Validation Report - bamlss@1.2.5
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 bamlss
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 172 |
| has_vignettes | 2 |
| export_help | 172 |
| has_website | TRUE |
| has_maintainer | Nikolaus Umlauf Nikolaus.Umlauf@uibk.ac.at |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| has_bug_reports_url | 0 |
| downloads_1yr | 11907 |
| reverse_dependencies | 5 |
| has_examples | 1 |
| dependencies | 12 |
| license | GPL-2 | GPL-3 |
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 | coda | Depends |
| 2 | colorspace | Depends |
| 3 | distributions3 (>= 0.2.1) | Depends |
| 4 | mgcv | Depends |
| 5 | Formula | Imports |
| 6 | MBA | Imports |
| 7 | mvtnorm | Imports |
| 8 | sp | Imports |
| 9 | Matrix | Imports |
| 10 | survival | Imports |
| 11 | methods | Imports |
| 12 | parallel | Imports |
Package dependencies
Reverse dependencies
Overall the package has 5 reverse dependencies:
distreg.vis, gmfamm, mevr, MJMbamlss, spiky
Namespace
Overall the package has 172 exported objects. 172 are documented:
ALD_bamlss AR1
TRUE TRUE
AR1_bamlss bamlss
TRUE TRUE
BAMLSS bamlss.engine.setup
TRUE TRUE
bamlss.family bamlss.formula
TRUE TRUE
bamlss.frame bamlss.model.frame
TRUE TRUE
BayesX BayesX.control
TRUE TRUE
bayesx2 bbfit
TRUE TRUE
bbfitp bboost
TRUE TRUE
bboost_plot beta_bamlss
TRUE TRUE
beta1_bamlss bfit
TRUE TRUE
bfit_glmnet bfit_iwls
TRUE TRUE
bfit_iwls_Matrix bfit_lm
TRUE TRUE
bfit_optim binomial_bamlss
TRUE TRUE
boost boost_frame
TRUE TRUE
boost_plot boost_summary
TRUE TRUE
boost2 boostm
TRUE TRUE
BUGSeta BUGSmodel
TRUE TRUE
c95 cnorm_bamlss
TRUE TRUE
colorlegend continue
TRUE TRUE
contribplot cox_bamlss
TRUE TRUE
cox_mcmc cox_mode
TRUE TRUE
cox_predict Crazy
TRUE TRUE
CRPS cv_ddnn
TRUE TRUE
ddnn DGP_bamlss
TRUE TRUE
DIC dirichlet_bamlss
TRUE TRUE
dist_mvnchol dw_bamlss
TRUE TRUE
ELF_bamlss engines
TRUE TRUE
GAMart gamlss_distributions
TRUE TRUE
gamma_bamlss gaussian_bamlss
TRUE TRUE
Gaussian_bamlss gaussian2_bamlss
TRUE TRUE
get_BayesXsrc get.par
TRUE TRUE
get.state GEV_bamlss
TRUE TRUE
gF glogis_bamlss
TRUE TRUE
GMCMC GMCMC_iwls
TRUE TRUE
GMCMC_iwlsC GMCMC_iwlsC_gp
TRUE TRUE
GMCMC_slice gpareto_bamlss
TRUE TRUE
gumbel_bamlss homstart_data
TRUE TRUE
JAGS jm_bamlss
TRUE TRUE
jm_mcmc jm_mode
TRUE TRUE
jm_predict jm_survplot
TRUE TRUE
la lasso
TRUE TRUE
lasso_coef lasso_plot
TRUE TRUE
lasso_stop lasso_transform
TRUE TRUE
lasso2 lin
TRUE TRUE
logNN_bamlss lognormal_bamlss
TRUE TRUE
make_formula make_weights
TRUE TRUE
mix_bamlss multinomial_bamlss
TRUE TRUE
mvn_chol mvn_modchol
TRUE TRUE
mvnchol_bamlss MVNORM
TRUE TRUE
mvnorm_bamlss n
TRUE TRUE
n.weights nbinom_bamlss
TRUE TRUE
neighbormatrix opt_bbfit
TRUE TRUE
opt_bbfitp opt_bfit
TRUE TRUE
opt_boost opt_boostm
TRUE TRUE
opt_Cox opt_JM
TRUE TRUE
opt_lasso parameters
TRUE TRUE
pathplot plot2d
TRUE TRUE
plot3d plotblock
TRUE TRUE
plotmap plotneighbors
TRUE TRUE
poisson_bamlss predict.bboost
TRUE TRUE
predict.ddnn Predict.matrix.kriging.smooth
TRUE TRUE
Predict.matrix.tensorX.smooth Predict.matrix.tensorX3.smooth
TRUE TRUE
predictn quant_bamlss
TRUE TRUE
randomize rb
TRUE TRUE
response_name results.bamlss.default
TRUE TRUE
rJM rmf
TRUE TRUE
rSurvTime2 s2
TRUE TRUE
sam_BayesX sam_Cox
TRUE TRUE
sam_GMCMC sam_JAGS
TRUE TRUE
sam_JM sam_MVNORM
TRUE TRUE
samples samplestats
TRUE TRUE
scale2 set.par
TRUE TRUE
set.starting.values Sichel_bamlss
TRUE TRUE
simJM simSurv
TRUE TRUE
sliceplot smooth_check
TRUE TRUE
smooth.construct smooth.construct.kr.smooth.spec
TRUE TRUE
smooth.construct.linear.smooth.spec smooth.construct.ms.smooth.spec
TRUE TRUE
smooth.construct.randombits.smooth.spec smooth.construct.tensorX.smooth.spec
TRUE TRUE
smooth.construct.tensorX3.smooth.spec stabsel
TRUE TRUE
surv_transform Surv2
TRUE TRUE
sx trans_AR1
TRUE TRUE
trans_random tx
TRUE TRUE
tx2 tx3
TRUE TRUE
tx4 Volcano
TRUE TRUE
WAIC weibull_bamlss
TRUE TRUE
ZANBI_bamlss ztnbinom_bamlss
TRUE TRUE Examples
There are 84 help pages with examples, from 84 (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 | 2025-02-21 13:12:39 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_1.9.0
[10] xfun_0.51 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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USER runner
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