Closed swihart closed 7 years ago
I add to NAMESPACE and rerun.
importFrom("grDevices", "gray")
importFrom("graphics", "hist", "lines", "par", "plot", "text")
importFrom("stats", "dcauchy", "dgamma", "dlnorm", "dlogis", "dnorm",
"glm", "model.frame", "na.fail", "nlm", "pbeta", "pcauchy",
"pgamma", "plnorm", "plogis", "pnorm", "poisson",
"pweibull", "qnorm", "terms")
Output (tail end):
hgamma: warning in pgamma(y, shape, scale = scale, lower = FALSE, log =
TRUE): partial argument match of 'lower' to 'lower.tail'
hgamma: warning in pgamma(y, shape, scale = scale, lower = FALSE, log =
TRUE): partial argument match of 'log' to 'log.p'
kalsurv : sh1: no visible binding for global variable ‘npl1’
Undefined global functions or variables:
npl1
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 7 warnings | 2 notes
R CMD check succeeded
hgamma
: easy fix. change lower to lower.tail; change log to log.pkalsurv
: a little harder. assume npl1 is npl+1.Rerun, tail end of output;
checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 7 warnings | 2 notes
R CMD check succeeded
survkit.R
.Rerun, tail end of output:
DUP is no longer supported and will be ignored.
R CMD check results
1 error | 7 warnings | 1 note
swihartbj:~/github/event$ find ./R -type f -print0 | xargs -0 grep -l 'DUP'
./R/kalsurv.r
./R/survkit.r
Rerun, tail end of output:
S3 methods shown with full name in documentation object 'km':
‘plot.km’ ‘plot.intensity.km’ ‘plot.dist.km’
S3 methods shown with full name in documentation object 'plot.intensity': ‘plot.intensity’ ‘plot.intensity.default’
The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
See ‘/Users/swihartbj/github/event.Rcheck/00check.log’ for details.
R CMD check results 1 error | 7 warnings | 0 notes
R CMD check succeeded
km.Rd
to\method{plot}{km}(z, add=FALSE, xlim, ylim=c(0,1), main=NULL, xlab="Time", ylab=NULL, lty=NULL, ...)
\method{plot.intensity}{km}(z, add=FALSE, xlab="Time", ylab="Intensity", type="l", lty=NULL, ...)
\method{plot.dist}{km}(z)
plot.intensity.Rd
to
\method{plot}{intensity}(z, ...)
\method{plot.intensity}{default}(times, censor=1, group=1, colour=TRUE, mix=1,
ylim=c(0,1), ylab="p", xlab="Time",
main="Empirical Intensity Function(s)")
Rerun, tail end of output:
checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'autointensity' ‘ylab’ ‘xlab’ ‘main’ ‘xlim’ ‘ylim’ ‘lty’ ‘...’ Documented arguments not in \usage in documentation object 'autointensity': ‘others’ Objects in \usage without \alias in documentation object 'autointensity': ‘autointensity’
Undocumented arguments in documentation object 'coxre' ‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘iterlim’ ‘fscale’ ... 35 lines ...
Undocumented arguments in documentation object 'pp' ‘censor’ Documented arguments not in \usage in documentation object 'pp': ‘cens’
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. R CMD check results 1 error | 7 warnings | 0 notes
R CMD check succeeded
Not going to lie, this part of the output above was introduced because of the edits, makes me nervous:
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
If push comes to shove, take things out of usage. Or, toggle what goes in the \method{}{}, e.g., is it \method{plot.intensity}{default} or \method{plot}{intensity.default} ? And or need to edit NAMESPACE, something similar to that of `rmutil` (which also forewent roxygen workflow):
S3method(finterp, data.frame) S3method(finterp, default) S3method(finterp, repeated) S3method(finterp, tccov) S3method(finterp, tvcov)
\item{ylab}{Plotting control options.}
\item{xlab}{Plotting control options.}
\item{main}{Plotting control options.}
\item{xlim}{Plotting control options.}
\item{ylim}{Plotting control options.}
\item{lty}{Plotting control options.}
\item{...}{Plotting control options.}
and right below usage (line 10) add:
\alias{autointensity}
take out
\item{others}{Plotting control options.}
Rerun, tail end of output:
checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'coxre'
‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘iterlim’ ‘fscale’
‘typsiz’ ‘stepmax’
Documented arguments not in \usage in documentation object 'coxre':
‘others’
Undocumented arguments in documentation object 'cprocess'
‘lty’ ‘xlim’ ‘ylim’ ‘xlab’ ‘ylab’ ‘...’
Documented arguments not in \usage in documentation object 'cprocess':
... 28 lines ...
