Running ‘testthat.R’ [6s/8s]
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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(survinger)
  > 
  > test_check("survinger")
  -- Lineage Prevalence Estimate -------------------------------------------------
  Lineage: "BA.2.86"
  Method: "hajek"
  Confidence level: 0.95
  Time periods: 1
  
  # A tibble: 1 x 5
    time     prevalence    se ci_lower ci_upper
    <chr>         <dbl> <dbl>    <dbl>    <dbl>
  1 2024-W01        0.3  0.05      0.2      0.4
  -- Optimal Sequencing Allocation -----------------------------------------------
  Objective: min_mse
  Total capacity: 100 sequences
  Strata: 1
  
  # A tibble: 1 x 2
    stratum n_allocated
    <chr>         <dbl>
  1 A               100
  -- Reporting Delay Distribution ------------------------------------------------
  Distribution: "negbin"
  Strata: none (pooled)
  Observations: 100
  Mean delay: 10 days
  
  # A tibble: 1 x 3
    stratum    mu  size
    <chr>   <dbl> <dbl>
  1 all        10     3
  -- Genomic Surveillance Design -------------------------------------------------
  Observations: 421
  Strata: 3 (region)
  Date range: 2024-01-01 to 2024-01-28
  Lineages: 4
  Sources: clinical, sentinel, wastewater
  Weight range: [5.354, 20.231]
  -- Surveillance Design Summary -------------------------------------------------
  Sequences: 421
  Strata: 3 (region)
  Period: 2024-01-01 to 2024-01-28
  
  -- Top lineages 
  BA.5: 252
  XBB.1.5: 121
  Other: 34
  BA.2.86: 14
  
  -- Sampling weights 
     Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    5.354   8.813  12.273  12.619  16.252  20.231 
  -- Optimal Sequencing Allocation -----------------------------------------------
  Objective: min_mse
  Total capacity: 100 sequences
  Strata: 3
  
  # A tibble: 3 x 3
    region   n_allocated proportion
    <chr>          <int>      <dbl>
  1 Region_A          24       0.24
  2 Region_B           8       0.08
  3 Region_C          68       0.68
  Saving _problems/test-03-prevalence-63.R
  -- Reporting Delay Distribution ------------------------------------------------
  Distribution: "negbin"
  Strata: none (pooled)
  Observations: 768
  Mean delay: 10 days
  
  # A tibble: 1 x 5
    stratum distribution    mu  size converged
    <chr>   <chr>        <dbl> <dbl> <lgl>    
  1 all     negbin        10.1  2.96 TRUE     
  -- Design-Weighted Delay-Adjusted Prevalence -----------------------------------
  Correction: "design:hajek+delay:direct"
  
  # A tibble: 10 x 9
     time     lineage n_obs_raw n_obs_adjusted prevalence     se ci_lower ci_upper
     <chr>    <chr>       <int>          <dbl>      <dbl>  <dbl>    <dbl>    <dbl>
   1 2024-W01 BA.2.86        56           56.0     0.0147 0.0256        0   0.0649
   2 2024-W02 BA.2.86        58           58.0     0.117  0.0726        0   0.260 
   3 2024-W03 BA.2.86        52           52.0     0      0             0   0     
   4 2024-W04 BA.2.86        53           53.0     0.0361 0.0257        0   0.0863
   5 2024-W05 BA.2.86        52           52.0     0.0135 0.0256        0   0.0638
   6 2024-W06 BA.2.86        68           68.0     0.0444 0.0409        0   0.125 
   7 2024-W07 BA.2.86        46           46.0     0      0             0   0     
   8 2024-W08 BA.2.86        51           51.0     0.0693 0.0518        0   0.171 
   9 2024-W09 BA.2.86        48           48.0     0.0659 0.0610        0   0.185 
  10 2024-W10 BA.2.86        66           66.2     0.0549 0.0465        0   0.146 
  # i 1 more variable: mean_report_prob <dbl>
  
  -- Surveillance System Report --------------------------------------------------
  
  -- Design Structure --
  
  Total sequences: 3,031
  Strata: 3
  Period: 2024-01-01 to 2024-02-25
  
  -- Sequencing Inequality --
  
  Rate range: 3.29% to 45.56%
  Rate ratio: 13.8x
  Gini coefficient: 0.365
  i Moderate inequality. Weighting recommended.
  
  -- Estimation Impact --
  
  Effective sample size: 1501 (49.5% of total)
  Mean |weighted - naive| bias: 2.07 percentage points
  
  -- Detection Power --
  
  Target: detect BA.5 at 1% prevalence
  Weekly detection probability: 97.8%
  Sequences needed for 95% detection: 299
  -- Detection Power Curve -------------------------------------------------------
  Prevalence range: 0.1% to 5%
  
  
  -- Thresholds 
  50% detection requires 0.2% prevalence
  80% detection requires 0.5% prevalence
  95% detection requires 0.8% prevalence
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 159 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-03-prevalence.R:63:3'): CI contains point estimate ───────────
  Expected `all(est$prevalence >= est$ci_lower)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 159 ]
  Error:
  ! Test failures.
  Execution halted