Last updated on 2025-02-04 02:50:05 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.2 | 2.30 | 41.84 | 44.14 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.2 | 1.96 | 31.81 | 33.77 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.2 | 72.97 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.2 | 96.91 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.2 | 4.00 | 66.00 | 70.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.2 | 2.64 | 89.07 | 91.71 | OK | |
| r-release-linux-x86_64 | 0.1.2 | 1.85 | 89.33 | 91.18 | OK | |
| r-release-macos-arm64 | 0.1.2 | 91.00 | OK | |||
| r-release-macos-x86_64 | 0.1.2 | 163.00 | OK | |||
| r-release-windows-x86_64 | 0.1.2 | 4.00 | 164.00 | 168.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.2 | 91.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.2 | 163.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.1.2 | 4.00 | 156.00 | 160.00 | OK |
Version: 0.1.2
Check: examples
Result: ERROR
Running examples in ‘cfr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cfr_rolling
> ### Title: Estimate static severity for an expanding time series
> ### Aliases: cfr_rolling
>
> ### ** Examples
>
> # load package data
> data("ebola1976")
>
> # estimate severity without correcting for delays
> cfr_static(ebola1976)
Error in cfr_static(ebola1976) :
Input data must have sequential dates with none missing or duplicated
Calls: cfr_static -> stopifnot
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.1.2
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(cfr)
>
> test_check("cfr")
`cfr_rolling()` is a convenience function to help understand how additional data influences the overall (static) severity. Use `cfr_time_varying()` instead to estimate severity changes over the course of the outbreak.
Total deaths = 99 and expected outcomes = 0 so setting expected outcomes = NA. If we were to assume
total deaths = expected outcomes, it would produce an estimate of 1.
[ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-estimate_outcomes.R:46:3',
'test-estimate_severity.R:47:3', 'test-prepare_data.R:35:3',
'test-prepare_data.R:126:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-delay_density.R:9:3'): CFR functions work with delay_density as lambda ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:9:3
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─rlang::try_fetch(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─cfr::cfr_static(ebola1976, delay_density = ddens)
9. └─base::stopifnot(...)
── Error ('test-delay_density.R:34:3'): CFR functions work with delay_density as <distcrete> ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:34:3
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─rlang::try_fetch(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─cfr::cfr_static(ebola1976, delay_density = ddens)
9. └─base::stopifnot(...)
── Error ('test-delay_density.R:59:3'): Input checking on delay_density works ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-delay_density.R:59:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─cfr::cfr_static(ebola1976, delay_density = ddens)
8. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:10:3'): Basic expectations for static ascertainment ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::estimate_ascertainment(data = ebola1976, severity_baseline = 0.7) at test-estimate_ascertainment.R:10:3
2. └─cfr::cfr_static(data, delay_density = delay_density)
3. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:40:3'): Correct for delays for static ascertainment ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::estimate_ascertainment(...) at test-estimate_ascertainment.R:40:3
2. └─cfr::cfr_static(data, delay_density = delay_density)
3. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:81:3'): Static ascertainment from vignette ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-estimate_ascertainment.R:81:3
2. └─rlang::cnd_signal(state$error)
── Error ('test-estimate_ascertainment.R:94:3'): Ascertainment > 1.0 throws a warning ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-estimate_ascertainment.R:94:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─cfr::estimate_ascertainment(...)
8. └─cfr::cfr_static(data, delay_density = delay_density)
9. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:119:3'): Ascertainment is statistically correct ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-estimate_ascertainment.R:119:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cfr::estimate_ascertainment(data, severity_baseline = 0.01)
5. └─cfr::cfr_static(data, delay_density = delay_density)
6. └─base::stopifnot(...)
── Error ('test-estimate_rolling.R:8:1'): (code run outside of `test_that()`) ──
Error in `cfr_rolling(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_rolling(data = ebola1976) at test-estimate_rolling.R:8:1
2. └─base::stopifnot(...)
── Error ('test-estimate_static.R:11:1'): (code run outside of `test_that()`) ──
Error in `cfr_static(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_static(data = ebola1976) at test-estimate_static.R:11:1
2. └─base::stopifnot(...)
── Error ('test-estimate_time_varying.R:11:1'): (code run outside of `test_that()`) ──
Error in `cfr_time_varying(ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_time_varying(ebola1976) at test-estimate_time_varying.R:11:1
2. └─base::stopifnot(...)
[ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cfr.Rmd’ using rmarkdown
Quitting from lines 93-97 [unnamed-chunk-3] (cfr.Rmd)
Error: processing vignette 'cfr.Rmd' failed with diagnostics:
Input data must have sequential dates with none missing or duplicated
--- failed re-building ‘cfr.Rmd’
--- re-building ‘data_from_incidence2.Rmd’ using rmarkdown
--- finished re-building ‘data_from_incidence2.Rmd’
--- re-building ‘delay_distributions.Rmd’ using rmarkdown
Quitting from lines 90-98 [unnamed-chunk-4] (delay_distributions.Rmd)
Error: processing vignette 'delay_distributions.Rmd' failed with diagnostics:
Input data must have sequential dates with none missing or duplicated
--- failed re-building ‘delay_distributions.Rmd’
--- re-building ‘estimate_ascertainment.Rmd’ using rmarkdown
Quitting from lines 115-121 [unnamed-chunk-3] (estimate_ascertainment.Rmd)
Error: processing vignette 'estimate_ascertainment.Rmd' failed with diagnostics:
Input data must have sequential dates with none missing or duplicated
--- failed re-building ‘estimate_ascertainment.Rmd’
--- re-building ‘estimate_static_severity.Rmd’ using rmarkdown
Quitting from lines 120-130 [unnamed-chunk-4] (estimate_static_severity.Rmd)
Error: processing vignette 'estimate_static_severity.Rmd' failed with diagnostics:
Input data must have sequential dates with none missing or duplicated
--- failed re-building ‘estimate_static_severity.Rmd’
--- re-building ‘estimate_time_varying_severity.Rmd’ using rmarkdown
Quitting from lines 113-133 [unnamed-chunk-4] (estimate_time_varying_severity.Rmd)
Error: processing vignette 'estimate_time_varying_severity.Rmd' failed with diagnostics:
Input data must have sequential dates with none missing or duplicated
--- failed re-building ‘estimate_time_varying_severity.Rmd’
--- re-building ‘software-permissions.Rmd’ using rmarkdown
--- finished re-building ‘software-permissions.Rmd’
SUMMARY: processing the following files failed:
‘cfr.Rmd’ ‘delay_distributions.Rmd’ ‘estimate_ascertainment.Rmd’
‘estimate_static_severity.Rmd’ ‘estimate_time_varying_severity.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.1.2
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(cfr)
>
> test_check("cfr")
`cfr_rolling()` is a convenience function to help understand how additional data influences the overall (static) severity. Use `cfr_time_varying()` instead to estimate severity changes over the course of the outbreak.
Total deaths = 99 and expected outcomes = 0 so setting expected outcomes = NA. If we were to assume
total deaths = expected outcomes, it would produce an estimate of 1.
[ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-estimate_outcomes.R:46:3',
'test-estimate_severity.R:47:3', 'test-prepare_data.R:35:3',
'test-prepare_data.R:126:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-delay_density.R:9:3'): CFR functions work with delay_density as lambda ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:9:3
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─rlang::try_fetch(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─cfr::cfr_static(ebola1976, delay_density = ddens)
9. └─base::stopifnot(...)
── Error ('test-delay_density.R:34:3'): CFR functions work with delay_density as <distcrete> ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:34:3
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─rlang::try_fetch(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─cfr::cfr_static(ebola1976, delay_density = ddens)
9. └─base::stopifnot(...)
── Error ('test-delay_density.R:59:3'): Input checking on delay_density works ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-delay_density.R:59:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─cfr::cfr_static(ebola1976, delay_density = ddens)
8. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:10:3'): Basic expectations for static ascertainment ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::estimate_ascertainment(data = ebola1976, severity_baseline = 0.7) at test-estimate_ascertainment.R:10:3
2. └─cfr::cfr_static(data, delay_density = delay_density)
3. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:40:3'): Correct for delays for static ascertainment ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::estimate_ascertainment(...) at test-estimate_ascertainment.R:40:3
2. └─cfr::cfr_static(data, delay_density = delay_density)
3. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:81:3'): Static ascertainment from vignette ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-estimate_ascertainment.R:81:3
2. └─rlang::cnd_signal(state$error)
── Error ('test-estimate_ascertainment.R:94:3'): Ascertainment > 1.0 throws a warning ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-estimate_ascertainment.R:94:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─cfr::estimate_ascertainment(...)
