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automating a script to read a file

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Steve_Friedman@nps.gov

automating a script to read a file

Hi,

The following script (which I did not develop) is used to calculate and
plot a skewed normal curve. The script currently requires the user to
input six parameters, rather than reading these directly from a file.

I've been spinning wheels here, trying to figure out how to modify the
script to automate it. I have four data sets, each in excess of 300
records that I need to process.

My initial thoughts were to use the lapply and use a pdf graphic device to
capture the plots to do this, but my R programming skills are too limited
to determine how to best accomplish this.

If any one can provide assistance I would appreciate the help.

Thanks,

Steve

## Function set to find values in a skewed normal distribution

print("syntax: plot.spdf(min, max, skewlocation, skewscale, skewshape,
skewmax, <skewtitle>)")
flush.console()

# sample input data could be the following:
# -100, 1000, 976.02, 230, -34, 0.7543
# 0, 500, 270, 350, -13, 0.7707
# or any other data of similar form

erf <- function(z) {
## Chebyshev fitting formula for erf(z) from
## Vetterling, W.T., , W.H. Press, S.A. Teukolsky, and B.P.
Flannery. 1999.
## Numerical Recipes: Example Book [C], Second Edition.
## Cambridge University Press, NY. , Chapter 6-2.

t <- 1.0/(1.0 + 0.5 * abs(z))
## use Horner's method
ans <- (1 - t * exp(-z * z - 1.26551223
+ t * (1.00002368
+ t * (0.37409196
+ t * (0.09678418
+ t * (-0.18628806
+ t * (0.27886807
+ t * (-1.13520398
+ t * (1.48851587
+ t * (-0.82215223
+ t * (0.17087277)))))))))))
if (z >= 0) return(ans) else return(-1 * ans)
}

pdf <- function(x) {
return((1 / sqrt(2 * pi)) * exp(-1 * ((x * x) / 2)))
}

cdf <- function(x) {
return( 0.5 * (1 + erf(x / sqrt(2))))
}

spdf <- function(x, skewlocation, skewscale, skewshape) {
xmod <- (x - skewlocation) / skewscale
return( 2 * pdf(xmod) * (cdf(xmod * skewshape)))
}

#### Plotting Function ################
plot.spdf <- function(xmin, xmax, skewlocation, skewscale, skewshape,
skewmax, skewtitle) {

if(missing(skewtitle)) {
plottitle <- "Skewed Probability Density Function"
} else {
plottitle <- skewtitle
}

skip <- (xmax - xmin) / 100.0
xArray <- numeric(100)
yArray <- numeric(100)

for (i in 1:100){
x <- xmin + i * skip
y <- (spdf(x, skewlocation, skewscale, skewshape))/skewmax
xArray[i] <- x
yArray[i] <- y
}

plot(xArray,yArray, main=plottitle)

}

Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034

[hidden email]
Office (305) 224 - 4282
Fax (305) 224 - 4147

______________________________________________
[hidden email] 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.

Petr Savicky

Re: automating a script to read a file

On Mon, Apr 23, 2012 at 04:02:45PM -0400, [hidden email] wrote:

>
> Hi,
>
>
> The following script (which I did not develop) is used to calculate and
> plot a skewed normal curve. The script currently requires the user to
> input six parameters, rather than reading these directly from a file.
>
> I've been spinning wheels here, trying to figure out how to modify the
> script to automate it. I have four data sets, each in excess of 300
> records that I need to process.
>
> My initial thoughts were to use the lapply and use a pdf graphic device to
> capture the plots to do this, but my R programming skills are too limited
> to determine how to best accomplish this.

Hi.

If you read the parameters from a file and put them to a matrix,
then all the plots may be produced using a loop like the following.

#some parameters
p <- matrix(1:18, nrow=3, ncol=6)
for (i in 1:nrow(p)) {
plot.spdf(p[i, 1], p[i, 2], p[i, 3], p[i, 4], p[i, 5], p[i, 6])
readline("press Enter to continue")
}

If you use pdf() for sending the graphics to a file, then remove
the "readline" command.

Hope this helps.

Petr Savicky.

______________________________________________
[hidden email] 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.

Steve_Friedman@nps.gov

Re: automating a script to read a file

Petr,

Thank you very much this works. A little more tweaking and I'll have what
I need.

Thanks

Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034

[hidden email]
Office (305) 224 - 4282
Fax (305) 224 - 4147

Petr Savicky
<[hidden email]
z> To
Sent by: [hidden email]
r-help-bounces@r- cc
project.org
Subject
Re: [R] automating a script to read
04/23/2012 04:42 a file
PM

On Mon, Apr 23, 2012 at 04:02:45PM -0400, [hidden email] wrote:

to
> capture the plots to do this, but my R programming skills are too limited
> to determine how to best accomplish this.

