[R] interaction plot and x axis

2012-01-04 Thread Lathouri, Maria
Dear all



 I am trying to make an interaction plot among 6 variables; e.g. PH to be in 
the x axis and the rest 5 variables in the y axis. The code that I am using is 
the below:



The name of my file is e.g. spec so



 spec-read.csv(spec.csv)

head (spec)

str(spec)

names-names(spec)[2:6]
speclong - reshape(spec, idvar = id, varying = list(names), 
v.names=outcome,direction = long)

speclong$time2-factor(speclong$time,labels=rep(   ,5))

interaction.plot(speclong$PH,speclong$time2,speclong$outcome, xaxt=n, 
type=l, log=y, trace.label=,col=rainbow(8))



what I want is to change the labels of the x axis. If for example I don't use 
xaxt=n, by default it shows some values of PH e.g. 4.93, 5.97, 6.23, 6.47, 
6.59, 6.77, 6.89, 7.35 but it don't show the ticks in each value. However I 
would like to define the x values e.g. 5.0, 5.5, 6.0, 6.5, 7.0. I used the xlim 
but it says error as well

axis(1, at=c(5.0, 5.5, 6.0, 6.5, 7.0)) but still there is a problem.



Does anyone know how I can define that?



Thank you in advance.



Kind regards

Maria

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[R] fitting a distribution to a ecdf plot

2011-03-15 Thread Lathouri, Maria
Dear all,

I need to plot an cumulative distribution plot of a variable and then to fit a 
distribution to that, probably a weibull or lognormal.

I have plotted the ecdf as
 plot(ecdf(x))

but I haven't managed to fit the distribution. I have as well attached the data.

I would appreciate if you could help me on that.

Thank you.

Kind regards
Maria
NOECCu
67.88904443
150.1397457
186.4661306
125.4586537
164.6450167
82.26572728
46.12957405
139.3670831
77.3140337
73.71616087
89.24381267
55.49698407
161.4744795
110.9611291
103.3427988
120.978441
121.3764833
100.1028412
145.5605989
142.3290787
145.3679277
93.62492361
55.48686698
128.11105
69.65897422
77.74185999
115.8001364
50.45232492
90.35071838
132.9893917
77.72242849
64.28160263
54.01295646
83.71891269
134.0958513
64.60377903
48.18032813
130.486115
56.73379201
52.23087454
50.33847793
54.88254634
109.1721021
48.20831769
87.10977697
47.02111749
63.29204939
48.15737916
59.51869418
63.70426227
83.97669506
93.56957986
94.13697821
49.81656675
41.49804514
51.05645798
61.76354398
60.6012629
54.42093914
93.51486665
60.54396105
48.85428234
166.7654584
146.810965
80.95967487
167.2626315
59.47330368
72.86066214
116.4378185
55.64725599
121.2565064
71.47595431
133.7136451
73.82132992
137.8096239
49.83650594
81.08199187
89.36373311
47.72963718
49.02577131
54.0245052
47.18943578
106.7524366
92.86330941
107.7602873
80.46842086
203.1770731
63.47382772
106.0130281
90.67128789
85.91406122
85.65280069
129.637575
81.89671307
115.5356497
65.53656745
129.3789983
83.07309212
95.3862417
47.64942729
44.58198126
65.91324525
85.98441643
173.7522613
68.43518477
62.19982961
60.48931609
79.84400257
196.0585861
79.15253575
198.4031949
188.8371774
67.2503906
76.7620257
154.1797827
84.26522759
70.97081638
56.37466386
129.0594303
114.5855536
73.67967762
536.9946813
78.95253975
71.19112816
51.24938953
67.10699555
93.07971733
52.55033118
48.98038035
71.99776449
87.15210545
120.8311727
63.00287326
67.90228061
87.24346937
170.9653141
174.1646464
51.72208312
55.25671981
67.79918864
52.23148551
68.94684451
58.64711247
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Re: [R] fitting a distribution to a ecdf plot

2011-03-15 Thread Lathouri, Maria
Actually I have already done a search on that but it was not much of a help. 
That is why I posted it in the r-help in case it was much more helpful. 

Thank you.

Kind regards
Maria


From: David Winsemius [dwinsem...@comcast.net]
Sent: 15 March 2011 16:19
To: Lathouri, Maria
Cc: r-help@r-project.org
Subject: Re: [R] fitting a distribution to a ecdf plot

On Mar 15, 2011, at 12:00 PM, Lathouri, Maria wrote:

 Dear all,

 I need to plot an cumulative distribution plot of a variable and
 then to fit a distribution to that, probably a weibull or lognormal.

