predab.resample: handled case where fitter doesn't include fail=FALSE

harrelfe · Apr 8, 2018 · 6bcaee4 · 6bcaee4
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Showing 4 changed files with 7 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rms
 Version: 5.1-3
-Date: 2018-04-07
+Date: 2018-04-08
 Title: Regression Modeling Strategies
 Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
 Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>

diff --git a/NEWS b/NEWS
@@ -1,11 +1,12 @@
-Changes in version 5.1-3 (2018-04-07)
+Changes in version 5.1-3 (2018-04-08)
    * lrm: when lrm.fit fails, don't stop altogether but print warning and return fit with fail=TRUE
    * summary.orm: stopped negating linear predictor before computing hazard ratio for orm fit with log-log family (confidence limits never attempted to do this).  See https://github.com/harrelfe/rms/issues/56
    * Design: stop with error message any any design matrix column name is duplicated as with a predictor X1 with factor level 2 (forming name X12 in model.matrix) and a numeric predictor named X12.  See https://github.com/harrelfe/rms/issues/55
    * contrast.rms: for conf.type='simultaneous' shortened fit$coefficients to only have one intercept so will work with multcomp::glht.  Thanks: Matthew Shun-Shin
    * orm: changed label for Unique Y to Distinct Y
    * survplotp: fixed bug in legends
-
+   * predab.resample: handled case where fitter doesn't include fail=FALSE
+
 Changes in version 5.1-2 (2018-01-06)
    * plot.pentrace: corrected lty for AIC if ! add, interchanged lty for AIC and BIC.  Thanks: Ferenci Tamas
    * removeFormulaTerms: added width.cutoff=500 to deparse call to avoid problems with long variable names.  Thanks: Ferenci Tamas

diff --git a/R/predab.resample.s b/R/predab.resample.s
@@ -280,6 +280,7 @@ predab.resample <-
     }
     f <- tryCatch(fit(x[xtrain, , drop=FALSE], y[train, , drop=FALSE],
                       strata=stra[train], iter=i, tol=tol, ...), error=efit)
+    if(! length(f$fail)) f$fail <- FALSE
     f$assign <- NULL  #Some programs put a NULL assign (e.g. ols.val fit)
     ni <- num.intercepts(f)
 
@@ -328,7 +329,7 @@ predab.resample <-
                             iter=i, tol=tol, xcol=xcol, ...), error=efit)
         }
 
-        if(f$fail) fail <- TRUE
+        if(length(f$fail) && f$fail) fail <- TRUE
         else coef <- f$coef
       }
     }

diff --git a/inst/tests/examples.Rmd b/inst/tests/examples.Rmd
@@ -88,7 +88,7 @@ plot(nomogram(f, fun=plogis, funlabel='Prob(survive)'))
 ```
 
 # Survival Plots for `r mu$code('pbc')` Dataset
-Hover over the curves to see particular probability estimates and numbers at risk.  click on legend components to show/hide components.
+Hover over the curves to see particular probability estimates and numbers at risk.  Click on legend components to show/hide components.
 ```{r pbc,fig.height=6,fig.width=7}
 getHdata(pbc)
 pbc <- upData(pbc,