Fresh .r, .rd, DESCRIPTION, NAMESPACE: 1 error | 7 warnings

swihart commented 7 years ago

NO MORE ROXYGEN / DEVTOOLS::DOCUMENT() FOR event

==> devtools::check(document = FALSE)

Setting env vars ---------------------------------------------------------------
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building event -----------------------------------------------------------------
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD build '/Users/swihartbj/github/event'  \
  --no-resave-data --no-manual 

* checking for file ‘/Users/swihartbj/github/event/DESCRIPTION’ ... OK
* preparing ‘event’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking whether ‘INDEX’ is up-to-date ... NO
* use ‘--force’ to remove the existing ‘INDEX’
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory ‘event/README_files/figure-html’
Removed empty directory ‘event/README_files’
* building ‘event_1.1.0.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Setting env vars ---------------------------------------------------------------
_R_CHECK_CRAN_INCOMING_ : FALSE
_R_CHECK_FORCE_SUGGESTS_: FALSE
Checking event -----------------------------------------------------------------
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD check  \
  '/var/folders/tv/9xflkyxs21j3747s8wd641t1bd7ntf/T//RtmpEX5Q15/event_1.1.0.tar.gz'  \
  --as-cran --timings --no-manual 

* using log directory ‘/Users/swihartbj/github/event.Rcheck’
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘event/DESCRIPTION’ ... OK
* this is package ‘event’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘event’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Rank mismatch in argument 'valrho' at (1) (rank-1 and scalar)
See ‘/Users/swihartbj/github/event.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
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)

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, ...)

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)

residuals:
  function(object, ...)
residuals.kalsurv:
  function(z, recursive)

residuals:
  function(object, ...)
residuals.survivalkit:
  function(z)

