Validation Report - EpiNow2@1.7.0
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 EpiNow2
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 90 |
| has_vignettes | 45 |
| export_help | 90 |
| has_website | TRUE |
| has_maintainer | Sebastian Funk sebastian.funk@lshtm.ac.uk |
| bugs_status | subscript out of bounds |
| has_source_control | https://github.com/epiforecasts/EpiNow2 |
| has_bug_reports_url | 1 |
| downloads_1yr | 13182 |
| reverse_dependencies | 0 |
| has_examples | 1 |
| dependencies | 27 |
| license | MIT + file LICENSE |
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 | checkmate | Imports |
| 2 | cli | Imports |
| 3 | data.table | Imports |
| 4 | futile.logger (>= 1.4) | Imports |
| 5 | ggplot2 | Imports |
| 6 | lifecycle | Imports |
| 7 | lubridate | Imports |
| 8 | methods | Imports |
| 9 | patchwork | Imports |
| 10 | posterior | Imports |
| 11 | purrr | Imports |
| 12 | R.utils (>= 2.0.0) | Imports |
| 13 | Rcpp (>= 0.12.0) | Imports |
| 14 | rlang (>= 0.4.7) | Imports |
| 15 | rstan (>= 2.26.0) | Imports |
| 16 | rstantools (>= 2.2.0) | Imports |
| 17 | runner | Imports |
| 18 | scales | Imports |
| 19 | stats | Imports |
| 20 | truncnorm | Imports |
| 21 | utils | Imports |
| 22 | BH (>= 1.66.0) | LinkingTo |
| 23 | Rcpp (>= 0.12.0) | LinkingTo |
| 24 | RcppEigen (>= 0.3.3.3.0) | LinkingTo |
| 25 | RcppParallel (>= 5.0.1) | LinkingTo |
| 26 | rstan (>= 2.26.0) | LinkingTo |
| 27 | StanHeaders (>= 2.26.0) | LinkingTo |
Package dependencies
Reverse dependencies
Overall the package has 0 reverse dependencies:
Namespace
Overall the package has 90 exported objects. 90 are documented:
add_breakpoints adjust_infection_to_report
TRUE TRUE
apply_tolerance backcalc_opts
TRUE TRUE
bootstrapped_dist_fit bound_dist
TRUE TRUE
calc_CrI calc_CrIs
TRUE TRUE
calc_summary_measures calc_summary_stats
TRUE TRUE
clean_nowcasts collapse
TRUE TRUE
convert_to_logmean convert_to_logsd
TRUE TRUE
convolve_and_scale delay_opts
TRUE TRUE
discretise discretize
TRUE TRUE
dist_fit dist_skel
TRUE TRUE
epinow epinow2_cmdstan_model
TRUE TRUE
estimate_delay estimate_infections
TRUE TRUE
estimate_secondary estimate_truncation
TRUE TRUE
expose_stan_fns extract_CrIs
TRUE TRUE
extract_inits extract_samples
TRUE TRUE
extract_stan_param fill_missing
TRUE TRUE
filter_leading_zeros fix_dist
TRUE TRUE
fix_parameters Fixed
TRUE TRUE
forecast_infections forecast_opts
TRUE TRUE
forecast_secondary Gamma
TRUE TRUE
gamma_dist_def generation_time_opts
TRUE TRUE
get_dist get_distribution
TRUE TRUE
get_generation_time get_incubation_period
TRUE TRUE
get_parameters get_pmf
TRUE TRUE
get_regional_results gp_opts
TRUE TRUE
growth_to_R gt_opts
TRUE TRUE
is_constrained lognorm_dist_def
TRUE TRUE
LogNormal make_conf
TRUE TRUE
map_prob_change new_dist_spec
TRUE TRUE
NonParametric Normal
TRUE TRUE
obs_opts opts_list
TRUE TRUE
plot_estimates plot_summary
TRUE TRUE
R_to_growth regional_epinow
TRUE TRUE
regional_runtimes regional_summary
TRUE TRUE
report_cases report_plots
TRUE TRUE
report_summary rstan_opts
TRUE TRUE
rstan_sampling_opts rstan_vb_opts
TRUE TRUE
rt_opts sample_approx_dist
TRUE TRUE
secondary_opts set_dt_single_thread
TRUE TRUE
setup_default_logging setup_future
TRUE TRUE
setup_logging simulate_infections
TRUE TRUE
simulate_secondary stan_laplace_opts
TRUE TRUE
stan_opts stan_pathfinder_opts
TRUE TRUE
stan_sampling_opts stan_vb_opts
TRUE TRUE
trunc_opts update_secondary_args
TRUE TRUE Examples
There are 173 help pages with examples, from 173 (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 04:18:06 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
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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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FALSE
ACCEPT_EULA Y
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HOMEBREW_NO_AUTO_UPDATE
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PHARMAPKGS_EXCLUDED_METRICS
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PHARMAPKGS_REMOTE_REPO
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PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
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