[R] Hint improve my code
Joshua Wiley
jwiley.psych at gmail.com
Sun Jul 3 07:24:01 CEST 2011
Hi Edward,
One hint to improve your code is simply stylistic. Everyone tends to
have their own favorite way, but adding spaces and line breaks can
help make code much easier to read. Also, you seemed to have used
brackets "[" instead of parentheses "(" for the first two calls to
sum(). As Berend suggested, some more clarification on what is
supposed to be happening will help you get more feedback. Lastly,
although your data is readable as is, a very convenient way to provide
the list with data is using the function, dput(). Here is a little
example demonstrating its use:
> x <- data.frame(x1 = c("c", "b", "a"),
+ x2 = factor(c("c", "b", "a")), stringsAsFactors = FALSE)
> x ## print to console, two columns appear identical
x1 x2
1 c c
2 b b
3 a a
> ## but looking at the str()ucture, they are different
> str(x)
'data.frame': 3 obs. of 2 variables:
$ x1: chr "c" "b" "a"
$ x2: Factor w/ 3 levels "a","b","c": 3 2 1
> ## use dput() to provide copy-and-pastable output
> ## that others can use to access the same data as you easy peasy
> dput(x)
structure(list(x1 = c("c", "b", "a"), x2 = structure(c(3L, 2L,
1L), .Label = c("a", "b", "c"), class = "factor")), .Names = c("x1",
"x2"), row.names = c(NA, -3L), class = "data.frame")
>
> ## now someone else is ready to go with your data
> newx <- structure(list(x1 = c("c", "b", "a"), x2 = structure(c(3L, 2L,
+ 1L), .Label = c("a", "b", "c"), class = "factor")), .Names = c("x1",
+ "x2"), row.names = c(NA, -3L), class = "data.frame")
>
> str(newx)
'data.frame': 3 obs. of 2 variables:
$ x1: chr "c" "b" "a"
$ x2: Factor w/ 3 levels "a","b","c": 3 2 1
>
And here is an example of how I might have written your function
(stylistically speaking). I am not advocating this as the "best",
"correct", or "ideal", way. Just giving another example that (I at
least) find easier to read and make sense of.
llik <- function(R_j, R_m) {
if (R_j < 0) {
sum(log(1 / (2 * pi * (sigma_j^2))) -
(1 / (2 * (sigma_j^2))*(R_j + al_j - b_j * R_m))^2)
} else if (R_j > 0) {
sum(log(1 / (2 * pi * (sigma_j^2))) -
(1 / (2 * (sigma_j^2)) * (R_j + au_j - b_j * R_m))^2)
} else if (R_j == 0) {
sum(log(pnorm(au_j, mean = b_j * R_m, sd = sigma_j) -
pnorm(al_j, mean = b_j * R_m, sd = sigma_j)))
}
}
Cheers,
Josh
On Sat, Jul 2, 2011 at 5:52 PM, EdBo <n.bowora at gmail.com> wrote:
> Hi
>
> I have developed the code below. I am worried that the parameters I want to
> be estimated are "not being found" when I ran my code. Is there a way I can
> code them so that R recognize that they should be estimated.
>
> This is the error I am getting.
>
>> out1=optim(llik,par=start.par)
> Error in pnorm(au_j, mean = b_j * R_m, sd = sigma_j) :
> object 'au_j' not found
>
> #Yet al_j,au_j,sigma_j and b_j are just estimates that balance the
> likelihood function?
>
> llik=function(R_j,R_m)
> if(R_j< 0)
> {
> sum[log(1/(2*pi*(sigma_j^2)))-(1/(2*(sigma_j^2))*(R_j+al_j-b_j*R_m))^2]
> }else if(R_j>0)
> {
> sum[log(1/(2*pi*(sigma_j^2)))-(1/(2*(sigma_j^2))*(R_j+au_j-b_j*R_m))^2]
> }else if(R_j==0)
> {
> sum(log(pnorm(au_j,mean=b_j*R_m,sd=sigma_j)-pnorm(al_j,mean=b_j*R_m,sd=sigma_j)))
> }
> start.par=c(al_j=0,au_j=0,sigma_j=0.01,b_j=1)
> out1=optim(par=start.par,llik)
>
> My Data
>
> R_j R_m
> 2e-03 0.026567295
> 3e-03 0.009798475
> 5e-02 0.008497274
> -1e-02 0.012464578
> -9e-04 0.002896023
> 9e-02 0.000879473
> 1e-02 0.003194435
> 6e-04 0.010281122
>
> Thank you in advance.
>
> Edward
> UCT
>
> --
> View this message in context: http://r.789695.n4.nabble.com/Hint-improve-my-code-tp3641354p3641354.html
> Sent from the R help mailing list archive at Nabble.com.
>
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> and provide commented, minimal, self-contained, reproducible code.
>
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
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