Undocumented arguments in documentation object 'pp'
‘censor’
Documented arguments not in \usage in documentation object 'pp':
‘cens’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 7 warnings | 0 notes
R CMD check succeeded
\item{print.level}{\code{nlm} control options.}
\item{ndigit}{\code{nlm} control options.}
\item{gradtol}{\code{nlm} control options.}
\item{steptol}{\code{nlm} control options.}
\item{iterlim}{\code{nlm} control options.}
\item{fscale}{\code{nlm} control options.}
\item{typsiz}{\code{nlm} control options.}
\item{stepmax}{\code{nlm} control options.}
take out
\item{others}{Plotting control options.}
Rerun, tail end of output:
checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'cprocess'
‘lty’ ‘xlim’ ‘ylim’ ‘xlab’ ‘ylab’ ‘...’
Documented arguments not in \usage in documentation object 'cprocess':
‘others’
Undocumented arguments in documentation object 'ehr'
‘print.level’ ‘typsiz’ ‘ndigit’ ‘gradtol’ ‘iterlim’ ‘fscale’
‘stepmax’ ‘steptol’
Documented arguments not in \usage in documentation object 'ehr':
... 22 lines ...
Undocumented arguments in documentation object 'pp'
‘censor’
Documented arguments not in \usage in documentation object 'pp':
‘cens’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 7 warnings | 0 notes
R CMD check succeeded
\item{ylab}{Plotting control options.}
\item{xlab}{Plotting control options.}
\item{xlim}{Plotting control options.}
\item{ylim}{Plotting control options.}
\item{lty}{Plotting control options.}
\item{...}{Plotting control options.}
take out
\item{others}{Plotting control options.}
Rerun, tail end of output:
checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'ehr'
‘print.level’ ‘typsiz’ ‘ndigit’ ‘gradtol’ ‘iterlim’ ‘fscale’
‘stepmax’ ‘steptol’
Documented arguments not in \usage in documentation object 'ehr':
‘others’
Undocumented arguments in documentation object 'kalsurv'
‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘iterlim’ ‘fscale’
‘typsiz’ ‘stepmax’
... 17 lines ...
Undocumented arguments in documentation object 'pp'
‘censor’
Documented arguments not in \usage in documentation object 'pp':
‘cens’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
R CMD check results
1 error | 7 warnings | 0 notes
R CMD check succeeded
\item{print.level}{\code{nlm} control options.}
\item{ndigit}{\code{nlm} control options.}
\item{gradtol}{\code{nlm} control options.}
\item{steptol}{\code{nlm} control options.}
\item{iterlim}{\code{nlm} control options.}
\item{fscale}{\code{nlm} control options.}
\item{typsiz}{\code{nlm} control options.}
\item{stepmax}{\code{nlm} control options.}
take out
\item{others}{Plotting control options.}
Rerun, tail end of output:
checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'kalsurv'
‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘iterlim’ ‘fscale’
‘typsiz’ ‘stepmax’
Documented arguments not in \usage in documentation object 'kalsurv':
‘others’
Undocumented arguments in documentation object 'km'
‘add’ ‘xlim’ ‘ylim’ ‘main’ ‘xlab’ ‘ylab’ ‘lty’ ‘...’ ‘type’
... 11 lines ...
Undocumented arguments in documentation object 'pp'
‘censor’
Documented arguments not in \usage in documentation object 'pp':
‘cens’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 7 warnings | 0 notes
R CMD check succeeded
\item{print.level}{\code{nlm} control options.}
\item{ndigit}{\code{nlm} control options.}
\item{gradtol}{\code{nlm} control options.}
\item{steptol}{\code{nlm} control options.}
\item{iterlim}{\code{nlm} control options.}
\item{fscale}{\code{nlm} control options.}
\item{typsiz}{\code{nlm} control options.}
\item{stepmax}{\code{nlm} control options.}
take out
\item{others}{Plotting control options.}
Rerun, tail end of output:
checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'km'
‘add’ ‘xlim’ ‘ylim’ ‘main’ ‘xlab’ ‘ylab’ ‘lty’ ‘...’ ‘type’
Undocumented arguments in documentation object 'pbirth'
‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘fscale’ ‘iterlim’
‘typsiz’ ‘stepmax’
Documented arguments not in \usage in documentation object 'pbirth':
‘others’
Undocumented arguments in documentation object 'plot.intensity'
‘z’ ‘...’ ‘mix’ ‘ylim’ ‘ylab’ ‘xlab’ ‘main’
Objects in \usage without \alias in documentation object 'plot.intensity':
‘plot.intensity.default’
Undocumented arguments in documentation object 'pp'
‘censor’
Documented arguments not in \usage in documentation object 'pp':
‘cens’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 7 warnings | 0 notes
R CMD check succeeded
\item{add}{Plotting control options.}
\item{main}{Plotting control options.}
\item{type}{Plotting control options.}
\item{ylab}{Plotting control options.}
\item{xlab}{Plotting control options.}
\item{xlim}{Plotting control options.}
\item{ylim}{Plotting control options.}