8. └─cfr::cfr_static(data, delay_density = delay_density)
9. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:119:3'): Ascertainment is statistically correct ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-estimate_ascertainment.R:119:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cfr::estimate_ascertainment(data, severity_baseline = 0.01)
5. └─cfr::cfr_static(data, delay_density = delay_density)
6. └─base::stopifnot(...)
── Error ('test-estimate_rolling.R:8:1'): (code run outside of `test_that()`) ──
Error in `cfr_rolling(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_rolling(data = ebola1976) at test-estimate_rolling.R:8:1
2. └─base::stopifnot(...)
── Error ('test-estimate_static.R:11:1'): (code run outside of `test_that()`) ──
Error in `cfr_static(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_static(data = ebola1976) at test-estimate_static.R:11:1
2. └─base::stopifnot(...)
── Error ('test-estimate_time_varying.R:11:1'): (code run outside of `test_that()`) ──
Error in `cfr_time_varying(ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_time_varying(ebola1976) at test-estimate_time_varying.R:11:1
2. └─base::stopifnot(...)
[ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.2
Check: examples
Result: ERROR
Running examples in ‘cfr-Ex.R’ failed
The error most likely occurred in:
> ### Name: cfr_rolling
> ### Title: Estimate static severity for an expanding time series
> ### Aliases: cfr_rolling
>
> ### ** Examples
>
> # load package data
> data("ebola1976")
>
> # estimate severity without correcting for delays
> cfr_static(ebola1976)
Error in cfr_static(ebola1976) :
Input data must have sequential dates with none missing or duplicated
Calls: cfr_static -> stopifnot
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 0.1.2
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [6s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(cfr)
>
> test_check("cfr")
`cfr_rolling()` is a convenience function to help understand how additional data influences the overall (static) severity. Use `cfr_time_varying()` instead to estimate severity changes over the course of the outbreak.
Total deaths = 99 and expected outcomes = 0 so setting expected outcomes = NA. If we were to assume
total deaths = expected outcomes, it would produce an estimate of 1.
[ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-estimate_outcomes.R:46:3',
'test-estimate_severity.R:47:3', 'test-prepare_data.R:35:3',
'test-prepare_data.R:126:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-delay_density.R:9:3'): CFR functions work with delay_density as lambda ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:9:3
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─rlang::try_fetch(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─cfr::cfr_static(ebola1976, delay_density = ddens)
9. └─base::stopifnot(...)
── Error ('test-delay_density.R:34:3'): CFR functions work with delay_density as <distcrete> ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:34:3
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─rlang::try_fetch(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─cfr::cfr_static(ebola1976, delay_density = ddens)
9. └─base::stopifnot(...)
── Error ('test-delay_density.R:59:3'): Input checking on delay_density works ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-delay_density.R:59:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─cfr::cfr_static(ebola1976, delay_density = ddens)
8. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:10:3'): Basic expectations for static ascertainment ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::estimate_ascertainment(data = ebola1976, severity_baseline = 0.7) at test-estimate_ascertainment.R:10:3
2. └─cfr::cfr_static(data, delay_density = delay_density)
3. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:40:3'): Correct for delays for static ascertainment ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::estimate_ascertainment(...) at test-estimate_ascertainment.R:40:3
2. └─cfr::cfr_static(data, delay_density = delay_density)
3. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:81:3'): Static ascertainment from vignette ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-estimate_ascertainment.R:81:3
2. └─rlang::cnd_signal(state$error)
── Error ('test-estimate_ascertainment.R:94:3'): Ascertainment > 1.0 throws a warning ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-estimate_ascertainment.R:94:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─cfr::estimate_ascertainment(...)
8. └─cfr::cfr_static(data, delay_density = delay_density)
9. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:119:3'): Ascertainment is statistically correct ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-estimate_ascertainment.R:119:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cfr::estimate_ascertainment(data, severity_baseline = 0.01)
5. └─cfr::cfr_static(data, delay_density = delay_density)
6. └─base::stopifnot(...)
── Error ('test-estimate_rolling.R:8:1'): (code run outside of `test_that()`) ──
Error in `cfr_rolling(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_rolling(data = ebola1976) at test-estimate_rolling.R:8:1
2. └─base::stopifnot(...)
── Error ('test-estimate_static.R:11:1'): (code run outside of `test_that()`) ──
Error in `cfr_static(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_static(data = ebola1976) at test-estimate_static.R:11:1
2. └─base::stopifnot(...)
