[R] Specifying interactions in rms package... error

[Frank Harrell]

Hi Rob,

rms wants symmetry in the sense that the interactions need to use the 
same number and location of spline knots as the main effects.   So if 
using the * notation omit the main effects (which are generated 
automatically) and live with the equal knots.  Or use the restricted 
interaction operator %ia% to not use doubly nonlinear terms in forming 
the interactions, which is a sensible restriction.
Frank

Frank E Harrell Jr   Professor and Chairman        School of Medicine
                      Department of Biostatistics   Vanderbilt University

On Mon, 2 Aug 2010, Rob James wrote:

> I am encountering an error I do not know how to debug. The error arises
> when I try to add an  interaction term involving two continuous
> variables (defined using rcs functions) to an existing (and working) model.
>
> The new model reads:
>
>  model5 <- lrm( B_fainting ~   gender+  rcs(exactage, 7) +
> rcs(DW_nadler_bv, 7) +           rcs(drawtimefrom8am, 7)+  DW_firsttime+
>   DW_race_eth +
>  rcs(DW_BPS, 5)+  rcs(DW_BPD, 5)+  rcs(pulse3, 5)+  locat2+
> (rcs(exactage, 3) * rcs(drawtimefrom8am, 3))
>   )
>
> This gives rise to the following error:
>
> ----
> Error in dimnames(X)[[2]] <- atr$colnames :
>   length of 'dimnames' [2] not equal to array extent
> In addition: Warning message:
> In names(nmiss)[jz] <- fname[asm != 9] :
>   number of items to replace is not a multiple of replacement length
> ----
>
> The sessionInfo() output is below, but I think relatively unremarkable.
> The dataset is very large (about 550K observations, although the outcome
> (B_fainting)  is relatively sparse with only 1500 events in this
> sample.   I do not get this error when the interaction term is replaced
> by two categorical variables (data not shown).  I can replicate this
> error when there is just one continuous variable and one categorical
> variable.
>
>
> I'd welcome suggestions. Thank you in advance.
>
>
>
>
>
> sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
> LC_TIME=en_CA.UTF-8
>  [4] LC_COLLATE=en_CA.UTF-8     LC_MONETARY=C
> LC_MESSAGES=en_CA.UTF-8
>  [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                  LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
> [1] gmodels_2.15.0  rms_3.0-0       Hmisc_3.8-2     survival_2.35-8
> odfWeave_0.7.14 XML_3.1-0
> [7] lattice_0.18-8
>
> loaded via a namespace (and not attached):
> [1] cluster_1.13.1 gdata_2.8.0    grid_2.11.0    gtools_2.6.2   MASS_7.3-7
>
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