\item{lty}{Plotting control options.}
\item{...}{Plotting control options.}
Rerun, tail end of output:
checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'pbirth'
‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘fscale’ ‘iterlim’
‘typsiz’ ‘stepmax’
Documented arguments not in \usage in documentation object 'pbirth':
‘others’
Undocumented arguments in documentation object 'plot.intensity'
‘z’ ‘...’ ‘mix’ ‘ylim’ ‘ylab’ ‘xlab’ ‘main’
Objects in \usage without \alias in documentation object 'plot.intensity':
‘plot.intensity.default’
Undocumented arguments in documentation object 'pp'
‘censor’
Documented arguments not in \usage in documentation object 'pp':
‘cens’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 7 warnings | 0 notes
R CMD check succeeded
\item{print.level}{\code{nlm} control options.}
\item{ndigit}{\code{nlm} control options.}
\item{gradtol}{\code{nlm} control options.}
\item{steptol}{\code{nlm} control options.}
\item{iterlim}{\code{nlm} control options.}
\item{fscale}{\code{nlm} control options.}
\item{typsiz}{\code{nlm} control options.}
\item{stepmax}{\code{nlm} control options.}
take out
\item{others}{Plotting control options.}
Rerun, tail end of output:
checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'plot.intensity'
‘z’ ‘...’ ‘mix’ ‘ylim’ ‘ylab’ ‘xlab’ ‘main’
Objects in \usage without \alias in documentation object 'plot.intensity':
‘plot.intensity.default’
Undocumented arguments in documentation object 'pp'
‘censor’
Documented arguments not in \usage in documentation object 'pp':
‘cens’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 7 warnings | 0 notes
R CMD check succeeded
\alias{plot.intensity.default}
\item{z}{An object produced by \code{km}.}
\item{mix}{...}
\item{main}{Plotting control options.}
\item{ylab}{Plotting control options.}
\item{xlab}{Plotting control options.}
\item{ylim}{Plotting control options.}
\item{...}{Plotting control options.}
Rerun, tail end of output:
checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'pp'
‘censor’
Documented arguments not in \usage in documentation object 'pp':
‘cens’
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
See ‘/Users/swihartbj/github/event.Rcheck/00check.log’ for details.
R CMD check results 1 error | 7 warnings | 0 notes
R CMD check succeeded
in pp.Rd, change
\item{cens}{Vector of censoring indicators.}
to
\item{censor}{Vector of censoring indicators.}
Rerun, tail end of output:
checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'autointensity':
autointensity
Code: function(times, window = NULL, maxlag = max(times), ylab =
"Conditional probability", xlab = "Lag", main =
"Autointensity function", xlim = c(0, max(times)),
ylim = c(0, if (plotse) max(se1) else max(z$density)),
lty = 1, plot = TRUE, plotse = TRUE, add = FALSE, ...)
Docs: function(times, window = NULL, maxlag = total/10, ylab =
"Conditional probability", xlab = "Lag", main =
... 105 lines ...
Codoc mismatches from documentation object 'plot.intensity':
plot.intensity.default
Code: function(times, censor = 1, group = 1, colour = TRUE, mix = 1,
ylim = c(0, 1), ylab = "p", xlab = "Time", main =
"Empirical Hazard Function(s)")
Docs: function(times, censor = 1, group = 1, colour = TRUE, mix = 1,
ylim = c(0, 1), ylab = "p", xlab = "Time", main =
"Empirical Intensity Function(s)")
Mismatches in argument default values:
Name: 'main' Code: "Empirical Hazard Function(s)" Docs: "Empirical Intensity Function(s)"
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 6 warnings | 0 notes
R CMD check succeeded
WE have eliminated a warning! On to these:
checking for code/documentation mismatches ... WARNING
plot.intensity.Rd
change
"Empirical Intensity Function(s)"
to
"Empirical Hazard Function(s)"
Rerun, tail end of output:
Codoc mismatches from documentation object 'pbirth':
pbirth
Code: function(frequencies, p, intensity = "negative binomial", type
= "spectral decomposition", print.level = 0, ndigit =
10, gradtol = 1e-05, steptol = 1e-05, fscale = 1,
iterlim = 100, typsize = abs(p), stepmax = 10 * sqrt(p
%*% p))
Docs: function(frequencies, p, intensity = "negative binomial", type
= "spectral decomposition", print.level = 0, ndigit =
10, gradtol = 1e-05, steptol = 1e-05, fscale = 1,
iterlim = 100, typsiz = abs(p), stepmax = 10 * sqrt(p
%*% p))
Argument names in code not in docs:
typsize
Argument names in docs not in code:
typsiz
Mismatches in argument names:
Position: 11 Code: typsize Docs: typsiz
Rerun, tail end of output:
Codoc mismatches from documentation object 'km':
plot.intensity.km
Code: function(z, add = FALSE, xlab = "Time", ylab = "Hazard", type =
"l", lty = NULL, ...)
Docs: function(z, add = FALSE, xlab = "Time", ylab = "Intensity",
type = "l", lty = NULL, ...)
