    -4  95864
3    -3  82322
4    -2  95591
5    -1  69378
6     0  74281
7     1 103261
8     2  92473
9     3  84344
10    4 127415
11    5 123826
12    6 100029
13    7  76205
14    8 105162
15    9 119533
16   10 106490
17   -5  82322
18   -4  95591
19   -3  69378
20   -2  74281
21   -1 103261
22    0  92473
23    1  84344
24    2 127415
25    3 123826
26    4 100029
27    5  76205
28    6 105162
29    7 119533
30    8 106490
31    9 114771
32   10  55593
33   -5  85694
34   -4  65205
35   -3  80995
36   -2  51723
37   -1  62310
38    0  53401
39    1  65677
40    2  76094
41    3  64035
42    4  68290
43    5  73306
44    6  82176
45    7  75566
46    8  89762
47    9  88063
48   10  94395
49   -5  80651
50   -4  81291
51   -3  63702
52   -2  70297
53   -1  64117
54    0  71219
55    1  57354
56    2  62111
57    3  42252
58    4  35454
59    5  33469
60    6  38899
61    7  64981
62    8  85694
63    9  79452
64   10  85216
65   -5  71219
66   -4  57354
67   -3  62111
68   -2  42252
69   -1  35454
70    0  33469
71    1  38899
72    2  64981
73    3  85694
74    4  79452
75    5  85216
76    6  81721
77    7  91231
78    8 107074
79    9 108103
80   10  7576

A<-matrix(rep(-5:10,71))
B<-matrix(data)
 AB<-data.frame(A,B)

x= B

 f<-factor(A)
AB<- tapply(x,f,mean)
x<--5:10
plot(x,AB,type="l")

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Re: tapply and error bars

Jim Lemon-4
Hi Ogbos,
This may help:

# assume your data frame is named "oodf"
oomean<-as.vector(by(oodf$B,oodf$A,mean))
oose<-as.vector(by(oodf$B,oodf$A,std.error))
plot(-5:10,oomean,type="b",ylim=c(50000,110000),
 xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
dispersion(-5:10,oomean,oose)

Jim

On Sat, Jun 23, 2018 at 4:35 PM, Ogbos Okike <[hidden email]> wrote:

> Dear workers,
> I have a data of length 1136. Below is the code I use to get the means B.
> It worked fine and I had the mean calculated and plotted.
>
> I wish to plot the error bars as well. I already plotted such means with
> error bars before. Please see attached for example.
>
> I tried to redo the same plot but unlikely could not get around it as I
> lost my system containing the script.
> Among many attempts, I tried:
> library(gplots)
>
>  plotmeans(errors~AB,xlab="Factor A",ylab="mean errors", p=.68, main="Main
>   effect Plot",barcol="black")
> Nothing worked.
>
> I would really be thankful should somebody return me to the track.
> Many, many thanks for your time.
> Ogbos
>
> A sample of the data is:
> S/N      A        B
> 1    -5  64833
> 2    -4  95864
> 3    -3  82322
> 4    -2  95591
> 5    -1  69378
> 6     0  74281
> 7     1 103261
> 8     2  92473
> 9     3  84344
> 10    4 127415
> 11    5 123826
> 12    6 100029
> 13    7  76205
> 14    8 105162
> 15    9 119533
> 16   10 106490
> 17   -5  82322
> 18   -4  95591
> 19   -3  69378
> 20   -2  74281
> 21   -1 103261
> 22    0  92473
> 23    1  84344
> 24    2 127415
> 25    3 123826
> 26    4 100029
> 27    5  76205
> 28    6 105162
> 29    7 119533
> 30    8 106490
> 31    9 114771
> 32   10  55593
> 33   -5  85694
> 34   -4  65205
> 35   -3  80995
> 36   -2  51723
> 37   -1  62310
> 38    0  53401
> 39    1  65677
> 40    2  76094
> 41    3  64035
> 42    4  68290
> 43    5  73306
> 44    6  82176
> 45    7  75566
> 46    8  89762
> 47    9  88063
> 48   10  94395
> 49   -5  80651
> 50   -4  81291
> 51   -3  63702
> 52   -2  70297
> 53   -1  64117
> 54    0  71219
> 55    1  57354
> 56    2  62111
> 57    3  42252
> 58    4  35454
> 59    5  33469
> 60    6  38899
> 61    7  64981
> 62    8  85694
> 63    9  79452
> 64   10  85216
> 65   -5  71219
> 66   -4  57354
> 67   -3  62111
> 68   -2  42252
> 69   -1  35454
> 70    0  33469
> 71    1  38899
> 72    2  64981
> 73    3  85694
> 74    4  79452
> 75    5  85216
> 76    6  81721
> 77    7  91231
> 78    8 107074
> 79    9 108103
> 80   10  7576
>
> A<-matrix(rep(-5:10,71))
> B<-matrix(data)
>  AB<-data.frame(A,B)
>
> x= B
>
>  f<-factor(A)
> AB<- tapply(x,f,mean)
> x<--5:10
> plot(x,AB,type="l")
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: tapply and error bars