 I have plotted the ecdf as
 plot(ecdf(x))

 but I haven't managed to fit the distribution. I have as well
 attached the data.

Try a search on one of the R search sites with:

Fitting distributions with R  # use the quotes



 I would appreciate if you could help me on that.

 Thank you.

 Kind regards
 Maria
 example.txt__
 R-help@r-project.org mailing list
 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.

David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
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Re: [R] fitting a distribution to a ecdf plot

2011-03-15 Thread Lathouri, Maria
Hallo
yes I tried it as well and it works;

Thank you a lot

Maria


From: Dennis Murphy [djmu...@gmail.com]
Sent: 15 March 2011 21:36
To: Lathouri, Maria
Cc: r-help@r-project.org
Subject: Re: [R] fitting a distribution to a ecdf plot

Hi:

The fitdistrplus package from CRAN may be useful. I tried it on your data and 
the lognormal seemed to fit well, apart from the outlier. I just followed the 
vignette that accompanies the package.

library(fitdistplus)

plotdist(NOEccu) # ecdf
descdist(NOEccu, boot = 1000)  # Cullen-Frey graph based on 1000 bootstrap 
samples

# The Cullen-Frey graph suggests that the distribution is somewhere between a 
Gamma and lognormal

# Weibull
N1w - fitdist(NOEccu, 'weibull')
# Warning messages:
# 1: In dweibull(x, shape, scale, log) : NaNs produced
# 2: In dweibull(x, shape, scale, log) : NaNs produced
plot(N1w)
summary(N1w)

# Gamma
N1g - fitdist(NOEccu, 'gamma')
# Warning messages:
# 1: In dgamma(x, shape, scale, log) : NaNs produced
# 2: In dgamma(x, shape, scale, log) : NaNs produced
# 3: In dgamma(x, shape, scale, log) : NaNs produced
# 4: In dgamma(x, shape, scale, log) : NaNs produced
plot(N1g)
summary(N1g)

# Lognormal
N1l - fitdist(NOEccu, 'lnorm')
plot(N1l)
summary(N1l)

Try it out and see if it suits your needs.

HTH,
Dennis

On Tue, Mar 15, 2011 at 9:00 AM, Lathouri, Maria 
m.lathour...@imperial.ac.ukmailto:m.lathour...@imperial.ac.uk wrote:
Dear all,

I need to plot an cumulative distribution plot of a variable and then to fit a 
distribution to that, probably a weibull or lognormal.

I have plotted the ecdf as
 plot(ecdf(x))

but I haven't managed to fit the distribution. I have as well attached the data.

I would appreciate if you could help me on that.

Thank you.

Kind regards
Maria

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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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and provide commented, minimal, self-contained, reproducible code.


[R] how to change the margins of a plot area

2011-03-13 Thread Lathouri, Maria
Dear all,

I am ploting two boxplot of two chemical variables using the format
boxplot(Alkalinity, logAlkalinity, log=y, col=c(lightblue), lwd=0.6, 
boxwex=0.3)

However when I plot like this, the distance between the two boxplots is very 
big and as well the distance of each boxplot from the plot area, left and 
right. How can I minimise that distance between the boxplots and as well the 
distance of each boxplot from the left and right margin of the plot area?

Another question is that when I write in the above ylab=Concentration, I get 
in the y axis as well in each tick and a number. How can I not have this but 
only the text?

Thank you.

Kind regards
Maria

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and provide commented, minimal, self-contained, reproducible code.


Re: [R] how to change the margins of a plot area

2011-03-13 Thread Lathouri, Maria
Dear all

I have attached a file in a csv format, with two variables; the code that I am 
using to plot the boxplots is 
boxplot(ALKY, CL, ylab=Concentration, lwd=0.7, boxwex=0.4)

I hope this will help.

Thanks
Maria


From: John Kane [jrkrid...@yahoo.ca]
Sent: 13 March 2011 13:19
To: r-help@r-project.org; Lathouri, Maria
Subject: Re: [R] how to change the margins of a plot area

Hi Maria,
I think we need some sample data and code to really be ablo to help.

in the meantime have have a look at ?par for general plotting info.