See section ‘Generic functions and methods’ in the ‘Writing R
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.
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Calls with DUP:
   .C("ksurvb", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), 
       pfamily = as.integer(!is.null(pfamily)), dep = as.integer(dep), 
       birth = as.integer(birth), tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), 
       fit = as.integer(0), pred = double(n), rpred = double(n), 
       renewal = as.integer(renewal), rf = as.integer(rf), bb = as.double(b), 
       sf = as.integer(sf), vv = as.double(v), like = double(1), 
       DUP = FALSE, PACKAGE = "event")
   .C("ksurvg", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), distribution = as.integer(dst), 
       density = as.integer(density), dep = as.integer(dep), birth = as.integer(birth), 
       tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), 
       fit = as.integer(0), pred = double(n), rpred = double(n), 
       renewal = as.integer(renewal), rf = as.integer(rf), bb = as.double(b), 
       sf = as.integer(sf), vv = as.double(v), like = double(1), 
       DUP = FALSE, PACKAGE = "event")
   .C("frailb", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), 
       dep = as.integer(dep), birth = as.integer(birth), tvc = as.integer(tvc), 
       tvcov = as.double(resp$tvcov$tvcov), fit = as.integer(0), 
       pred = double(n), rpred = double(n), rf = as.integer(rf), 
       bb = as.double(b), sf = as.integer(sf), vv = as.double(v), 
       frser = as.integer(frser), like = double(1), DUP = FALSE, 
       PACKAGE = "event")
   .C("frailb", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), 
       dep = as.integer(dep), birth = as.integer(birth), tvc = as.integer(tvc), 
       tvcov = as.double(resp$tvcov$tvcov), fit = as.integer(1), 
       pred = double(n), rpred = double(n), rf = as.integer(rf), 
       bb = as.double(b), sf = as.integer(sf), vv = as.double(v), 
       frser = as.integer(frser), like = double(1), DUP = FALSE, 
       PACKAGE = "event")
   .C("ksurvb", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), 
       pfamily = as.integer(!is.null(pfamily)), dep = as.integer(dep), 
       birth = as.integer(birth), tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), 
       fit = as.integer(1), pred = double(n), rpred = double(n), 
       renewal = as.integer(renewal), rf = as.integer(rf), bb = as.double(b), 
       sf = as.integer(sf), vv = as.double(v), like = double(1), 
       DUP = FALSE, PACKAGE = "event")
   .C("ksurvg", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), distribution = as.integer(dst), 
       density = as.integer(density), dep = as.integer(dep), birth = as.integer(birth), 
       tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), 
       fit = as.integer(1), pred = double(n), rpred = double(n), 
       renewal = as.integer(renewal), rf = as.integer(rf), bb = as.double(b), 
       sf = as.integer(sf), vv = as.double(v), like = double(1), 
       DUP = FALSE, PACKAGE = "event")
   .Fortran("weibull", iconst = as.integer(iconst), rconst = as.double(rconst), 
       istime = as.integer(istime), squant = as.double(squant), 
       valrho = as.double(valrho), includ = as.integer(includ), 
       info = as.integer(info), itabl = as.integer(itabl), xtabl = as.double(xtabl), 
       nrr = as.integer(nrr), info2 = as.integer(info2), itabl2 = as.integer(itabl2), 
       xtabl2 = as.double(xtabl2), ipedig = as.integer(pedigree), 
       nrr2 = as.integer(nrr2), nccov = as.integer(nccov), ndcov = as.integer(ndcov), 
       nstime = as.integer(nstime), nquant = as.integer(nquant), 
       igam = as.integer(igam), inor = as.integer(inor), xgam = as.double(xgam), 
       xnor = as.double(xnor), bound = as.double(bound), icons = as.integer(icons), 
       beta = double(ndimax), stder = double(ndimax), grad = double(ndimax), 
       hess = double(ndimax * ndimax), xmom = double(4), surv = double(3 * 
           nstimax * nrr), like = double(2), df = integer(2), DUP = FALSE, 
       PACKAGE = "event")
   .Fortran("cox", iconst = as.integer(iconst), rconst = as.double(rconst), 
       istime = as.integer(istime), squant = as.double(squant), 
       includ = as.integer(includ), info = as.integer(info), itabl = as.integer(itabl), 
       xtabl = as.double(xtabl), nrr = as.integer(nrr), info2 = as.integer(info2), 
       itabl2 = as.integer(itabl2), xtabl2 = as.double(xtabl2), 
       iplus1 = as.integer(iplus1), iplus2 = as.integer(iplus2), 
       ipedig = as.integer(pedigree), nrr2 = as.integer(nrr2), nccov = as.integer(nccov), 
       ndcov = as.integer(ndcov), nstime = as.integer(nstime), nquant = as.integer(nquant), 
       igam = as.integer(igam), inor = as.integer(inor), xgam = as.double(xgam), 
       xnor = as.double(xnor), bound = as.double(bound), icons = as.integer(icons), 
       beta = double(ndimax), stder = double(ndimax), grad = double(ndimax), 
       hess = double(ndimax * ndimax), xmom = double(4), surv = double(3 * 
           nstimax * nrr), like = double(2), df = integer(2), km = double(nrr * 
           nstrata * 4), resid = double(nrr * nstrata * 3), ut = as.integer(nrr * 
           nstrata), DUP = FALSE, PACKAGE = "event")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