Jim Lemon-4
Hi Ogbos,
If I use the example data that you sent, I get the error after this line:

oose<-as.vector(by(oodf$B,oodf$A,std.error))
Error in FUN(X[[i]], ...) : object 'std.error' not found

The reason is that you have not defined std.error as a function, but
as the result of a calculation. When I rewrite it like this:

std.error<-function(x) return(sd(x)/(sum(!is.na(x))))
oose<-as.vector(by(oodf$B,oodf$A,std.error))
plot(-5:10,oomean,type="b",ylim=c(50000,110000),
 xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
dispersion(-5:10,oomean,oose)

I get the expected plot.

Jim


On Sat, Jun 23, 2018 at 9:36 PM, Ogbos Okike <[hidden email]> wrote:

> Hi Jim,
>
> Thanks for assisting. Here is what I did:
>
> A<-matrix(rep(-5:10,71))
> B<-matrix(data)
> std.error = sd(B)/sqrt(sum(!is.na(B)))
>  oodf<-data.frame(A,B)
>
>  oomean<-as.vector(by(oodf$B,oodf$A,mean))
> oose<-as.vector(by(oodf$B,oodf$A,std.error))
> plot(-5:10,oomean,type="b",ylim=c(50000,110000),
>  xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
> dispersion(-5:10,oomean,oose)
>
> And the error says:
> Error in FUN(X[[1L]], ...) : could not find function "FUN"
>
> Please note that I use:
> std.error = sd(B)/sqrt(sum(!is.na(B)))
>  to calculate the standard error as it requested for it.
>
> Thanks
> Ogbos
>
> On Sat, Jun 23, 2018 at 10:09 AM, Jim Lemon <[hidden email]> wrote:
>>
>> Hi Ogbos,
>> This may help:
>>
>> # assume your data frame is named "oodf"
>> oomean<-as.vector(by(oodf$B,oodf$A,mean))
>> oose<-as.vector(by(oodf$B,oodf$A,std.error))
>> plot(-5:10,oomean,type="b",ylim=c(50000,110000),
>>  xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
>> dispersion(-5:10,oomean,oose)
>>
>> Jim
>>
>> On Sat, Jun 23, 2018 at 4:35 PM, Ogbos Okike <[hidden email]>
>> wrote:
>> > Dear workers,
>> > I have a data of length 1136. Below is the code I use to get the means
>> > B.
>> > It worked fine and I had the mean calculated and plotted.
>> >
>> > I wish to plot the error bars as well. I already plotted such means with
>> > error bars before. Please see attached for example.
>> >
>> > I tried to redo the same plot but unlikely could not get around it as I
>> > lost my system containing the script.
>> > Among many attempts, I tried:
>> > library(gplots)
>> >
>> >  plotmeans(errors~AB,xlab="Factor A",ylab="mean errors", p=.68,
>> > main="Main
>> >   effect Plot",barcol="black")
>> > Nothing worked.
>> >
>> > I would really be thankful should somebody return me to the track.
>> > Many, many thanks for your time.
>> > Ogbos
>> >
>> > A sample of the data is:
>> > S/N      A        B
>> > 1    -5  64833
>> > 2    -4  95864
>> > 3    -3  82322
>> > 4    -2  95591
>> > 5    -1  69378
>> > 6     0  74281
>> > 7     1 103261
>> > 8     2  92473
>> > 9     3  84344
>> > 10    4 127415
>> > 11    5 123826
>> > 12    6 100029
>> > 13    7  76205
>> > 14    8 105162
>> > 15    9 119533
>> > 16   10 106490
>> > 17   -5  82322
>> > 18   -4  95591
>> > 19   -3  69378
>> > 20   -2  74281
>> > 21   -1 103261
>> > 22    0  92473
>> > 23    1  84344
>> > 24    2 127415
>> > 25    3 123826
>> > 26    4 100029
>> > 27    5  76205
>> > 28    6 105162
>> > 29    7 119533
>> > 30    8 106490
>> > 31    9 114771
>> > 32   10  55593
>> > 33   -5  85694
>> > 34   -4  65205
>> > 35   -3  80995
>> > 36   -2  51723
>> > 37   -1  62310
>> > 38    0  53401
>> > 39    1  65677
>> > 40    2  76094
>> > 41    3  64035
>> > 42    4  68290
>> > 43    5  73306
>> > 44    6  82176
>> > 45    7  75566
>> > 46    8  89762
>> > 47    9  88063
>> > 48   10  94395
>> > 49   -5  80651
>> > 50   -4  81291
>> > 51   -3  63702
>> > 52   -2  70297
>> > 53   -1  64117
>> > 54    0  71219
>> > 55    1  57354
>> > 56    2  62111
>> > 57    3  42252
>> > 58    4  35454
>> > 59    5  33469
>> > 60    6  38899
>> > 61    7  64981
>> > 62    8  85694
>> > 63    9  79452
>> > 64   10  85216
>> > 65   -5  71219
>> > 66   -4  57354
>> > 67   -3  62111
>> > 68   -2  42252
>> > 69   -1  35454
>> > 70    0  33469
>> > 71    1  38899
>> > 72    2  64981
>> > 73    3  85694
>> > 74    4  79452
>> > 75    5  85216
>> > 76    6  81721
>> > 77    7  91231
>> > 78    8 107074
>> > 79    9 108103
>> > 80   10  7576
>> >
>> > A<-matrix(rep(-5:10,71))
>> > B<-matrix(data)
>> >  AB<-data.frame(A,B)
>> >
>> > x= B
>> >
>> >  f<-factor(A)
>> > AB<- tapply(x,f,mean)
>> > x<--5:10
>> > plot(x,AB,type="l")
>> >
>> > ______________________________________________
>> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> > http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>> >
>
>