--- On Sun, 3/13/11, Lathouri, Maria m.lathour...@imperial.ac.uk wrote:

 From: Lathouri, Maria m.lathour...@imperial.ac.uk
 Subject: [R] how to change the margins of a plot area
 To: r-help@r-project.org r-help@r-project.org
 Received: Sunday, March 13, 2011, 8:15 AM
 Dear all,

 I am ploting two boxplot of two chemical variables using
 the format
 boxplot(Alkalinity, logAlkalinity, log=y,
 col=c(lightblue), lwd=0.6, boxwex=0.3)

 However when I plot like this, the distance between the two
 boxplots is very big and as well the distance of each
 boxplot from the plot area, left and right. How can I
 minimise that distance between the boxplots and as well the
 distance of each boxplot from the left and right margin of
 the plot area?

 Another question is that when I write in the above
 ylab=Concentration, I get in the y axis as well in each
 tick and a number. How can I not have this but only the
 text?

 Thank you.

 Kind regards
 Maria

 [[alternative HTML version deleted]]

 __
 R-help@r-project.org
 mailing list
 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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and provide commented, minimal, self-contained, reproducible code.


[R] FW: how to change the margins of a plot area

2011-03-13 Thread Lathouri, Maria
Dear all

I am sorry about that; I thought that since in R csv formats are acceptable, it 
will be here as well. I have attached it in a text format.

I hope now it is better.

Thank you
Maria


From: David Winsemius [dwinsem...@comcast.net]
Sent: 13 March 2011 18:24
To: Lathouri, Maria
Subject: Re: [R] how to change the margins of a plot area

Please read the Posting Guide and note that .csv files are NOT
mentioned as one of the acceptable formats for attachments to postings!


On Mar 13, 2011, at 1:00 PM, Lathouri, Maria wrote:

 Dear all

 I have attached a file in a csv format, with two variables; the code
 that I am using to plot the boxplots is
 boxplot(ALKY, CL, ylab=Concentration, lwd=0.7, boxwex=0.4)

 I hope this will help.

 Thanks
 Maria

 
 From: John Kane [jrkrid...@yahoo.ca]
 Sent: 13 March 2011 13:19
 To: r-help@r-project.org; Lathouri, Maria
 Subject: Re: [R] how to change the margins of a plot area

 Hi Maria,
 I think we need some sample data and code to really be ablo to help.

 in the meantime have have a look at ?par for general plotting info.

 --- On Sun, 3/13/11, Lathouri, Maria m.lathour...@imperial.ac.uk
 wrote:

 From: Lathouri, Maria m.lathour...@imperial.ac.uk
 Subject: [R] how to change the margins of a plot area
 To: r-help@r-project.org r-help@r-project.org
 Received: Sunday, March 13, 2011, 8:15 AM
 Dear all,

 I am ploting two boxplot of two chemical variables using
 the format
 boxplot(Alkalinity, logAlkalinity, log=y,
 col=c(lightblue), lwd=0.6, boxwex=0.3)

 However when I plot like this, the distance between the two
 boxplots is very big and as well the distance of each
 boxplot from the plot area, left and right. How can I
 minimise that distance between the boxplots and as well the
 distance of each boxplot from the left and right margin of
 the plot area?

 Another question is that when I write in the above
 ylab=Concentration, I get in the y axis as well in each
 tick and a number. How can I not have this but only the
 text?

 Thank you.

 Kind regards
 Maria

[[alternative HTML version deleted]]

 __
 R-help@r-project.org
 mailing list
 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.
 __
 R-help@r-project.org mailing list
 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.

David Winsemius, MD
West Hartford, CTALKYCL
24  17
42  16.8
20  15.2
33  15.8
34  14.7
38  14.8
32  13.2
27  13.3
37  15.7
31  12.7
31  14
35  14.8
30  14.6
31  14.7
34  15.6
39  16
44  15.2
40  14.3
51  17.2
41  16.3
30  12
48  15.1
40  14
46  15.8
33  13.9
44  15.2
33  14.1
33.42520849 14.6906392
31  14.6
31  10.6
49.65524516 15.8163576
49  15
47  14.3
33  13
39  12.5
38  12.8
30  12
30  12.2
29.82656017 14.29424761
34  14.2
34  12.8
56  16
60  17.4
61  18.4
59  15.7
44  15.3
41  16.2
33  13.8
38  13
41  13.5
37  17.1
21  12.8
39  16.1
36.412.5
50.717.1
37.312.1
41.711.9
62.117.5
43.413.8
42  13.5
40  14.1
40.16876216 15.9
36.48094861 16.4
41.4029284  15.5
55.16932486 17
56.74926517 17.2
40.75086976 14.9
57.92527479 15.5
61.0741 16.4
47.58835403 15.8
26.78666719 19.8
29.11069914 18.5
43.89296089 15.7
29.80014395 15.3
45.43326189 17.9
21.52111069 14.8
34.28668871 16.3
51.33203813 15.4
61.16524423 19.1
33.08808335 16
28.45357602 13.1
46.95762322 15
41.2184536  14.6
41.67606216 14
34.53359965 17.6
34.88690373 17.4
34.61562996 15.5
44.29030259 17
39.68692169 16.3
39.43498713 19.5
37.04679913 16.6
58.97385637 16.1
44.08944815 14.9
42.07100781 13.8
40.29932265 15.4
43.10896392 16.6
34.27550906 13.6
28.53052378 11.9
46.85048052 15.9
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[R] please help with interaction.plot

