serocalculator
Estimating Infection Rates from Serological Data
Description
Translates antibody levels measured in cross-sectional population samples into estimates of the frequency with which seroconversions (infections) occur in the sampled populations. Replaces the previous `seroincidence` package.
Downloads
763
Last 30 days
4330th
8K
Last 90 days
16.8K
Last year
Trend: +41.8% (30d vs prior 30d)
28
Last 30 days
124
Last 90 days
442
Last year
Trend: -30% (30d vs prior 30d)
6
Last 7 days
26
Last 30 days
0
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
Package required but not available: ‘labelled’ Packages suggested but not available for checking: 'mixtools', 'tidyverse' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 3, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE May 30, 2026
examples
Running examples in ‘serocalculator-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: strat_ests_scatterplot
> ### Title: Scatterplot method for 'summary.seroincidence.by' objects
>
...[truncated]...
serverSocket
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
graph.curve.params 4.198 0.037 5.469
autoplot.summary.seroincidence.by 2.192 0.111 8.390
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 2, 2026
ERROR 11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 25, 2026
package dependencies
Package required but not available: ‘labelled’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 8 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 26, 2026
Code & tests
Open call graph →Code intelligence has not been computed for this package yet.
Code
Structure
Lines of code
31,693
Files
309
Compiled share
1.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
42
Internal functions
80
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
4.20
testthat edition
3
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
78.6%
\dontrun example ratio
31.3%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
4
First release
2024-07-21
Latest release
2026-03-25
Avg cadence
188 days
Cold removal rate
100%
Dep drift
10
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.