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: tapply and error bars

Ogbos
Hi Jim

Thanks again for returning to this.
please not that the line "oomean<-as.vector(by(oodf$B,oodf$A,mean))" was
omitted (not sure whether deliberate)  after you introduced the standard
error function.
When I used it, empty plot window with the correct axes were generated but
no data was displayed. No error too.

library(plotrix)
std.error<-function(x) return(sd(x)/(sum(!is.na(x))))
oose<-as.vector(by(oodf$B,oodf$A,std.error))
plot(-5:10,oomean,type="b",ylim=c(50000,110000),
 xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
dispersion(-5:10,oomean,oose)

When I included the line, the same empty graph window was generated but
with the former error "Error in FUN(X[[1L]], ...) : could not find function
"FUN""
library(plotrix)
std.error<-function(x) return(sd(x)/(sum(!is.na(x))))
oomean<-as.vector(by(oodf$B,oodf$A,mean))
oose<-as.vector(by(oodf$B,oodf$A,std.error))
plot(-5:10,oomean,type="b",ylim=c(50000,110000),
 xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
dispersion(-5:10,oomean,oose)

I am sure am missing something but can't place it. Please have a look again
to track my mistake.

Warmest regards
Ogbos

On Sun, Jun 24, 2018 at 11:24 AM, Jim Lemon <[hidden email]> wrote:

> Hi Ogbos,
> If I use the example data that you sent, I get the error after this line:
>
> oose<-as.vector(by(oodf$B,oodf$A,std.error))
> Error in FUN(X[[i]], ...) : object 'std.error' not found
>
> The reason is that you have not defined std.error as a function, but
> as the result of a calculation. When I rewrite it like this:
>
> std.error<-function(x) return(sd(x)/(sum(!is.na(x))))
> oose<-as.vector(by(oodf$B,oodf$A,std.error))
> plot(-5:10,oomean,type="b",ylim=c(50000,110000),
>  xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
> dispersion(-5:10,oomean,oose)
>
> I get the expected plot.
>
> Jim
>
>
> On Sat, Jun 23, 2018 at 9:36 PM, Ogbos Okike <[hidden email]>
> wrote:
> > Hi Jim,
> >
> > Thanks for assisting. Here is what I did:
> >
> > A<-matrix(rep(-5:10,71))
> > B<-matrix(data)
> > std.error = sd(B)/sqrt(sum(!is.na(B)))
> >  oodf<-data.frame(A,B)
> >
> >  oomean<-as.vector(by(oodf$B,oodf$A,mean))
> > oose<-as.vector(by(oodf$B,oodf$A,std.error))
> > plot(-5:10,oomean,type="b",ylim=c(50000,110000),
> >  xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
> > dispersion(-5:10,oomean,oose)
> >
> > And the error says:
> > Error in FUN(X[[1L]], ...) : could not find function "FUN"
> >
> > Please note that I use:
> > std.error = sd(B)/sqrt(sum(!is.na(B)))
> >  to calculate the standard error as it requested for it.
> >
> > Thanks
> > Ogbos
> >
> > On Sat, Jun 23, 2018 at 10:09 AM, Jim Lemon <[hidden email]>
> wrote:
> >>
> >> Hi Ogbos,
> >> This may help:
> >>
> >> # assume your data frame is named "oodf"
> >> oomean<-as.vector(by(oodf$B,oodf$A,mean))
> >> oose<-as.vector(by(oodf$B,oodf$A,std.error))
> >> plot(-5:10,oomean,type="b",ylim=c(50000,110000),
> >>  xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
> >> dispersion(-5:10,oomean,oose)
> >>
> >> Jim
> >>
> >> On Sat, Jun 23, 2018 at 4:35 PM, Ogbos Okike <[hidden email]>
> >> wrote:
> >> > Dear workers,
> >> > I have a data of length 1136. Below is the code I use to get the means
> >> > B.
> >> > It worked fine and I had the mean calculated and plotted.
> >> >
> >> > I wish to plot the error bars as well. I already plotted such means
> with
> >> > error bars before. Please see attached for example.
> >> >
> >> > I tried to redo the same plot but unlikely could not get around it as
> I
> >> > lost my system containing the script.
> >> > Among many attempts, I tried:
> >> > library(gplots)
> >> >
> >> >  plotmeans(errors~AB,xlab="Factor A",ylab="mean errors", p=.68,
> >> > main="Main
> >> >   effect Plot",barcol="black")
> >> > Nothing worked.
> >> >
> >> > I would really be thankful should somebody return me to the track.
> >> > Many, many thanks for your time.
> >> > Ogbos
> >> >
> >> > A sample of the data is:
> >> > S/N      A        B
> >> > 1    -5  64833
> >> > 2    -4  95864
> >> > 3    -3  82322
> >> > 4    -2  95591
> >> > 5    -1  69378
> >> > 6     0  74281
> >> > 7     1 103261
> >> > 8     2  92473
> >> > 9     3  84344
> >> > 10    4 127415
> >> > 11    5 123826
> >> > 12    6 100029
> >> > 13    7  76205
> >> > 14    8 105162
> >> > 15    9 119533
> >> > 16   10 106490
> >> > 17   -5  82322
> >> > 18   -4  95591
> >> > 19   -3  69378
> >> > 20   -2  74281
> >> > 21   -1 103261
> >> > 22    0  92473
> >> > 23    1  84344
> >> > 24    2 127415
> >> > 25    3 123826
> >> > 26    4 100029
> >> > 27    5  76205
> >> > 28    6 105162
> >> > 29    7 119533
> >> > 30    8 106490
> >> > 31    9 114771
> >> > 32   10  55593
> >> > 33   -5  85694
> >> > 34   -4  65205
> >> > 35   -3  80995
> >> > 36   -2  51723
> >> > 37   -1  62310
> >> > 38    0  53401
> >> > 39    1  65677
> >> > 40    2  76094
> >> > 41    3  64035
> >> > 42    4  68290
> >> > 43    5  73306
> >> > 44    6  82176
> >> > 45    7  75566
> >> > 46    8  89762
> >> > 47    9  88063
> >> > 48   10  94395
> >> > 49   -5  80651
> >> > 50   -4  81291
> >> > 51   -3  63702
> >> > 52   -2  70297
> >> > 53   -1  64117
> >> > 54    0  71219
> >> > 55    1  57354
> >> > 56    2  62111
> >> > 57    3  42252
> >> > 58    4  35454
> >> > 59    5  33469
> >> > 60    6  38899
> >> > 61    7  64981
> >> > 62    8  85694
> >> > 63    9  79452
> >> > 64   10  85216
> >> > 65   -5  71219
> >> > 66   -4  57354
> >> > 67   -3  62111
> >> > 68   -2  42252
> >> > 69   -1  35454
> >> > 70    0  33469
> >> > 71    1  38899
> >> > 72    2  64981
> >> > 73    3  85694
> >> > 74    4  79452
> >> > 75    5  85216
> >> > 76    6  81721
> >> > 77    7  91231
> >> > 78    8 107074
> >> > 79    9 108103
> >> > 80   10  7576
> >> >
> >> > A<-matrix(rep(-5:10,71))
> >> > B<-matrix(data)
> >> >  AB<-data.frame(A,B)
> >> >
> >> > x= B
> >> >
> >> >  f<-factor(A)
> >> > AB<- tapply(x,f,mean)
> >> > x<--5:10
> >> > plot(x,AB,type="l")
> >> >
> >> > ______________________________________________
> >> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> >> > https://stat.ethz.ch/mailman/listinfo/r-help
> >> > PLEASE do read the posting guide
> >> > http://www.R-project.org/posting-guide.html
> >> > and provide commented, minimal, self-contained, reproducible code.
> >> >
> >
> >
>