2011-03-02 Thread Lathouri, Maria
Dear all

I have the following code to produce a graph of 5 different variables in the 
same graph; however when I follow it in the end it produces the plot of the 5 
variables and a legend in right but the problem is that the legend is too close 
to the margin of the plot and when I try to write the text for each line it 
does not fit. How can I change the location of the legend to be placed a little 
bit to the left?

example-read.csv(file=example.csv)
example$date-as.Date(example$Date,format=%d/%m/%Y,order=dmy)
head(example)
str(example)
names-names(example)[2:5]
examplelong - reshape(example, idvar = id, varying = list(names), 
v.names=outcome,direction = long)
examplelong$time2-factor(examplelong$time,labels=rep(   ,4))
d3-c((examplelong$date[1]),(examplelong$date[103]))
d4-as.Date((d3[1])+150*(0:20))
interaction.plot(examplelong$date, 
examplelong$time2,examplelong$outcome,xaxt=n,type=l,pch=20,xlab=, 
log=y, ylab=expression(paste(Concentration~(~mu~g/L))), 
trace.label=,col=rainbow(4))

Thank you
Maria

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[R] barplot with errorbars

2011-02-17 Thread Lathouri, Maria
Dear all

I have six variables of the average metal concentrations

Var1 4.77
Var2 23.5
Var3 5.2
Var4 12.3
Var5 42.1
Var6 121.2

I want to plot them as a barplot with error bars. Could you help me?

Cheers
Maria

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[R] please help-DTK package

2011-02-08 Thread Lathouri, Maria
Dear all

I am trying to do a multiple pairwise comparison test with Tukey-Kramer test as 
I have unequal sample sizes and variance. I have downloaded the DTK package 
from CRAN website in my computer for Windows, however I have difficulties in 
installing it in R.

I have unzipped the compressed file in my computer and then I open R, I try to 
install the package through File - Source R code - DTK but there is always an 
error.

Could you please help me? I can't understand what I am doing wrong.

Thank you.

Maria

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[R] add error bars in a plot

2011-02-08 Thread Lathouri, Maria
Dear all

I have a dataset of how metal concentrations change through time. I have made a 
plot of date versus metal concentration. However I want to add error bars in 
the plot.

Could you help me?

Thanks
Maria

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[R] Uncertainty analysis

2010-09-09 Thread Lathouri, Maria
Dear all

I would like to run in R an uncertainty/sensitivity analysis. I know that these 
two are performed together. I have a geochemical model where I have the inputs, 
the water variables (e.g. pH, temperature, oxygen ect) and as well an output of 
different variables. What I would like to do is to estimate the uncertainty 
that the output variables have considering the uncertainty of the input 
variables as well how the variations of my inputs contribute most to the 
variations of my output (probably though the sensitivity analysis). I was 
thinking perhaps with Monte Carlo analysis.

Is there a way to do that?

Thanks a lot.

Maria



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[R] change the type of lines and colours in interaction.plot

2010-09-03 Thread Lathouri, Maria
Dear all,

I want to plot 8 chemical variables in the same plot. I have used the 
interaction.plot command:

 interaction.plot(speclong$Date,speclong$time2,speclong$outcome,xaxt=n,type=l,pch=20,xlab=,
  log=y, ylab=Concentration (ug/L),trace.label=,col=rainbow(8))
However, what it gives me is dotted lines and the colours are very fade. I was 
wondering if I can change the lines to be solid and as well to specify for each 
line the colour that I want.

Thanks a lot.

Maria

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[R] specify axis range

2010-08-31 Thread Lathouri, Maria
Dear all,

I want to make a plot where I can specify the range of y axis. I am using the 
interaction.plot command and because the values of y axis are from 2 to 500, I 
am using a logarithmic scale.

interaction.plot(speclong$Date,speclong$time2,speclong$outcome,xaxt=n,type=l,pch=20,xlab=,
 log=y, ylab=Concentration (ug/L),trace.label=,col=rainbow(7))



The plot itself gives me a y scale displaying ticks at 2, 5, 10, 20, 100, 200, 
500. I would like to get a y scale where it would display ticks at every 4 
marks, at 2, 20, 100 and 500.