autointensity: no visible global function definition for ‘hist’
autointensity: no visible global function definition for ‘lines’
coxre : like: no visible global function definition for ‘glm’
coxre : like: no visible binding for global variable ‘poisson’
coxre : likel: no visible global function definition for ‘glm’
coxre : likel: no visible binding for global variable ‘poisson’
coxre: no visible global function definition for ‘glm’
coxre: no visible binding for global variable ‘poisson’
coxre: no visible global function definition for ‘nlm’
cprocess: no visible global function definition for ‘lines’
cprocess: no visible global function definition for ‘plot’
cprocess: no visible global function definition for ‘text’
ehr: no visible global function definition for ‘nlm’
hboxcox: no visible global function definition for ‘pnorm’
hcauchy: no visible global function definition for ‘dcauchy’
hcauchy: no visible global function definition for ‘pcauchy’
hgamma: no visible global function definition for ‘dgamma’
hgamma: no visible global function definition for ‘pgamma’
hgextval: no visible global function definition for ‘pweibull’
hggamma: no visible global function definition for ‘pgamma’
hinvgauss: no visible global function definition for ‘pnorm’
hlnorm: no visible global function definition for ‘dlnorm’
hlnorm: no visible global function definition for ‘plnorm’
hlogis: no visible global function definition for ‘dlogis’
hlogis: no visible global function definition for ‘plogis’
hnorm: no visible global function definition for ‘dnorm’
hnorm: no visible global function definition for ‘pnorm’
hstudent : pst: no visible global function definition for ‘pbeta’
kalsurv: no visible global function definition for ‘terms’
kalsurv : sh1: no visible binding for global variable ‘npl1’
kalsurv: no visible global function definition for ‘nlm’
pbirth: no visible global function definition for ‘nlm’
plot.dist.km: no visible global function definition for ‘par’
plot.dist.km: no visible global function definition for ‘plot’
plot.dist.km: no visible global function definition for ‘lines’
plot.dist.km: no visible global function definition for ‘qnorm’
plot.intensity.default: no visible global function definition for
  ‘plot’
plot.intensity.default: no visible global function definition for
  ‘lines’
plot.intensity.default: no visible global function definition for
  ‘gray’
plot.intensity.km: no visible global function definition for ‘lines’
plot.intensity.km: no visible global function definition for ‘plot’
plot.km: no visible global function definition for ‘lines’
plot.km: no visible global function definition for ‘plot’
plot.surv: no visible global function definition for ‘lines’
plot.surv: no visible global function definition for ‘plot’
survkit: no visible global function definition for ‘model.frame’
survkit: no visible global function definition for ‘terms’
survkit: no visible binding for global variable ‘na.fail’
Undefined global functions or variables:
  dcauchy dgamma dlnorm dlogis dnorm glm gray hist lines model.frame
  na.fail nlm npl1 par pbeta pcauchy pgamma plnorm plogis plot pnorm
  poisson pweibull qnorm terms text
Consider adding
  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")
to your NAMESPACE file.
* 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
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'event.Rd':
  ‘[event]{hboxcox}’ ‘[event]{hburr}’ ‘[event]{hgextval}’
  ‘[event]{hggamma}’ ‘[event]{hglogis}’ ‘[event]{hgweibull}’
  ‘[event]{hhjorth}’ ‘[event]{hinvgauss}’ ‘[event]{hlaplace}’
  ‘[event]{hpareto}’ ‘[event]{hskewlaplace}’ ‘[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 'hlogis.Rd':
  ‘hboxcox’ ‘hburr’ ‘hgextval’ ‘hggamma’ ‘hhjorth’ ‘hinvgauss’
  ‘hlaplace’ ‘hglogis’ ‘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}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘autointensity’ ‘baseline’ ‘baseline.survivalkit’
  ‘deviance.intensity’ ‘deviance.kalsurv’ ‘deviance.pbirth’
  ‘fitted.kalsurv’ ‘hboxcox’ ‘hburr’ ‘hgextval’ ‘hggamma’ ‘hglogis’
  ‘hgweibull’ ‘hhjorth’ ‘hinvgauss’ ‘hlaplace’ ‘hpareto’ ‘hskewlaplace’
  ‘plot.intensity.default’ ‘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.
* 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

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

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

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

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"

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

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)"

* 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’
  ‘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':
  ‘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':
  ‘others’

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’