Mismatches in argument default values:
Name: 'ylab' Code: "Hazard" Docs: "Intensity"
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 6 warnings | 0 notes
R CMD check succeeded
km.Rd
change ylab = "Intensity",
to ylab = "Hazard",
Rerun, tail end of output:
Codoc mismatches from documentation object 'kalsurv':
kalsurv
Code: function(response = NULL, intensity = "exponential",
distribution = "Pareto", depend = "independence",
update = "Markov", mu = NULL, shape = NULL, renewal =
TRUE, density = FALSE, censor = NULL, delta = NULL,
ccov = NULL, tvcov = NULL, preg = NULL, ptvc = NULL,
pbirth = NULL, pintercept = NULL, pshape = NULL,
pinitial = 1, pdepend = NULL, pfamily = NULL, envir =
parent.frame(), print.level = 0, ndigit = 10, gradtol
= 1e-05, steptol = 1e-05, iterlim = 100, fscale = 1,
typsize = abs(p), stepmax = 10 * sqrt(p %*% p))
Docs: function(response, intensity = "exponential", distribution =
"Pareto", depend = "independence", update = "Markov",
mu = NULL, shape = NULL, renewal = TRUE, density =
FALSE, censor = NULL, delta = NULL, ccov = NULL, tvcov
= NULL, preg = 1, ptvc = NULL, pbirth = NULL,
pintercept = NULL, pshape = NULL, pinitial = 1,
pdepend = NULL, pfamily = NULL, envir =
parent.frame(), print.level = 0, ndigit = 10, gradtol
= 1e-05, steptol = 1e-05, iterlim = 100, fscale = 1,
typsiz = abs(p), stepmax = 10 * sqrt(p %*% p))
Argument names in code not in docs:
typsize
Argument names in docs not in code:
typsiz
Mismatches in argument names:
Position: 29 Code: typsize Docs: typsiz
Mismatches in argument default values:
Name: 'response' Code: NULL Docs:
Name: 'preg' Code: NULL Docs: 1
kalsurv.Rd
and kalsurv.R
, fix the typo typsiz
and then make the default values for preg=NULL and remove any default value for response.Rerun, tail end of output:
Codoc mismatches from documentation object 'ehr':
ehr
Code: function(point, lambda = NULL, linear = NULL, plambda = NULL,
delta = 1, envir = parent.frame(), print.level = 0,
typsize = rep(1, length(plambda)), ndigit = 10,
gradtol = 1e-05, iterlim = 100, fscale = 1, stepmax =
max(10 * sqrt(plambda %*% plambda), 10), steptol =
4e-04)
Docs: function(point, lambda = NULL, linear = NULL, plambda = NULL,
delta = 1, envir = parent.frame(), print.level = 0,
typsiz = rep(1, length(plambda)), ndigit = 10, gradtol
= 1e-05, iterlim = 100, fscale = 1, stepmax = max(10 *
sqrt(plambda %*% plambda), 10), steptol = 4e-04)
Argument names in code not in docs:
typsize
Argument names in docs not in code:
typsiz
Mismatches in argument names:
Position: 8 Code: typsize Docs: typsiz
Rerun, tail end of output:
Codoc mismatches from documentation object 'coxre':
coxre
Code: function(response, censor, nest = NULL, cov = NULL, stratified
= FALSE, cumul = FALSE, estimate = 1, iter = 10,
print.level = 0, ndigit = 10, gradtol = 1e-05, steptol
= 1e-05, iterlim = 100, fscale = 1, typsize =
abs(estimate), stepmax = estimate)
Docs: function(response, censor, nest = NULL, cov = NULL, stratified
= FALSE, cumul = FALSE, estimate = 1, iter = 10,
print.level = 0, ndigit = 10, gradtol = 1e-05, steptol
= 1e-05, iterlim = 100, fscale = 1, typsiz =
abs(estimate), stepmax = estimate)
Argument names in code not in docs:
typsize
Argument names in docs not in code:
typsiz
Mismatches in argument names:
Position: 15 Code: typsize Docs: typsiz
Rerun, tail end of output:
checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'autointensity':
autointensity
Code: function(times, window = NULL, maxlag = max(times), ylab =
"Conditional probability", xlab = "Lag", main =
"Autointensity function", xlim = c(0, max(times)),
ylim = c(0, if (plotse) max(se1) else max(z$density)),
lty = 1, plot = TRUE, plotse = TRUE, add = FALSE, ...)
Docs: function(times, window = NULL, maxlag = total/10, ylab =
"Conditional probability", xlab = "Lag", main =
"Autointensity function", xlim = c(0, max(times)),
ylim = c(0, if (plotse) max(se1) else max(z$density)),
lty = 1, plot = TRUE, plotse = TRUE, add = FALSE, ...)