I tried ylim=c(2,20,100,500) but nothing happened. Actually I got an error.



Could you help me?



Thank you.



Maria


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[R] superscript in ylab

2009-10-28 Thread Lathouri, Maria
Dear all

I am doing some plots in R.

I want to have as label in y-axis Temperature (oC). I have used 
ylab=expression(paste({Temperature} ^o*C)) but what I get is TemperatureoC.
How can I have a space between Temperature and the units and also the units to 
be in brackets?

Many thanks
Maria



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and provide commented, minimal, self-contained, reproducible code.


[R] plot dates in x-axis

2009-10-13 Thread Lathouri, Maria
Hallo,

I am trying to plot dates in x-axis. The format of my dates are in dd/mm/. 
At first I install zoo package. After R reads my file, I change the default 
format of dates to the format that I have,

myfile-read.csv
DATE-as.Date(DATE,format=%d/%m/%Y)

up till now everything goes ok; when however I go and plot for example
plot(DATE, Discharge)

in the x-axis I only get the years, 1998, 2000, 2002...

How can I see in the x-axis the whole format of the dates that I have e.g. 
29/01/1998?



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[R] Trendline and R square value

2009-09-28 Thread Lathouri, Maria
Hi

I would like to display the trendline and the R-square value in a xy scatter in 
R. For example if I want to plot f vs g I add the trendline using the commands 
below

library(quantreg)
plot(f,g)
abline(rq(g~f))

however I don't know how to display the R2 in the graph.

Thank you in advance.

Kind regards
Maria

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[R] Time plots

2008-11-17 Thread Lathouri, Maria
Dear all, 
I want to do some time plots and actually the dates are in the format of 
dd/mm/. So first I input my dataframe in R in a csv form. What I do is 
 
DF-read.csv(C:/Documents and Settings/DF.csv)
DATE-as.Date(DATE, %d/%m/%Y)  # to tell R that DATE column is indeed dates
with(DF, plot(DATE,pH))
 
Until here it works fine, but I have the graph plotting only the points. What I 
want is to have a line (join these points) so to have a time plot. I have tried 
different commands such as lines(DATE,pH) or with(DF, lines(DATE,pH) but 
nothing works. 
 
What can I do?
 
Yours
Lathouri Maria

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[R] Boxplots with different variables and different ranges in R

2008-11-13 Thread Lathouri, Maria
Dear all,
 
I am trying to make boxplots in one diagram but it is not working. Actually I 
have a large dataset, around 35 water quality variables with different units 
and of course in different ranges (some are orders of magnitude bigger than 
others). I want to produce one diagram with all the boxplots of the variables 
of my dataset. 
 
I tried these series of commands:
oldpar - par(mfrow=c(1,ncol(R)))
 invisible(apply(R, 2,boxplot))
 for (i in 1:ncol(R)) boxplot(R[,i], main=colnames(R)[i])
 par(oldpar)

(where R is the name of my dataset)

The problem is that after the second command, there is an error in plot.new( ): 
figure margins too large. 

Is there a way to overcome this and put all my variables in a same diagram? I 
tried with less number of variables, but I had the same warning.

Thank you very much for your time and help.

Kind regards

Maria Lathouri




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[R] Enquiries about time plots in R

2008-11-12 Thread Lathouri, Maria
Dear all,
 
My name is Maria Lathouri and I am currently doing a PhD at Imperial College of 
London about time series of environmental variables in surface waters. I am 
trying to do some time plots with R but it seems that it is not working. 
The problem is that the time is not regular, for example, a small dataset can 
be seen below:
Date  pH
1/02/1998  5.5
5/03/1998  5
8/12/1998  6
1/02/1999  6.1
...
08/10/20007.2
 
I have used the function plot(DATE, pH) and then lines(pH), but the line does 
not join the points. I have used many combinations, e.g. plot(DATE, pH) and 
then lines(DATE, pH), where I get a plot with full of lines inside or just 
plot(pH) and then lines(pH) where the line connects the points but in x-axis 
I do not have the DATE. It says Index from 0 to 80. 
 
Do you know if there is a function where I can have in x-axis the DATE 
(irregular dates) and in y-axis the variable with a continuous line, showing 
how it changes through time?
 
I know that your time is valuable but I would appreciate it if you could help 
me. 
 
Thank you very much in advance for your time and help.
 
I am looking forward to hearing from you.
 
Sincerely yours 
Lathouri Maria

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