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Re: tapply and error bars

Jim Lemon-4
Hi Ogbos,
The problem is almost certainly with the data. I get the plot I expect
with the sample data that you first posted, so I know that the code
works. If you try thIs what do you get?

oodf<-read.table(text="S/N      A        B
1    -5  64833
2    -4  95864
3    -3  82322
4    -2  95591
5    -1  69378
6     0  74281
7     1 103261
8     2  92473
9     3  84344
10    4 127415
11    5 123826
12    6 100029
13    7  76205
14    8 105162
15    9 119533
16   10 106490
17   -5  82322
18   -4  95591
19   -3  69378
20   -2  74281
21   -1 103261
22    0  92473
23    1  84344
24    2 127415
25    3 123826
26    4 100029
27    5  76205
28    6 105162
29    7 119533
30    8 106490
31    9 114771
32   10  55593
33   -5  85694
34   -4  65205
35   -3  80995
36   -2  51723
37   -1  62310
38    0  53401
39    1  65677
40    2  76094
41    3  64035
42    4  68290
43    5  73306
44    6  82176
45    7  75566
46    8  89762
47    9  88063
48   10  94395
49   -5  80651
50   -4  81291
51   -3  63702
52   -2  70297
53   -1  64117
54    0  71219
55    1  57354
56    2  62111
57    3  42252
58    4  35454
59    5  33469
60    6  38899
61    7  64981
62    8  85694
63    9  79452
64   10  85216
65   -5  71219
66   -4  57354
67   -3  62111
68   -2  42252
69   -1  35454
70    0  33469
71    1  38899
72    2  64981
73    3  85694
74    4  79452
75    5  85216
76    6  81721
77    7  91231
78    8 107074
79    9 108103
80   10  7576",
header=TRUE)
library(plotrix)
std.error<-function(x) return(sd(x)/(sum(!is.na(x))))
oomean<-as.vector(by(oodf$B,oodf$A,mean))
oose<-as.vector(by(oodf$B,oodf$A,std.error))
plot(-5:10,oomean,type="b",ylim=c(50000,110000),
 xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
dispersion(-5:10,oomean,oose)

I get the attached plot;

Jim

On Mon, Jun 25, 2018 at 1:58 AM, Ogbos Okike <[hidden email]> wrote:

> Hi Jim
>
> Thanks again for returning to this.
> please not that the line "oomean<-as.vector(by(oodf$B,oodf$A,mean))" was
> omitted (not sure whether deliberate)  after you introduced the standard
> error function.
> When I used it, empty plot window with the correct axes were generated but
> no data was displayed. No error too.
>
> library(plotrix)
> std.error<-function(x) return(sd(x)/(sum(!is.na(x))))
> oose<-as.vector(by(oodf$B,oodf$A,std.error))
> plot(-5:10,oomean,type="b",ylim=c(50000,110000),
>  xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
> dispersion(-5:10,oomean,oose)
>
> When I included the line, the same empty graph window was generated but with
> the former error "Error in FUN(X[[1L]], ...) : could not find function
> "FUN""
> library(plotrix)
> std.error<-function(x) return(sd(x)/(sum(!is.na(x))))
> oomean<-as.vector(by(oodf$B,oodf$A,mean))
> oose<-as.vector(by(oodf$B,oodf$A,std.error))
> plot(-5:10,oomean,type="b",ylim=c(50000,110000),
>  xlab="days (epoch is the day of Fd)",ylab="strikes/km2/day")
> dispersion(-5:10,oomean,oose)
>
> I am sure am missing something but can't place it. Please have a look again
> to track my mistake.
>
> Warmest regards
> Ogbos
>

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