Mismatches in argument default values:
Name: 'maxlag' Code: max(times) Docs: total/10
R CMD check results
1 error | 6 warnings | 0 notes
R CMD check succeeded
autointensity.Rd
change maxlag=total/10,
to maxlag = max(times),
.Rerun, tail end of output:
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘baseline’ ‘baseline.survivalkit’ ‘deviance.intensity’
‘deviance.kalsurv’ ‘deviance.pbirth’ ‘fitted.kalsurv’ ‘hboxcox’
‘hburr’ ‘hgextval’ ‘hggamma’ ‘hglogis’ ‘hgweibull’ ‘hhjorth’
‘hinvgauss’ ‘hlaplace’ ‘hpareto’ ‘hskewlaplace’ ‘plot.surv’
‘print.intensity’ ‘print.kalsurv’ ‘print.km’ ‘print.llrf’
‘print.pbirth’ ‘print.survivalkit’ ‘residuals.kalsurv’
‘residuals.survivalkit’ ‘survival’ ‘survival.survivalkit’ ‘vdm’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
R CMD check results
1 error | 5 warnings | 0 notes
R CMD check succeeded
We have eliminated a warning! On to these:
checking for missing documentation entries ... WARNING
This next warning I think has to do with the \alias
and \S3methods
.
The original documentation has grouped certain functions together for their documentation...
swihartbj@L01950966:~/github/event$ find ./R -type f -print0 | xargs -0 grep -l 'hboxcox'
./R/intensity.r
swihartbj@L01950966:~/github/event$ find ./man -type f -print0 | xargs -0 grep -l 'hboxcox'
./man/event.Rd
./man/hcauchy.Rd
./man/hexp.Rd
./man/hgamma.Rd
./man/hlnorm.Rd
./man/hlogis.Rd
./man/hnorm.Rd
./man/hstudent.Rd
./man/hweibull.Rd
What I mean is that intensity.R
houses all the h[dist]() functions. Only some of them have an .Rd file. I suppose I"ll have to make a few by hand...since I'm not using roxygen for this package.
What's interesting is that some hdist functions have .Rd and some don't. Cracking one of them open, I see in the @seealso that the hdist that don't have .Rd have links to rmutil. Oh, that's right! It's all coming back to me. I had to remove a bunch of hdist functions from documentation in rmutil. Maybe I can, in Terminal, copy those .Rd files over and edit them. To be on CRAN they need to be standalone.
Need to grab the jim-lindsey-hompage-version-1.0 .Rds...
swihartbj@L01950966:~/github/event$ cp ../../Downloads/rmutil/man/BoxCox.Rd ./man/hboxcox.Rd
swihartbj@L01950966:~/github/event$ head ./man/hboxcox.Rd
\name{Box-Cox}
\title{Box-Cox Distribution}
\usage{
dboxcox(y, m, s=1, f=1, log=FALSE)
pboxcox(q, m, s=1, f=1)
qboxcox(p, m, s=1, f=1)
hboxcox(y, m, s=1, f=1)
rboxcox(n, m, s=1, f=1)
}
\alias{dboxcox}
and then delete all the usage
and alias
lines not pertaining to hboxcox
.
continued ...
swihartbj@L01950966:~/github/event$ cp ../../Downloads/rmutil/man/Burr.Rd ./man/hburr.Rd
swihartbj@L01950966:~/github/event$ head ./man/hburr.Rd
\name{Burr}
\title{Burr Distribution}
\usage{
dburr(y, m, s, f, log=FALSE)
pburr(q, m, s, f)
qburr(p, m, s, f)
hburr(y, m, s, f)
rburr(n, m, s, f)
}
\alias{dburr}
continued
swihartbj@L01950966:~/github/event$ cp ../../Downloads/rmutil/man/GExtVal.Rd ./man/hgextval.Rd
swihartbj@L01950966:~/github/event$ head ./man/hgextval.Rd
\name{Generalized Extreme Value}
\title{Generalized Extreme Value Distribution}
\usage{
dgextval(y, s, m, f, log=FALSE)
pgextval(q, s, m, f)
qgextval(p, s, m, f)
hgextval(y, s, m, f)
rgextval(n, s, m, f)
}
\alias{dgextval}
continued
swihartbj@L01950966:~/github/event$ cp ../../Downloads/rmutil/man/GGamma.Rd ./man/hggamma.Rd
swihartbj@L01950966:~/github/event$ head ./man/hggamma.Rd
\name{Generalized Gamma}
\title{Generalized Gamma Distribution}
\usage{
dggamma(y, s, m, f, log=FALSE)
pggamma(q, s, m, f)
qggamma(p, s, m, f)
hggamma(y, s, m, f)
rggamma(n, s, m, f)
}
\alias{dggamma}
continued
swihartbj@L01950966:~/github/event$ cp ../../Downloads/rmutil/man/GLogis.Rd ./man/hglogis.Rd
swihartbj@L01950966:~/github/event$ head ./man/hglogis.Rd
\name{Generalized Logistic}
\title{Generalized Logistic Distribution}
\usage{
dglogis(y, m=0, s=1, f=1, log=FALSE)
