R help - Jun 2010 - Documentation of B-spline function

Goodmorning, 
 
This is a documentation related question about the B-spline function in R. 
In the help file it is stated that: 
 
"df  degrees of freedom; one can specify df rather than knots; bs() then
chooses df-degree-1 knots at suitable quantiles of x (which will ignore missing
values)."
 
So if one were to specify a spline with 6 degrees of freedom (and no intercept)
then a basis with 6-3-1 =2  internal knots should be created. However this is
not what happens:
 
> library(splines)
> s1<-bs(women$height, df = 6,deg=3)
> s2<-bs(women$height, df = 6,deg=2)
> 
> attributes(s1)$knots
 25%  50%  75% 
61.5 65.0 68.5 
> attributes(s2)$knots
 20%  40%  60%  80% 
60.8 63.6 66.4 69.2 
> 
 
i.e. basis is created with an extra knot i.e. bs() chooses df-degree internal
knots
 
The documentation of "ns" states that: " .... ns() then chooses
df - 1 - intercept knots ..." suggesting that the spline functions create
the basis with df-degree internal knots if no intercept is specified but
df-degree-1 internal knots if the caller explicitly asks for an intercept.
 
> s1<-bs(women$height, df = 6,deg=3,intercept=T)
> s2<-bs(women$height, df = 6,deg=2,intercept=T)
> 
> attributes(s1)$knots
33.33333% 66.66667% 
 62.66667  67.33333 
> attributes(s2)$knots
 25%  50%  75% 
61.5 65.0 68.5 
 
 
Is it possible to change the documentation of these functions to reflect their
actual behaviour. For example something like the following:
"df  degrees of freedom; one can specify df rather than knots; bs() then
chooses df-degree-1 knots at suitable quantiles of x (which will ignore missing
values) if the intercept argument is TRUE and df-degree if
intercept=FALSE."
 
 
Christos Argyropoulos
  		 	   		  
_________________________________________________________________
Hotmail: Trusted email with Microsoft?s powerful SPAM protection.

On Fri, 11 Jun 2010, Christos Argyropoulos wrote:
>
> Goodmorning,
>
> This is a documentation related question about the B-spline function in R.
> In the help file it is stated that:
>
> "df degrees of freedom; one can specify df rather than knots; bs()
then
> chooses df-degree-1 knots at suitable quantiles of x (which will ignore 
> missing values)."
Not in R 2.11.1 where help("bs") says:

df	   degrees of freedom; one can specify df rather than knots; bs()
            then chooses df-degree (minus one if there is an intercept)
            knots at suitable quantiles of x (which will ignore missing
            values).
>
> So if one were to specify a spline with 6 degrees of freedom (and no
intercept) then a basis with 6-3-1 =2  internal knots should be created. However
this is not what happens:
>
>> library(splines)
>> s1<-bs(women$height, df = 6,deg=3)
>> s2<-bs(women$height, df = 6,deg=2)
>>
>> attributes(s1)$knots
> 25%  50%  75%
> 61.5 65.0 68.5
>> attributes(s2)$knots
> 20%  40%  60%  80%
> 60.8 63.6 66.4 69.2
>>
>
> i.e. basis is created with an extra knot i.e. bs() chooses df-degree
internal knots
>
> The documentation of "ns" states that: " .... ns() then
chooses df - 1 -
> intercept knots ..." suggesting that the spline functions create the 
> basis with df-degree internal knots if no intercept is specified but 
> df-degree-1 internal knots if the caller explicitly asks for an 
> intercept.

If you  knew that 1 - TRUE == 0, then you know that is what it says.
>
>> s1<-bs(women$height, df = 6,deg=3,intercept=T)
>> s2<-bs(women$height, df = 6,deg=2,intercept=T)
>>
>> attributes(s1)$knots
> 33.33333% 66.66667%
> 62.66667  67.33333
>> attributes(s2)$knots
> 25%  50%  75%
> 61.5 65.0 68.5
>
>
> Is it possible to change the documentation of these functions to reflect 
> their actual behaviour. For example something like the following: "df 
> degrees of freedom; one can specify df rather than knots; bs() then 
> chooses df-degree-1 knots at suitable quantiles of x (which will ignore 
> missing values) if the intercept argument is TRUE and df-degree if 
> intercept=FALSE."
R-devel is where you post stuff like this, but be sure to refer to current 
versions to avoid being flamed for non-compliance with posting guidelines.

HTH,

Chuck


>
>
> Christos Argyropoulos
>
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>
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>
Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901