── Error ('test-estimate_time_varying.R:11:1'): (code run outside of `test_that()`) ──
Error in `cfr_time_varying(ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_time_varying(ebola1976) at test-estimate_time_varying.R:11:1
2. └─base::stopifnot(...)
[ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘cfr.Rmd’ using rmarkdown
Quitting from lines 93-97 [unnamed-chunk-3] (cfr.Rmd)
Error: processing vignette 'cfr.Rmd' failed with diagnostics:
Input data must have sequential dates with none missing or duplicated
--- failed re-building ‘cfr.Rmd’
--- re-building ‘data_from_incidence2.Rmd’ using rmarkdown
--- finished re-building ‘data_from_incidence2.Rmd’
--- re-building ‘delay_distributions.Rmd’ using rmarkdown
Quitting from lines 90-98 [unnamed-chunk-4] (delay_distributions.Rmd)
Error: processing vignette 'delay_distributions.Rmd' failed with diagnostics:
Input data must have sequential dates with none missing or duplicated
--- failed re-building ‘delay_distributions.Rmd’
--- re-building ‘estimate_ascertainment.Rmd’ using rmarkdown
Quitting from lines 115-121 [unnamed-chunk-3] (estimate_ascertainment.Rmd)
Error: processing vignette 'estimate_ascertainment.Rmd' failed with diagnostics:
Input data must have sequential dates with none missing or duplicated
--- failed re-building ‘estimate_ascertainment.Rmd’
--- re-building ‘estimate_static_severity.Rmd’ using rmarkdown
Quitting from lines 120-130 [unnamed-chunk-4] (estimate_static_severity.Rmd)
Error: processing vignette 'estimate_static_severity.Rmd' failed with diagnostics:
Input data must have sequential dates with none missing or duplicated
--- failed re-building ‘estimate_static_severity.Rmd’
--- re-building ‘estimate_time_varying_severity.Rmd’ using rmarkdown
Quitting from lines 113-133 [unnamed-chunk-4] (estimate_time_varying_severity.Rmd)
Error: processing vignette 'estimate_time_varying_severity.Rmd' failed with diagnostics:
Input data must have sequential dates with none missing or duplicated
--- failed re-building ‘estimate_time_varying_severity.Rmd’
--- re-building ‘software-permissions.Rmd’ using rmarkdown
--- finished re-building ‘software-permissions.Rmd’
SUMMARY: processing the following files failed:
‘cfr.Rmd’ ‘delay_distributions.Rmd’ ‘estimate_ascertainment.Rmd’
‘estimate_static_severity.Rmd’ ‘estimate_time_varying_severity.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 0.1.2
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [19s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(cfr)
>
> test_check("cfr")
`cfr_rolling()` is a convenience function to help understand how additional data influences the overall (static) severity. Use `cfr_time_varying()` instead to estimate severity changes over the course of the outbreak.
Total deaths = 99 and expected outcomes = 0 so setting expected outcomes = NA. If we were to assume
total deaths = expected outcomes, it would produce an estimate of 1.
[ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-estimate_outcomes.R:46:3',
'test-estimate_severity.R:47:3', 'test-prepare_data.R:35:3',
'test-prepare_data.R:126:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-delay_density.R:9:3'): CFR functions work with delay_density as lambda ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:9:3
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─rlang::try_fetch(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─cfr::cfr_static(ebola1976, delay_density = ddens)
9. └─base::stopifnot(...)
── Error ('test-delay_density.R:34:3'): CFR functions work with delay_density as <distcrete> ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:34:3
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─rlang::try_fetch(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─cfr::cfr_static(ebola1976, delay_density = ddens)
9. └─base::stopifnot(...)
── Error ('test-delay_density.R:59:3'): Input checking on delay_density works ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-delay_density.R:59:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─cfr::cfr_static(ebola1976, delay_density = ddens)
8. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:10:3'): Basic expectations for static ascertainment ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::estimate_ascertainment(data = ebola1976, severity_baseline = 0.7) at test-estimate_ascertainment.R:10:3
2. └─cfr::cfr_static(data, delay_density = delay_density)
3. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:40:3'): Correct for delays for static ascertainment ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::estimate_ascertainment(...) at test-estimate_ascertainment.R:40:3
2. └─cfr::cfr_static(data, delay_density = delay_density)
3. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:81:3'): Static ascertainment from vignette ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-estimate_ascertainment.R:81:3
2. └─rlang::cnd_signal(state$error)
── Error ('test-estimate_ascertainment.R:94:3'): Ascertainment > 1.0 throws a warning ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-estimate_ascertainment.R:94:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─cfr::estimate_ascertainment(...)