pglogis(q, m=0, s=1, f=1)
qglogis(p, m=0, s=1, f=1)
hglogis(y, m=0, s=1, f=1)
rglogis(n, m=0, s=1, f=1)
}
\alias{dglogis}
continued
swihartbj@L01950966:~/github/event$ cp ../../Downloads/rmutil/man/GWeibull.Rd ./man/hgweibull.Rd
swihartbj@L01950966:~/github/event$ head ./man/hgweibull.Rd
\name{Generalized Weibull}
\title{Generalized Weibull Distribution}
\usage{
dgweibull(y, s, m, f, log=FALSE)
pgweibull(q, s, m, f)
qgweibull(p, s, m, f)
hgweibull(y, s, m, f)
rgweibull(n, s, m, f)
}
\alias{dgweibull}
continued
swihartbj@L01950966:~/github/event$ cp ../../Downloads/rmutil/man/Hjorth.Rd ./man/hhjorth.Rd
swihartbj@L01950966:~/github/event$ head ./man/hhjorth.Rd
\name{Hjorth}
\title{Hjorth Distribution}
\usage{
dhjorth(y, m, s, f, log=FALSE)
phjorth(q, m, s, f)
qhjorth(p, m, s, f)
hhjorth(y, m, s, f)
rhjorth(n, m, s, f)
}
\alias{dhjorth}
continued
swihartbj@L01950966:~/github/event$ cp ../../Downloads/rmutil/man/InvGauss.Rd ./man/hinvgauss.Rd
swihartbj@L01950966:~/github/event$ head ./man/hinvgauss.Rd
\name{Inverse Gaussian}
\title{Inverse Gaussian Distribution}
\usage{
dinvgauss(y, m, s, log=FALSE)
pinvgauss(q, m, s)
qinvgauss(p, m, s)
hinvgauss(y, m, s)
rinvgauss(n, m, s)
}
\alias{dinvgauss}
continued
swihartbj@L01950966:~/github/event$ cp ../../Downloads/rmutil/man/Laplace.Rd ./man/hlaplace.Rd
swihartbj@L01950966:~/github/event$ head ./man/hl
hlaplace.Rd hlnorm.Rd hlogis.Rd
swihartbj@L01950966:~/github/event$ head ./man/hlaplace.Rd
\name{Laplace}
\title{Laplace Distribution}
\usage{
dlaplace(y, m=0, s=1, log=FALSE)
plaplace(q, m=0, s=1)
qlaplace(p, m=0, s=1)
hlaplace(y, m=0, s=1)
rlaplace(n, m=0, s=1)
}
\alias{dlaplace}
continued
swihartbj@L01950966:~/github/event$ cp ../../Downloads/rmutil/man/Pareto.Rd ./man/hpareto.Rd
swihartbj@L01950966:~/github/event$ head ./man/hpareto.Rd
\name{Pareto}
\title{Pareto Distribution}
\usage{
dpareto(y, m, s, log=FALSE)
ppareto(q, m, s)
qpareto(p, m, s)
hpareto(y, m, s)
rpareto(n, m, s)
}
\alias{dpareto}
continued
swihartbj@L01950966:~/github/event$ cp ../../Downloads/rmutil/man/SkewLaplace.Rd ./man/hskewlaplace.Rd
swihartbj@L01950966:~/github/event$ head ./man/hskewlaplace.Rd
\name{SkewLaplace}
\title{Skew Laplace Distribution}
\usage{
dskewlaplace(y, m=0, s=1, f=1, log=FALSE)
pskewlaplace(q, m=0, s=1, f=1)
qskewlaplace(p, m=0, s=1, f=1)
hskewlaplace(y, m=0, s=1, f=1)
rskewlaplace(n, m=0, s=1, f=1)
}
\alias{dskewlaplace}
okay! That's the last of the log hazard .Rd files. But we still have some Undocumented code objects:
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘baseline’ ‘baseline.survivalkit’ ‘deviance.intensity’
‘deviance.kalsurv’ ‘deviance.pbirth’ ‘fitted.kalsurv’ ‘plot.surv’
‘print.intensity’ ‘print.kalsurv’ ‘print.km’ ‘print.llrf’
‘print.pbirth’ ‘print.survivalkit’ ‘residuals.kalsurv’
‘residuals.survivalkit’ ‘survival’ ‘survival.survivalkit’ ‘vdm’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Seems ‘baseline’ ‘baseline.survivalkit’ ‘residuals.survivalkit’ ‘survival’ ‘survival.survivalkit’
are all tucked into
survkit.R
so add
\alias{baseline}
\alias{baseline.survivalkit}
\alias{print.survivalkit}
\alias{residuals.survivalkit}
\alias{survival}
\alias{survival.survivalkit}
into survkit.Rd
Do likewise for remaining:
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘deviance.intensity’ ‘deviance.kalsurv’ ‘deviance.pbirth’
‘fitted.kalsurv’ ‘plot.surv’ ‘print.intensity’ ‘print.kalsurv’
‘print.km’ ‘print.llrf’ ‘print.pbirth’ ‘residuals.kalsurv’ ‘vdm’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
put
\alias{deviance.kalsurv}
\alias{fitted.kalsurv}
\alias{print.kalsurv}
\alias{residuals.kalsurv}
into
kalsurv.Rd
put
\alias{deviance.pbirth}
\alias{print.pbirth}
into pbirth.Rd
put
\alias{print.intensity}
\alias{deviance.intensity}
\alias{vdm}
into
ehr.Rd
put
\alias{plot.surv}
\alias{print.km}
into
km.Rd
put
\alias{print.llrf}
into coxre.Rd
And that's how you drop another warning!