Hi.

If you read the parameters from a file and put them to a matrix,
then all the plots may be produced using a loop like the following.

#some parameters
p <- matrix(1:18, nrow=3, ncol=6)
for (i in 1:nrow(p)) {
plot.spdf(p[i, 1], p[i, 2], p[i, 3], p[i, 4], p[i, 5], p[i, 6])
readline("press Enter to continue")
}

If you use pdf() for sending the graphics to a file, then remove
the "readline" command.

Hope this helps.

Petr Savicky.

______________________________________________
[hidden email] 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.

______________________________________________
[hidden email] 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.

Steve_Friedman@nps.gov

Re: automating a script to read a file

In reply to this post by Petr Savicky

Petr, R- Users

The scheme you provided yesterday worked very well. I am now trying to add
more information to the graph(s) to make them more informative for my
purposes.

Essentially, I am trying to use a double Y axis graphic that will include
the skew normal curves that I wrote about yesterday and a histogram.

The graph is very similar to the one produced by the following:

library(latticeExtra)
> doubleYScale(histogram(x), densityplot(x), use.style = FALSE)

However, I'd like to substitute the following syntax:

> doubleYScale(hist("mydata", breaks=20, prob=T, xlim=c(-100, 2000),
plot.spdf(x), use.style=FALSE)

This does not work as doubleYScale expects histogram and densityplot, and
I'd like to use the plot.spdf routine in its place.

Any Suggestions would be greatly appreciated.

I'm working with
R 2.15.0 (2012-03-12)
Platform i386-pc-mingw32/ie86 (32-bit)

Thanks
Steve

Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034

[hidden email]
Office (305) 224 - 4282
Fax (305) 224 - 4147

Petr Savicky
<[hidden email]
z> To
Sent by: [hidden email]
r-help-bounces@r- cc
project.org
Subject
Re: [R] automating a script to read
04/23/2012 04:42 a file
PM

On Mon, Apr 23, 2012 at 04:02:45PM -0400, [hidden email] wrote:

ilai-2

Re: automating a script to read a file

On Tue, Apr 24, 2012 at 2:09 PM, <[hidden email]> wrote:

> library(latticeExtra)
>> doubleYScale(hist("mydata", breaks=20, prob=T, xlim=c(-100, 2000),
> plot.spdf(x), use.style=FALSE)
>
> This does not work as doubleYScale expects histogram and densityplot, and
> I'd like to use the plot.spdf routine in its place.

Maybe it doesn't work because ?hist is base graphics, not the same as
?histogram in lattice. You did not provide plot.spdf or any data, so
this just a "place to start" type response.

Cheers

>
> Any Suggestions would be greatly appreciated.
>
> I'm working with
> R 2.15.0 (2012-03-12)
> Platform i386-pc-mingw32/ie86 (32-bit)
>
> Thanks
> Steve
>
>
> Steve Friedman Ph. D.
> Ecologist / Spatial Statistical Analyst
> Everglades and Dry Tortugas National Park
> 950 N Krome Ave (3rd Floor)
> Homestead, Florida 33034
>
> [hidden email]
> Office (305) 224 - 4282
> Fax (305) 224 - 4147
>
>
>
> Petr Savicky
> <[hidden email]
> z> To
> Sent by: [hidden email]
> r-help-bounces@r- cc
> project.org
> Subject
> Re: [R] automating a script to read
> 04/23/2012 04:42 a file
> PM
>
>
>
>
>
>
>
>
>
> On Mon, Apr 23, 2012 at 04:02:45PM -0400, [hidden email] wrote:
>>
>> Hi,
>>
>>
>> The following script (which I did not develop) is used to calculate and
>> plot a skewed normal curve. The script currently requires the user to
>> input six parameters, rather than reading these directly from a file.
>>
>> I've been spinning wheels here, trying to figure out how to modify the
>> script to automate it. I have four data sets, each in excess of 300
>> records that I need to process.
>>
>> My initial thoughts were to use the lapply and use a pdf graphic device
> to
>> capture the plots to do this, but my R programming skills are too limited
>> to determine how to best accomplish this.
>
> Hi.
>
> If you read the parameters from a file and put them to a matrix,
> then all the plots may be produced using a loop like the following.
>
> #some parameters
> p <- matrix(1:18, nrow=3, ncol=6)
> for (i in 1:nrow(p)) {
> plot.spdf(p[i, 1], p[i, 2], p[i, 3], p[i, 4], p[i, 5], p[i, 6])
> readline("press Enter to continue")
> }
>
> If you use pdf() for sending the graphics to a file, then remove
> the "readline" command.
>
> Hope this helps.
>
> Petr Savicky.
>
> ______________________________________________
> [hidden email] 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.
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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.

ilai-2

Re: automating a script to read a file

On Tue, Apr 24, 2012 at 6:00 PM, Steve Friedman <[hidden email]> wrote:

> The original post does contain the function plot.spdf and some sample data.