8. └─cfr::cfr_static(data, delay_density = delay_density)
9. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:119:3'): Ascertainment is statistically correct ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-estimate_ascertainment.R:119:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cfr::estimate_ascertainment(data, severity_baseline = 0.01)
5. └─cfr::cfr_static(data, delay_density = delay_density)
6. └─base::stopifnot(...)
── Error ('test-estimate_rolling.R:8:1'): (code run outside of `test_that()`) ──
Error in `cfr_rolling(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_rolling(data = ebola1976) at test-estimate_rolling.R:8:1
2. └─base::stopifnot(...)
── Error ('test-estimate_static.R:11:1'): (code run outside of `test_that()`) ──
Error in `cfr_static(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_static(data = ebola1976) at test-estimate_static.R:11:1
2. └─base::stopifnot(...)
── Error ('test-estimate_time_varying.R:11:1'): (code run outside of `test_that()`) ──
Error in `cfr_time_varying(ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_time_varying(ebola1976) at test-estimate_time_varying.R:11:1
2. └─base::stopifnot(...)
[ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.2
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(cfr)
>
> test_check("cfr")
`cfr_rolling()` is a convenience function to help understand how additional data influences the overall (static) severity. Use `cfr_time_varying()` instead to estimate severity changes over the course of the outbreak.
Total deaths = 99 and expected outcomes = 0 so setting expected outcomes = NA. If we were to assume
total deaths = expected outcomes, it would produce an estimate of 1.
[ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-estimate_outcomes.R:46:3',
'test-estimate_severity.R:47:3', 'test-prepare_data.R:35:3',
'test-prepare_data.R:126:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-delay_density.R:9:3'): CFR functions work with delay_density as lambda ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:9:3
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─rlang::try_fetch(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─cfr::cfr_static(ebola1976, delay_density = ddens)
9. └─base::stopifnot(...)
── Error ('test-delay_density.R:34:3'): CFR functions work with delay_density as <distcrete> ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:34:3
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─rlang::try_fetch(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─cfr::cfr_static(ebola1976, delay_density = ddens)
9. └─base::stopifnot(...)
── Error ('test-delay_density.R:59:3'): Input checking on delay_density works ──
Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-delay_density.R:59:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─cfr::cfr_static(ebola1976, delay_density = ddens)
8. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:10:3'): Basic expectations for static ascertainment ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::estimate_ascertainment(data = ebola1976, severity_baseline = 0.7) at test-estimate_ascertainment.R:10:3
2. └─cfr::cfr_static(data, delay_density = delay_density)
3. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:40:3'): Correct for delays for static ascertainment ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::estimate_ascertainment(...) at test-estimate_ascertainment.R:40:3
2. └─cfr::cfr_static(data, delay_density = delay_density)
3. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:81:3'): Static ascertainment from vignette ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-estimate_ascertainment.R:81:3
2. └─rlang::cnd_signal(state$error)
── Error ('test-estimate_ascertainment.R:94:3'): Ascertainment > 1.0 throws a warning ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-estimate_ascertainment.R:94:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─cfr::estimate_ascertainment(...)
8. └─cfr::cfr_static(data, delay_density = delay_density)
9. └─base::stopifnot(...)
── Error ('test-estimate_ascertainment.R:119:3'): Ascertainment is statistically correct ──
Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-estimate_ascertainment.R:119:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cfr::estimate_ascertainment(data, severity_baseline = 0.01)
5. └─cfr::cfr_static(data, delay_density = delay_density)
6. └─base::stopifnot(...)
── Error ('test-estimate_rolling.R:8:1'): (code run outside of `test_that()`) ──
Error in `cfr_rolling(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_rolling(data = ebola1976) at test-estimate_rolling.R:8:1
2. └─base::stopifnot(...)
── Error ('test-estimate_static.R:11:1'): (code run outside of `test_that()`) ──
Error in `cfr_static(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_static(data = ebola1976) at test-estimate_static.R:11:1
2. └─base::stopifnot(...)
── Error ('test-estimate_time_varying.R:11:1'): (code run outside of `test_that()`) ──
Error in `cfr_time_varying(ebola1976)`: Input data must have sequential dates with none missing or duplicated
Backtrace:
▆
1. └─cfr::cfr_time_varying(ebola1976) at test-estimate_time_varying.R:11:1
2. └─base::stopifnot(...)
[ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64