AMISforInfectiousDiseases
Implement the AMIS Algorithm for Infectious Disease Models
Description
Implements the Adaptive Multiple Importance Sampling (AMIS) algorithm, as described by Retkute et al. (2021, <doi:10.1214/21-AOAS1486>), to estimate key epidemiological parameters by combining outputs from a geostatistical model of infectious diseases (such as prevalence, incidence, or relative risk) with a disease transmission model. Utilising the resulting posterior distributions, the package enables forward projections at the local level.
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16091st
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Last 90 days
2.8K
Last year
Trend: +59.2% (30d vs prior 30d)
24
Last 30 days
120
Last 90 days
444
Last year
Trend: -40% (30d vs prior 30d)
10
Last 7 days
47
Last 30 days
2
All-time
autoCRAN-only: this name is served only by autoCRAN, so the count is exact.
CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
package dependencies
Packages required but not available: 'Hmisc', 'weights' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 2, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 10, 2026
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'ascariasis.Rmd' using rmarkdown File figure/asc_plot_mixt-1.png not found in resource path Error: processing vignette 'ascariasis.Rmd' failed with diagnostics: pandoc document conversion failed with ...[truncated]... iagnostics: pandoc document conversion failed with error 99 --- failed re-building 'simulation_study.Rmd' SUMMARY: processing the following files failed: 'ascariasis.Rmd' 'simulation_study.Rmd' Error: Vignette re-building failed. Execution halted
Code & tests
Open call graph →Line coverage
–
Expression
–
Tests / Examples
–
Functions
66 5 exported
Complexity
8.8 avg / 76 max
Call network
66 nodes / 57 edges
Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
5,773
Files
46
Compiled share
28.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
5
Internal functions
32
Recent export changes
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
0%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
No
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2025-01-20
Latest release
2025-01-20
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.
Dependency Network
Version History
1 trackedR Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Jan 20, 2025. Releases before tracking aren’t shown.