Re: [R] Probit Analysis

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From: apjaworski@mmm.com
Date: Wed 01 Jan 2003 - 11:36:51 EST

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Message-id: <OFF6F29251.377B5E75-ON86256CA1.0000B093@mmm.com>

Jacquelin,

Here is an answer to your question wrapped in much longer question of my
own.

Cheers,

Andy

-----------------------------------------------------------------------------------------

Extracting components from complex objects is, in my opinion, not easy to
do unless I am missing something very obvious. Take the glm.dose object as
an example. Following the example on the dose.p help page I ran

zz <- dose.p(budworm.lg0, cf = c(1,3), p = 1:3/4)

Typing zz applies print method to the zz object and shows

                          Dose SE
      p = 0.25: 2.231264 0.2498235
      p = 0.50: 3.263587 0.2297039
      p = 0.75: 4.295910 0.2746190

If I now want to extract some of the numbers from zz, I have to go through
some hoops. What I usually do first is

str(zz)

This gives me

      Class 'glm.dose' atomic [1:3] 2.23 3.26 4.30
        ..- attr(*, "SE")= num [1:3, 1] 0.250 0.230 0.275
        .. ..- attr(*, "dimnames")=List of 2
       .. .. ..$ : chr [1:3] "p = 0.25:" "p = 0.50:" "p = 0.75:"
        .. .. ..$ : NULL
        ..- attr(*, "p")= num [1:3] 0.25 0.5 0.75

The format of this output is not really described on the str help page, so
I am guessing that what this means is that the "basic" object is a vector
of length 3 with a couple of attributes called SE and p, the SE attribute
having additional nested attribute called dimnames. We can onfirm that by

attributes(zz)

giving

$names
[1] "p = 0.25:" "p = 0.50:" "p = 0.75:"

$SE

                   [,1]
       p = 0.25: 0.2498235
       p = 0.50: 0.2297039
       p = 0.75: 0.2746190

$p
[1] 0.25 0.50 0.75

$class
[1] "glm.dose"

So, If I want to extract the actual dose value from zz I just need

zz[1]

geting

p = 0.25:
2.231264

but if I want to get the first standard error I have to do

attributes(zz)$SE[1]

getting

p = 0.25:
0.2498235

Is this a correct general method of extracting components from complex
objects? Is there a simpler way?

Thanks in advance and sorry for this longish post, but this is something I
have been having problems with for a long time and it seems that every time
I run into this "extraction problem" I have to reinvent the wheel.

Andy

__________________________________
Andy Jaworski
Engineering Systems Technology Center
3M Center, 518-1-01
St. Paul, MN 55144-1000
-----
E-mail: apjaworski@mmm.com
Tel: (651) 733-6092
Fax: (651) 736-3122

|---------+---------------------------------->
| | "Ngayee J Law" |
| | <Ngayee.Law@celeradiagn|
| | ostics.com> |
| | |
| | 12/31/2002 17:18 |
| | |
|---------+---------------------------------->
>-----------------------------------------------------------------------------------------------------------------------------|
  | |
  | To: apjaworski@mmm.com |
  | cc: r-help@stat.math.ethz.ch |
  | Subject: Re: [R] Probit Analysis |
>-----------------------------------------------------------------------------------------------------------------------------|

Hi Andy,

Thanks! glm and dose.p can do exaclty what I want to do. Just a quick
question,
how can I extract the numbers in the glm.dose object created by the dose.p?
My
goal is to calculate a 95% CI for the 'LD50'.

- Jacqueline

apjaworski@mm

m.com To: "Ngayee J Law"
<Ngayee.Law@celeradiagnostics.com>
cc: r-help@stat.math.ethz.ch

12/31/2002 Subject: Re: [R] Probit
Analysis
02:47 PM

Jacqueline,

This should be a simple application of GLM. Check the help pages for glm,
family and dose.p in library MASS. Look at the example at the bottom of
the dose.p help page - it does almost exactly what you need.

Hope this helps,

Andy

|---------+---------------------------------->
| | "Ngayee J Law" |
| | <Ngayee.Law@celeradiagn|
| | ostics.com> |
| | Sent by: |
| | r-help-admin@stat.math.|
| | ethz.ch |
| | |
| | |
| | 12/31/2002 16:17 |
| | |
|---------+---------------------------------->
>
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  |
|
  | To: r-help@stat.math.ethz.ch
|
  | cc:
|
  | Subject: [R] Probit Analysis
|
>
-----------------------------------------------------------------------------------------------------------------------------|

Hello all,

I have a very simple set of data and I would like to analyze them with
probit analysis.
The data are:

X Event Trial
100 8 8
75 8 8
50 6 8
25 4 8
10 2 8
0 0 8

I want to estimate the value of X that will give a 95% hit rate
(Event/Trial) and the corresponding
95% CI. Anyone can offer some help? Thanks!!

- Jacqueline

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Next message: Frank E Harrell Jr: "[R] Updates to Hmisc and Design Libraries"
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