Validation Report - Epi@2.59
Context
This report is fully automated and builds on rhub/ref-image image. Documents the installation of this package on an open source R environment, focusing on:
- Installation environment description
- Testing coverage
It is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful.
Package Epi
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 185 |
| has_vignettes | 18 |
| export_help | 185 |
| has_website | TRUE |
| has_maintainer | Bendix Carstensen b@bxc.dk |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| has_bug_reports_url | 0 |
| downloads_1yr | 102479 |
| reverse_dependencies | 17 |
| has_examples | 1 |
| dependencies | 14 |
| license | GPL-2 |
Package general assessment: Coverage, check results, size, download the last year, reverse dependencies and number of dependencies.
Dependencies
Overall the package has these dependencies:
| package | type | |
|---|---|---|
| 1 | utils | Depends |
| 2 | cmprsk | Imports |
| 3 | etm | Imports |
| 4 | splines | Imports |
| 5 | MASS | Imports |
| 6 | survival | Imports |
| 7 | plyr | Imports |
| 8 | dplyr | Imports |
| 9 | Matrix | Imports |
| 10 | numDeriv | Imports |
| 11 | data.table | Imports |
| 12 | zoo | Imports |
| 13 | mgcv | Imports |
| 14 | magrittr | Imports |
Package dependencies
Reverse dependencies
Overall the package has 17 reverse dependencies:
biostat3, bshazard, catregs, codeCollection, cohorttools, dani, flexrsurv, fmsb, Greg, mable, MCARtest, metafor, pander, popEpi, pubh, shinyPredict, TwoTimeScales
Namespace
Overall the package has 185 exported objects. 185 are documented:
[.Lexis AaJ.Lexis absorbing
TRUE TRUE TRUE
addCov.Lexis addDrug.Lexis after
TRUE TRUE TRUE
apc.fit apc.frame apc.LCa
TRUE TRUE TRUE
apc.lines apc.plot Aplot
TRUE TRUE TRUE
as.Date.cal.yr before bootLexis
TRUE TRUE TRUE
boxarr boxes boxes.Lexis
TRUE TRUE TRUE
boxes.matrix boxes.MS breaks
TRUE TRUE TRUE
cal.yr cbind.Lexis ccwc
TRUE TRUE TRUE
ci.Crisk ci.cum ci.eta
TRUE TRUE TRUE
ci.exp ci.lin ci.mat
TRUE TRUE TRUE
ci.pd ci.pred ci.ratio
TRUE TRUE TRUE
ci.surv clear clogistic
TRUE TRUE TRUE
coarse.Lexis contr.2nd contr.cum
TRUE TRUE TRUE
contr.diff contr.orth countLexis
TRUE TRUE TRUE
coxph.Lexis coxphLexis cp.lines
TRUE TRUE TRUE
cp.matlines cp.matpoints cp.matshade
TRUE TRUE TRUE
cp.points Cplot crr.Lexis
TRUE TRUE TRUE
cutLexis dbox decurve
TRUE TRUE TRUE
detrend dur effx
TRUE TRUE TRUE
effx.match entry erl
TRUE TRUE TRUE
erl1 etm.Lexis exit
TRUE TRUE TRUE
factorize factorize.Lexis fgrep
TRUE TRUE TRUE
fillarr fit.add fit.mult
TRUE TRUE TRUE
float ftrend gam.Lexis
TRUE TRUE TRUE
gamLexis gen.exp glm.Lexis
TRUE TRUE TRUE
glmLexis harm Icens
TRUE TRUE TRUE
id.span idSpan in.span
TRUE TRUE TRUE
inSpan LCa.fit legendbox
TRUE TRUE TRUE
levels.Lexis Lexis Lexis.diagram
TRUE TRUE TRUE
Lexis.lines Lexis2msm lgrep
TRUE TRUE TRUE
Life.lines lines.apc lines.Lexis
TRUE TRUE TRUE
lines.pState linesEst lls
TRUE TRUE TRUE
mat2pol matshade mcutLexis
TRUE TRUE TRUE
merge.Lexis mh msdata
TRUE TRUE TRUE
msdata.Lexis N2Y NArray
TRUE TRUE TRUE
ncut ngrep nice
TRUE TRUE TRUE
nid nid.Lexis Ns
TRUE TRUE TRUE
nState order.Lexis orderLexis
TRUE TRUE TRUE
paths.Lexis pc.lines pc.matlines
TRUE TRUE TRUE
pc.matpoints pc.matshade pc.points
TRUE TRUE TRUE
pctab plot.apc plot.LCa
TRUE TRUE TRUE
plot.Lexis plot.pState plotCIF
TRUE TRUE TRUE
plotEst plotevent points.Lexis
TRUE TRUE TRUE
pointsEst poisreg Pplot
TRUE TRUE TRUE
preceding predict.LCa print.floated
TRUE TRUE TRUE
print.Icens print.LCa print.Lexis
TRUE TRUE TRUE
print.mh print.summary.Lexis projection.ip
TRUE TRUE TRUE
pState PY.ann PY.ann.Lexis
TRUE TRUE TRUE
rateplot rbind.Lexis rcutLexis
TRUE TRUE TRUE