That's great. And who's responsibility is it to make sure we have
context for THIS post ? This is a mailing list, not a forum and MY
mail client doesn't keep track of YOUR postings.

BTW, you are the one seeking our help, so even if you think it was a
picky request, a proper response would be to simply post your
function+data set. Not send us looking for some "original post".

> I thought I also made it clear that I understood that hist and histogram are
> not the same.

No you didn't. But now IT IS clear you don't realize grid and base
graphics don't mix.

> I am looking for a way to use the alternatives in a function similar to but
> not identical to doubleYScale.

LatticeExtra functions expect any lattice plots, including local (user
defined) panel/plot functions, if only you would have posted plot.spdf
maybe you would have gotten a solution by now...
If plot.spdf is actually a base graphics plotter and you just stumbled
upon DoubleYscale somehow, ?par ?axis hist(...,add=T) are all
available to you.

Best

>
> Steve
>
> On Apr 24, 2012 7:45 PM, "ilai" <[hidden email]> wrote:
>>
>> On Tue, Apr 24, 2012 at 2:09 PM, <[hidden email]> wrote:
>>
>> > library(latticeExtra)
>> >> doubleYScale(hist("mydata", breaks=20, prob=T, xlim=c(-100, 2000),
>> > plot.spdf(x), use.style=FALSE)
>> >
>> > This does not work as doubleYScale expects histogram and densityplot,
>> > and
>> > I'd like to use the plot.spdf routine in its place.
>>
>> Maybe it doesn't work because ?hist is base graphics, not the same as
>> ?histogram in lattice. You did not provide plot.spdf or any data, so
>> this just a "place to start" type response.
>>
>> Cheers
>>
>>
>>
>> >
>> > Any Suggestions would be greatly appreciated.
>> >
>> > I'm working with
>> > R 2.15.0 (2012-03-12)
>> > Platform i386-pc-mingw32/ie86 (32-bit)
>> >
>> > Thanks
>> > Steve
>> >
>> >
>> > Steve Friedman Ph. D.
>> > Ecologist / Spatial Statistical Analyst
>> > Everglades and Dry Tortugas National Park
>> > 950 N Krome Ave (3rd Floor)
>> > Homestead, Florida 33034
>> >
>> > [hidden email]
>> > Office (305) 224 - 4282
>> > Fax (305) 224 - 4147
>> >
>> >
>> >
>> > Petr Savicky
>> > <[hidden email]
>> > z>
>> > To
>> > Sent by: [hidden email]
>> > r-help-bounces@r-
>> > cc
>> > project.org
>> >
>> > Subject
>> > Re: [R] automating a script to
>> > read
>> > 04/23/2012 04:42 a file
>> > PM
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Mon, Apr 23, 2012 at 04:02:45PM -0400, [hidden email] wrote:
>> >>
>> >> Hi,
>> >>
>> >>
>> >> The following script (which I did not develop) is used to calculate and
>> >> plot a skewed normal curve. The script currently requires the user to
>> >> input six parameters, rather than reading these directly from a file.
>> >>
>> >> I've been spinning wheels here, trying to figure out how to modify the
>> >> script to automate it. I have four data sets, each in excess of 300
>> >> records that I need to process.
>> >>
>> >> My initial thoughts were to use the lapply and use a pdf graphic
>> >> device
>> > to
>> >> capture the plots to do this, but my R programming skills are too
>> >> limited
>> >> to determine how to best accomplish this.
>> >
>> > Hi.
>> >
>> > If you read the parameters from a file and put them to a matrix,
>> > then all the plots may be produced using a loop like the following.
>> >
>> > #some parameters
>> > p <- matrix(1:18, nrow=3, ncol=6)
>> > for (i in 1:nrow(p)) {
>> > plot.spdf(p[i, 1], p[i, 2], p[i, 3], p[i, 4], p[i, 5], p[i, 6])
>> > readline("press Enter to continue")
>> > }
>> >
>> > If you use pdf() for sending the graphics to a file, then remove
>> > the "readline" command.
>> >
>> > Hope this helps.
>> >
>> > Petr Savicky.
>> >
>> > ______________________________________________
>> > [hidden email] 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.
>> >
>> > ______________________________________________
>> > [hidden email] 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.
>>
>> ______________________________________________
>> [hidden email] 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.