Validation Report - epiworldR@0.6.1.0
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 epiworldR
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 162 |
| has_vignettes | 10 |
| export_help | 162 |
| has_website | TRUE |
| has_maintainer | Andrew Pulsipher pulsipher.a@gmail.com |
| bugs_status | subscript out of bounds |
| has_source_control | https://github.com/UofUEpiBio/epiworldR |
| has_bug_reports_url | 1 |
| downloads_1yr | 4035 |
| reverse_dependencies | 1 |
| has_examples | 1 |
| dependencies | 2 |
| 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 | cpp11 | LinkingTo |
| 2 | utils | Imports |
Package dependencies
Reverse dependencies
Overall the package has 1 reverse dependencies:
epiworldRShiny
Namespace
Overall the package has 162 exported objects. 162 are documented:
add_entity add_globalevent
TRUE TRUE
add_param add_tool
TRUE TRUE
add_tool_agent add_tool_n
TRUE TRUE
add_virus add_virus_agent
TRUE TRUE
add_virus_n agents_from_edgelist
TRUE TRUE
agents_smallworld change_state
TRUE TRUE
clone_model distribute_entity_randomly
TRUE TRUE
distribute_entity_to_set distribute_tool_randomly
TRUE TRUE
distribute_tool_to_set distribute_virus_randomly
TRUE TRUE
distribute_virus_set entity
TRUE TRUE
entity_add_agent entity_get_agents
TRUE TRUE
get_agents get_agents_data_ncols
TRUE TRUE
get_agents_states get_agents_tools
TRUE TRUE
get_all_accepted_kernel_scores get_all_accepted_params
TRUE TRUE
get_all_accepted_stats get_all_sample_acceptance
TRUE TRUE
get_all_sample_drawn_prob get_all_sample_kernel_scores
TRUE TRUE
get_all_sample_params get_all_sample_stats
TRUE TRUE
get_current_accepted_params get_current_accepted_stats
TRUE TRUE
get_current_proposed_params get_current_proposed_stats
TRUE TRUE
get_entities get_entity_name
TRUE TRUE
get_entity_size get_generation_time
TRUE TRUE
get_hist_tool get_hist_total
TRUE TRUE
get_hist_transition_matrix get_hist_virus
TRUE TRUE
get_initial_params get_mean_params
TRUE TRUE
get_mean_stats get_n_params
TRUE TRUE
get_n_replicates get_n_samples
TRUE TRUE
get_n_stats get_n_tools
TRUE TRUE
get_n_viruses get_name
TRUE TRUE
get_name_tool get_name_virus
TRUE TRUE
get_ndays get_network
TRUE TRUE
get_observed_stats get_param
TRUE TRUE
get_reproductive_number get_state
TRUE TRUE
get_states get_today_total
TRUE TRUE
get_tool get_transition_probability
TRUE TRUE
get_transmissions get_virus
TRUE TRUE
globalaction_fun globalaction_set_params
TRUE TRUE
globalaction_tool globalaction_tool_logit
TRUE TRUE
globalevent_fun globalevent_set_params
TRUE TRUE
globalevent_tool globalevent_tool_logit
TRUE TRUE
has_tool has_virus
TRUE TRUE
initial_states LFMCMC
TRUE TRUE
load_agents_entities_ties make_saver
TRUE TRUE
ModelDiffNet ModelSEIR
TRUE TRUE
ModelSEIRCONN ModelSEIRD
TRUE TRUE
ModelSEIRDCONN ModelSEIRMixing
TRUE TRUE
ModelSIR ModelSIRCONN
TRUE TRUE
ModelSIRD ModelSIRDCONN
TRUE TRUE
ModelSIRLogit ModelSIRMixing
TRUE TRUE
ModelSIS ModelSISD
TRUE TRUE
ModelSURV plot_generation_time
TRUE TRUE
plot_incidence plot_reproductive_number
TRUE TRUE
queuing_off queuing_on
TRUE TRUE
rm_entity rm_globalevent
TRUE TRUE
rm_tool rm_virus
TRUE TRUE
run run_lfmcmc
TRUE TRUE
run_multiple run_multiple_get_results
TRUE TRUE
set_agents_data set_death_reduction
TRUE TRUE
set_death_reduction_fun set_death_reduction_ptr
TRUE TRUE
set_distribution_entity set_distribution_tool
TRUE TRUE
set_distribution_virus set_incubation
TRUE TRUE
set_incubation_fun set_incubation_ptr
TRUE TRUE
set_kernel_fun set_name
TRUE TRUE
set_name_tool set_name_virus
TRUE TRUE
set_observed_data set_param
TRUE TRUE
set_params_names set_prob_death
TRUE TRUE
set_prob_death_fun set_prob_death_ptr
TRUE TRUE
set_prob_infecting set_prob_infecting_fun
TRUE TRUE
set_prob_infecting_ptr set_prob_recovery
TRUE TRUE
set_prob_recovery_fun set_prob_recovery_ptr
TRUE TRUE
set_proposal_fun set_recovery_enhancer
TRUE TRUE
set_recovery_enhancer_fun set_recovery_enhancer_ptr
TRUE TRUE
set_simulation_fun set_stats_names
TRUE TRUE
set_summary_fun set_susceptibility_reduction
TRUE TRUE
set_susceptibility_reduction_fun set_susceptibility_reduction_ptr
TRUE TRUE
set_transmission_reduction set_transmission_reduction_fun
TRUE TRUE
set_transmission_reduction_ptr size
TRUE TRUE
today tool
TRUE TRUE
tool_fun_logit use_kernel_fun_gaussian
TRUE TRUE
use_proposal_norm_reflective verbose_off
TRUE TRUE
verbose_on virus
TRUE TRUE
virus_fun_logit virus_set_state
TRUE TRUE Examples
There are 26 help pages with examples, from 26 (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 04:20:12 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
_R_CHECK_SYSTEM_CLOCK_
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ACCEPT_EULA Y
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GITHUB_TRIGGERING_ACTOR
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GRADLE_HOME /usr/share/gradle-8.12.1
HOME /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
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HOMEBREW_NO_AUTO_UPDATE
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MAKE make
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PERFLOG_LOCATION_SETTING
RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
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PHARMAPKGS_LIMIT 1000
PHARMAPKGS_PLATFORM ubuntu-22.04
PHARMAPKGS_R_VERSION 4.4
PHARMAPKGS_REMOTE_REPO
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PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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POWERSHELL_DISTRIBUTION_CHANNEL
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YES
PWD /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_BIN_PATH /opt/quarto/bin
QUARTO_DENO /opt/quarto/bin/tools/x86_64/deno
QUARTO_DOCUMENT_PATH /home/runner/work/pharmapkgs/pharmapkgs/inst/report
QUARTO_PROFILE
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R_PLATFORM x86_64-pc-linux-gnu
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RUNNER_ENVIRONMENT github-hosted
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TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
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XDG_CONFIG_HOME /home/runner/.config
XDG_RUNTIME_DIR /run/user/1001These are the options set to generate the report:
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$bitmapType
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$browser
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$callr.condition_handler_cli_message
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<bytecode: 0x55afbdf12910>
<environment: namespace:cli>
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<environment: namespace:knitr>
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$rlang_trace_top_env
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$str
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$str$deparse.lines
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$str$formatNum
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<environment: 0x55afbd3ea520>
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mode "w+b"
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can read "yes"
can write "yes"
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$width
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