R CMD check results
1 error | 4 warnings | 0 notes
Now onto:
checking Rd cross-references ... WARNING
I know from experience that we will need to comment out a lot of @seealso
blocks.
Let's try to do this on another branch so we can merge back later.
Here's all of them:
* checking Rd cross-references ... WARNING
Unknown package ‘gnlm’ in Rd xrefs
Missing link or links in documentation object 'event.Rd':
‘[event]{read.list}’ ‘[event]{read.surv}’
Missing link or links in documentation object 'hcauchy.Rd':
‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’
Missing link or links in documentation object 'hexp.Rd':
‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’
Missing link or links in documentation object 'hgamma.Rd':
‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’
Missing link or links in documentation object 'hlnorm.Rd':
‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’
Missing link or links in documentation object 'hnorm.Rd':
‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’
Missing link or links in documentation object 'hstudent.Rd':
‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’
Missing link or links in documentation object 'hweibull.Rd':
‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
‘[rmutil]{hggamma}’ ‘[rmutil]{hhjorth}’ ‘[rmutil]{hinvgauss}’
‘[rmutil]{hlaplace}’ ‘[rmutil]{hglogis}’ ‘[rmutil]{hgweibull}’
Missing link or links in documentation object 'km.Rd':
‘[event]{plot.survivor}’
Missing link or links in documentation object 'plot.intensity.Rd':
‘[event]{plot.survivor}’
Change
\code{\link[event]{plot.survivor}
to
\code{\link[event]{plot.surv}
in km.Rd and plot.intensity.Rd
Change
\code{\link[event]{read.list}} Read a List of Matrices of Unbalanced Repeated Measurements from a File
\code{\link[event]{read.surv}} Read a List of Vectors of Event Histories from a File
to
\code{\link[rmutil]{read.list}} Read a List of Matrices of Unbalanced Repeated Measurements from a File
\code{\link[rmutil]{read.surv}} Read a List of Vectors of Event Histories from a File
in event.Rd
For the remaining, just go into .Rd file and change rmutil to event. In getting passed CRAN checks, needed to make .Rd files for the log-hazard h[dist] in event
and remove the \alias tags in rmutil
distributional pages.
Maybe one day we will reassemble. For now... every h[dist].R/Rd in event
.
comment out \link[gnlm] in kalsurv.Rd and you...
....wait for it .....
ELIMINATE yet another warning:
R CMD check results
1 error | 3 warnings | 0 notes
R CMD check succeeded
onto the next warning:
checking Rd files ... WARNING
checkRd: (5) bp.Rd:0-32: Must have a \description
checkRd: (5) hcauchy.Rd:0-31: Must have a \description
checkRd: (5) hexp.Rd:0-30: Must have a \description
checkRd: (5) hgamma.Rd:0-32: Must have a \description
checkRd: (5) hlnorm.Rd:0-31: Must have a \description
checkRd: (5) hlogis.Rd:0-29: Must have a \description
checkRd: (5) hnorm.Rd:0-31: Must have a \description
checkRd: (5) hstudent.Rd:0-32: Must have a \description
checkRd: (5) hweibull.Rd:0-31: Must have a \description
checkRd: (5) ident.Rd:0-31: Must have a \description
checkRd: (5) pp.Rd:0-29: Must have a \description
checkRd: (5) tccov.Rd:0-33: Must have a \description
checkRd: (5) tpast.Rd:0-27: Must have a \description
checkRd: (5) ttime.Rd:0-31: Must have a \description
checkRd: (5) tvcov.Rd:0-32: Must have a \description
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 3 warnings | 0 notes
R CMD check succeeded
For the h....Rd, I just copied the title over as a description after adding "Log" to the title text.
For the remaining, I copied \value as the \description.
And we eliminate another warning:
checking S3 generic/method consistency ... WARNING
baseline:
function(z, ...)
baseline.survivalkit:
function(z)
plot.dist:
function(z, ...)
plot.dist.km:
function(z)
... 109 lines ...
Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
baseline.survivalkit deviance.intensity deviance.kalsurv
deviance.pbirth fitted.kalsurv plot.dist plot.dist.km plot.dist.km
plot.intensity plot.intensity.default plot.intensity.default
plot.intensity.km plot.intensity.km plot.km plot.surv print.intensity
print.kalsurv print.km print.llrf print.pbirth print.survivalkit
residuals.kalsurv residuals.survivalkit survival.survivalkit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
See
‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.
R CMD check results
1 error | 2 warnings | 0 notes
R CMD check succeeded
Add
S3method( baseline, survivalkit )
S3method( deviance, intensity )
S3method( deviance, kalsurv)
S3method( deviance, pbirth )
S3method( fitted, kalsurv )
S3method( plot, dist )
S3method( plot, dist.km)
S3method( plot, intensity)
S3method( plot, intensity.default )
S3method( plot, intensity.km )
S3method( plot, km )
S3method( plot, surv)
S3method( print, intensity)
S3method( print, kalsurv )
S3method( print, km )
S3method( print, llrf)
S3method( print, pbirth)
S3method( print, survivalkit)
S3method( residuals, kalsurv )
S3method( residuals, survivalkit )
S3method( survival, survivalkit)
to
NAMESPACE
Now we focus on consistency problems...
* checking S3 generic/method consistency ... WARNING
baseline:
function(z, ...)
baseline.survivalkit:
function(z)
baseline:
function(z, ...)
baseline.survivalkit:
function(z)
plot.dist:
function(z, ...)
plot.dist.km:
function(z)
plot.intensity:
function(z, ...)
plot.intensity.default:
function(times, censor, group, colour, mix, ylim, ylab, xlab, main)
survival:
function(z, ...)
survival.survivalkit:
function(z)
survival:
function(z, ...)
survival.survivalkit:
function(z)
print:
function(x, ...)
print.intensity:
function(z)
print:
function(x, ...)
print.kalsurv:
function(z, digits, correlation)
print:
function(x, ...)
print.km:
function(z)
print:
function(x, ...)
print.llrf:
function(z)
print:
function(x, ...)
print.pbirth:
function(z)
print:
function(x, ...)
print.survivalkit:
function(z)
print:
function(x, ...)
print.intensity:
function(z)
print:
function(x, ...)
print.kalsurv:
function(z, digits, correlation)
print:
function(x, ...)
print.km:
function(z)
print:
function(x, ...)
print.llrf:
function(z)
print:
function(x, ...)
print.pbirth:
function(z)
print:
function(x, ...)
print.survivalkit:
function(z)
plot:
function(x, ...)
plot.dist:
function(z, ...)
plot:
function(x, ...)
plot.dist.km:
function(z)
plot:
function(x, ...)
plot.intensity:
function(z, ...)
plot:
function(x, ...)
plot.intensity.default:
function(times, censor, group, colour, mix, ylim, ylab, xlab, main)
plot:
function(x, ...)
plot.intensity.km:
function(z, add, xlab, ylab, type, lty, ...)
plot:
function(x, ...)
plot.km:
function(z, add, xlim, ylim, main, xlab, ylab, lty, ...)
plot:
function(x, ...)
plot.surv:
function(times, survivor, group, cdf, add, xlim, ylim, main, xlab,
ylab, lty, ...)
plot:
function(x, ...)
plot.dist:
function(z, ...)
plot:
function(x, ...)
plot.dist.km:
function(z)
plot:
function(x, ...)
plot.intensity:
function(z, ...)
plot:
function(x, ...)
plot.intensity.default:
function(times, censor, group, colour, mix, ylim, ylab, xlab, main)
plot:
function(x, ...)
plot.intensity.km:
function(z, add, xlab, ylab, type, lty, ...)
plot:
function(x, ...)
plot.km:
function(z, add, xlim, ylim, main, xlab, ylab, lty, ...)
plot:
function(x, ...)
plot.surv:
function(times, survivor, group, cdf, add, xlim, ylim, main, xlab,
ylab, lty, ...)
deviance:
function(object, ...)
deviance.intensity:
function(z)
deviance:
function(object, ...)
deviance.kalsurv:
function(z)
deviance:
function(object, ...)
deviance.pbirth:
function(z)
deviance:
function(object, ...)
deviance.intensity:
function(z)
deviance:
function(object, ...)
deviance.kalsurv:
function(z)
deviance:
function(object, ...)
deviance.pbirth:
function(z)
fitted:
function(object, ...)
fitted.kalsurv:
function(z, recursive)
fitted:
function(object, ...)
fitted.kalsurv:
function(z, recursive)
residuals:
function(object, ...)
residuals.kalsurv:
function(z, recursive)
residuals:
function(object, ...)
residuals.survivalkit:
function(z)
residuals:
function(object, ...)
residuals.kalsurv:
function(z, recursive)
residuals:
function(object, ...)
residuals.survivalkit:
function(z)
NO MORE ROXYGEN / DEVTOOLS::DOCUMENT() FOR
event