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Patch fix for long formula names #152

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Patch fix for long formula names #152

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257ac74
Patch fix for long formula names
jwallib Jul 7, 2021
667d647
Move patch to noweb and make all
jwallib Jul 8, 2021
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10 changes: 8 additions & 2 deletions R/coxph.R
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,10 @@ coxph <- function(formula, data, weights, subset, na.action,
terms(formula[[1]], specials=ss, data=data)
else Terms <- if (missing(data)) terms(formula, specials=ss) else
terms(formula, specials=ss, data=data)

attr(Terms,'term.labels') = gsub('\n',' ', attr(Terms,'term.labels'))
colnames(attr(Terms,'factors')) = gsub('\n',' ', colnames(attr(Terms,'factors')))
rownames(attr(Terms,'factors')) = gsub('\n',' ', rownames(attr(Terms,'factors')))

tcl <- attr(Terms, 'specials')$cluster
if (length(tcl) > 1) stop("a formula cannot have multiple cluster terms")

Expand Down Expand Up @@ -127,7 +130,10 @@ coxph <- function(formula, data, weights, subset, na.action,
# okay, now evaluate the formula
mf <- eval(tform, parent.frame())
Terms <- terms(mf)

attr(Terms,'term.labels') = gsub('\n',' ', attr(Terms,'term.labels'))
colnames(attr(Terms,'factors')) = gsub('\n',' ', colnames(attr(Terms,'factors')))
rownames(attr(Terms,'factors')) = gsub('\n',' ', rownames(attr(Terms,'factors')))

# Grab the response variable, and deal with Surv2 objects
n <- nrow(mf)
Y <- model.response(mf)
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35 changes: 35 additions & 0 deletions noweb/code.aux
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@@ -0,0 +1,35 @@
\relax
\providecommand\hyper@newdestlabel[2]{}
\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
\global\let\oldcontentsline\contentsline
\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
\global\let\oldnewlabel\newlabel
\gdef\newlabel#1#2{\newlabelxx{#1}#2}
\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
\AtEndDocument{\ifx\hyper@anchor\@undefined
\let\contentsline\oldcontentsline
\let\newlabel\oldnewlabel
\fi}
\fi}
\global\let\hyper@last\relax
\gdef\HyperFirstAtBeginDocument#1{#1}
\providecommand\HyField@AuxAddToFields[1]{}
\providecommand\HyField@AuxAddToCoFields[2]{}
\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{1}{section.1}}
\@writefile{toc}{\contentsline {section}{\numberline {2}Cox Models}{2}{section.2}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Coxph}{2}{subsection.2.1}}
\citation{Gail81}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2}Exact partial likelihood}{28}{subsection.2.2}}
\newlabel{d0}{{1}{29}{Exact partial likelihood}{equation.2.1}{}}
\newlabel{d1}{{2}{29}{Exact partial likelihood}{equation.2.2}{}}
\newlabel{d2}{{3}{29}{Exact partial likelihood}{equation.2.3}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.3}Andersen-Gill fits}{38}{subsection.2.3}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.4}Predicted survival}{57}{subsection.2.4}}
\@writefile{toc}{\contentsline {subsubsection}{\numberline {2.4.1}Multi-state models}{80}{subsubsection.2.4.1}}
\@writefile{toc}{\contentsline {section}{\numberline {3}The Fine-Gray model}{87}{section.3}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}The predict method}{93}{subsection.3.1}}
\newlabel{eq:eta}{{7}{100}{The predict method}{equation.3.7}{}}
\@writefile{toc}{\contentsline {section}{\numberline {4}Concordance}{104}{section.4}}
\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Main routine}{104}{subsection.4.1}}
\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Methods}{112}{subsection.4.2}}
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