Relevel Relevel.factor Relevel.Lexis
TRUE TRUE TRUE
rm.tr ROC show.apc.LCa
TRUE TRUE TRUE
simLexis sortLexis splitLexis
TRUE TRUE TRUE
stack.Lexis stackedCIF stat.table
TRUE TRUE TRUE
status subset.Lexis subset.stacked.Lexis
TRUE TRUE TRUE
succeeding summary.Icens summary.LCa
TRUE TRUE TRUE
summary.Lexis surv1 surv2
TRUE TRUE TRUE
tbox Termplot thinCol
TRUE TRUE TRUE
timeBand timeScales timeSince
TRUE TRUE TRUE
tmat tmat.Lexis transform.Lexis
TRUE TRUE TRUE
transform.stacked.Lexis transient tsNA20
TRUE TRUE TRUE
twoby2 unLexis Wald
TRUE TRUE TRUE
yll ZArray
TRUE TRUE Examples
There are 111 help pages with examples, from 111 (100.00 %).
NEWS
The package has NEWS file and it is current.
License
The package uses .
Installation environment
System Info
| Field | Value |
|---|---|
| Image | rhub/ref-image |
| OS | Ubuntu 24.04.1 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-02-19 04:14:31 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
loaded via a namespace (and not attached):
[1] riskreports_0.0.0.9003 compiler_4.4.2 fastmap_1.2.0
[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.49 jsonlite_1.8.9
[10] xfun_0.50 digest_0.6.37 rlang_1.1.5
[13] evaluate_1.0.3 Platform used:
OS.type file.sep dynlib.ext GUI endian pkgType path.sep
"unix" "/" ".so" "X11" "little" "source" ":"
r_arch
"" R’s capabilities:
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE FALSE TRUE FALSE TRUE
NLS Rprof profmem cairo ICU long.double
TRUE TRUE TRUE TRUE TRUE TRUE
libcurl
TRUE External software:
zlib
"1.3"
bzlib
"1.0.8, 13-Jul-2019"
xz
"5.4.5"
libdeflate
"1.19"
PCRE
"10.42 2022-12-11"
ICU
"74.2"
TRE
"TRE 0.8.0 R_fixes (BSD)"
iconv
"glibc 2.39"
readline
"8.2"
BLAS
"/usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3" Graphics external software:
cairo cairoFT pango
"1.18.0" "" "1.52.1"
libpng jpeg libtiff
"1.6.43" "8.0" "LIBTIFF, Version 4.5.1" Numerical characteristics of the machine:
double.eps double.neg.eps double.xmin
2.220446e-16 1.110223e-16 2.225074e-308
double.xmax double.base double.digits
1.797693e+308 2.000000e+00 5.300000e+01
double.rounding double.guard double.ulp.digits
5.000000e+00 0.000000e+00 -5.200000e+01
double.neg.ulp.digits double.exponent double.min.exp
-5.300000e+01 1.100000e+01 -1.022000e+03
double.max.exp integer.max sizeof.long
1.024000e+03 2.147484e+09 8.000000e+00
sizeof.longlong sizeof.longdouble sizeof.pointer
8.000000e+00 1.600000e+01 8.000000e+00
sizeof.time_t longdouble.eps longdouble.neg.eps
8.000000e+00 1.084202e-19 5.421011e-20
longdouble.digits longdouble.rounding longdouble.guard
6.400000e+01 5.000000e+00 0.000000e+00
longdouble.ulp.digits longdouble.neg.ulp.digits longdouble.exponent
-6.300000e+01 -6.400000e+01 1.500000e+01
longdouble.min.exp longdouble.max.exp
-1.638200e+04 1.638400e+04 Random number generation process:
[1] "Mersenne-Twister" "Inversion" "Rejection" Information about the environment
Environmental and options variables affect how package checks and software in it might behave. Here is the environmental variables when running this report
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PHARMAPKGS_EXCLUDED_METRICS
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PHARMAPKGS_REMOTE_REPO
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PKGLOAD_PARENT_TEMPDIR
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$bitmapType
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$browser
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$callr.condition_handler_cli_message
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<bytecode: 0x56120fdaf910>
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can write "yes"
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