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.
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.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ... ERROR
Running examples in ‘event-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pbirth
> ### Title: Fit Overdispersed Count Data as a Birth Process
> ### Aliases: pbirth
> ### Keywords: models
> 
> ### ** Examples
> 
> y <- rnbinom(100,2,0.6)
> fr <- tabulate(y)
> pbirth(fr, p=log(-log(0.7)), intensity="Poisson", type="series")
Error in log(prob1(p)) : non-numeric argument to mathematical function
Calls: pbirth -> nlm -> <Anonymous> -> f
Execution halted
* DONE
Status: 1 ERROR, 7 WARNINGs, 2 NOTEs
checking examples ... ERROR
Running examples in ‘event-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pbirth
> ### Title: Fit Overdispersed Count Data as a Birth Process
> ### Aliases: pbirth
> ### Keywords: models
> 
> ### ** Examples
> 
> y <- rnbinom(100,2,0.6)
> fr <- tabulate(y)
> pbirth(fr, p=log(-log(0.7)), intensity="Poisson", type="series")
Error in log(prob1(p)) : non-numeric argument to mathematical function
Calls: pbirth -> nlm -> <Anonymous> -> f
Execution halted

checking whether package ‘event’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Rank mismatch in argument 'valrho' at (1) (rank-1 and scalar)
See ‘/Users/swihartbj/github/event.Rcheck/00install.out’ for details.

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.

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

checking Rd cross-references ... WARNING
Missing link or links in documentation object 'event.Rd':
  ‘[event]{hboxcox}’ ‘[event]{hburr}’ ‘[event]{hgextval}’
  ‘[event]{hggamma}’ ‘[event]{hglogis}’ ‘[event]{hgweibull}’
  ‘[event]{hhjorth}’ ‘[event]{hinvgauss}’ ‘[event]{hlaplace}’
  ‘[event]{hpareto}’ ‘[event]{hskewlaplace}’ ‘[event]{read.list}’
  ‘[event]{read.surv}’

Missing link or links in documentation object 'hcauchy.Rd':
  ‘[rmutil]{hboxcox}’ ‘[rmutil]{hburr}’ ‘[rmutil]{hgextval}’
... 34 lines ...
  ‘[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}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘autointensity’ ‘baseline’ ‘baseline.survivalkit’
  ‘deviance.intensity’ ‘deviance.kalsurv’ ‘deviance.pbirth’
  ‘fitted.kalsurv’ ‘hboxcox’ ‘hburr’ ‘hgextval’ ‘hggamma’ ‘hglogis’
  ‘hgweibull’ ‘hhjorth’ ‘hinvgauss’ ‘hlaplace’ ‘hpareto’ ‘hskewlaplace’
  ‘plot.intensity.default’ ‘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.

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)"

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’
... 45 lines ...
Extensions’ manual.
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.

checking foreign function calls ... NOTE
Calls with DUP:
   .C("ksurvb", p = as.double(p), y = as.double(resp$response$y), 
       x = as.double(resp$ccov$ccov), cens = as.integer(resp$response$censor), 
       nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), 
       nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), 
       pfamily = as.integer(!is.null(pfamily)), dep = as.integer(dep), 
       birth = as.integer(birth), tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), 
       fit = as.integer(0), pred = double(n), rpred = double(n), 
       renewal = as.integer(renewal), rf = as.integer(rf), bb = as.double(b), 
... 72 lines ...
       iplus1 = as.integer(iplus1), iplus2 = as.integer(iplus2), 
       ipedig = as.integer(pedigree), nrr2 = as.integer(nrr2), nccov = as.integer(nccov), 
       ndcov = as.integer(ndcov), nstime = as.integer(nstime), nquant = as.integer(nquant), 
       igam = as.integer(igam), inor = as.integer(inor), xgam = as.double(xgam), 
       xnor = as.double(xnor), bound = as.double(bound), icons = as.integer(icons), 
       beta = double(ndimax), stder = double(ndimax), grad = double(ndimax), 
       hess = double(ndimax * ndimax), xmom = double(4), surv = double(3 * 
           nstimax * nrr), like = double(2), df = integer(2), km = double(nrr * 
           nstrata * 4), resid = double(nrr * nstrata * 3), ut = as.integer(nrr * 
           nstrata), DUP = FALSE, PACKAGE = "event")
DUP is no longer supported and will be ignored.

checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

autointensity: no visible global function definition for ‘hist’
autointensity: no visible global function definition for ‘lines’
coxre : like: no visible global function definition for ‘glm’
coxre : like: no visible binding for global variable ‘poisson’
coxre : likel: no visible global function definition for ‘glm’
coxre : likel: no visible binding for global variable ‘poisson’
coxre: no visible global function definition for ‘glm’
... 46 lines ...
  dcauchy dgamma dlnorm dlogis dnorm glm gray hist lines model.frame
  na.fail nlm npl1 par pbeta pcauchy pgamma plnorm plogis plot pnorm
  poisson pweibull qnorm terms text
Consider adding
  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")
to your NAMESPACE file.

See
  ‘/Users/swihartbj/github/event.Rcheck/00check.log’
for details.

R CMD check results
1 error  | 7 warnings | 2 notes

R CMD check succeeded

swihart commented 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

swihart commented 7 years ago

hgamma: easy fix. change lower to lower.tail; change log to log.p
kalsurv: 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

swihart commented 7 years ago

Comment out the .First.lib on line 33 of 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

swihart commented 7 years ago

Comment out all the DUPs. Tip: use terminal

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

swihart commented 7 years ago

Change lines 5-7 of 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)

Change lines 5-8 of 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)

swihart commented 7 years ago

in autointensity.Rd, add

\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

swihart commented 7 years ago

in coxre.Rd, add

\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

swihart commented 7 years ago

in cprocess.Rd, add

\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

swihart commented 7 years ago

in ehr.Rd, add

\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

swihart commented 7 years ago

in kalsurv.Rd, add

\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

swihart commented 7 years ago

in km.Rd, add

\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

swihart commented 7 years ago

in pbirth.Rd, add

\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

swihart commented 7 years ago

in plot.intensity.Rd add

\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

swihart commented 7 years ago

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

swihart commented 7 years ago

in 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

swihart commented 7 years ago

in pbirth.Rd, change typesiz to typsize.

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

swihart commented 7 years ago

in 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

swihart commented 7 years ago

between 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

swihart commented 7 years ago

in ehr.Rd, change typesiz to typsize.

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

swihart commented 7 years ago

in coxre.Rd, change typesiz to typsize.

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

swihart commented 7 years ago

in 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

swihart commented 7 years ago

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.

swihart commented 7 years ago

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}

swihart commented 7 years ago

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}

swihart commented 7 years ago

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}

swihart commented 7 years ago

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}

swihart commented 7 years ago

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}

swihart commented 7 years ago

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}

swihart commented 7 years ago

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}

swihart commented 7 years ago

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}

swihart commented 7 years ago

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}

swihart commented 7 years ago

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}

swihart commented 7 years ago

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.

swihart commented 7 years ago

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

swihart commented 7 years ago

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.

swihart commented 7 years ago

put

\alias{deviance.kalsurv}
\alias{fitted.kalsurv}
\alias{print.kalsurv}
\alias{residuals.kalsurv}

into

kalsurv.Rd

swihart commented 7 years ago

put

\alias{deviance.pbirth}
\alias{print.pbirth}

into pbirth.Rd

swihart commented 7 years ago

put

\alias{print.intensity}
\alias{deviance.intensity}
\alias{vdm}

into

ehr.Rd

swihart commented 7 years ago

put

\alias{plot.surv}
\alias{print.km}

into

km.Rd

swihart commented 7 years ago

put

\alias{print.llrf}

into coxre.Rd

swihart commented 7 years ago

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.

swihart commented 7 years ago

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}’

swihart commented 7 years ago

Change

\code{\link[event]{plot.survivor}

to

\code{\link[event]{plot.surv}

in km.Rd and plot.intensity.Rd

swihart commented 7 years ago

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

swihart commented 7 years ago

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.

swihart commented 7 years ago

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

swihart commented 7 years ago

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

swihart commented 7 years ago

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

swihart commented 7 years ago

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

swihart commented 7 years ago

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)

swihart / event

Fresh .r, .rd, DESCRIPTION, NAMESPACE: 1 error | 7 warnings | 2 notes #2