Running ‘testthat.R’ [78s/121s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SimplyAgree)
  > 
  > test_check("SimplyAgree")
  Limit of Agreement = 95%
  Nested Data Points (true value may vary)
  
  Hypothesis Test: don't reject h0
  
  ###- Bland-Altman Limits of Agreement (LoA) -###
            Estimate Lower CI Upper CI CI Level
  Bias        0.7255  -0.6694   2.1204     0.95
  Lower LoA  -2.1404  -7.5748  -0.5891     0.90
  Upper LoA   3.5915   2.0402   9.0259     0.90
  
  ###- Concordance Correlation Coefficient (CCC) -###
  CCC: 0.4454, 95% C.I. [0.2432, 0.6105]
  *Estimated via U-statistics; may be biased
  Limit of Agreement = 95%
  Nested Data Points (true value may vary)
  
  Hypothesis Test: don't reject h0
  
  ###- Bland-Altman Limits of Agreement (LoA) -###
            Estimate Lower CI Upper CI CI Level
  Bias        0.7255  -0.6694   2.1204     0.95
  Lower LoA  -2.1404  -7.5748  -0.5891     0.90
  Upper LoA   3.5915   2.0402   9.0259     0.90
  
  ###- Concordance Correlation Coefficient (CCC) -###
  CCC: 0.4454, 95% C.I. [0.2432, 0.6105]
  *Estimated via U-statistics; may be biased
  Limit of Agreement = 95%
  Nested Data Points (true value may vary)
  
  Hypothesis Test: don't reject h0
  
  ###- Bland-Altman Limits of Agreement (LoA) -###
            Estimate Lower CI Upper CI CI Level
  Bias        0.7255  -0.6694   2.1204     0.95
  Lower LoA  -2.1404  -7.5748  -0.5891     0.90
  Upper LoA   3.5915   2.0402   9.0259     0.90
  
  ###- Concordance Correlation Coefficient (CCC) -###
  CCC: 0.4454, 95% C.I. [0.2432, 0.6105]
  *Estimated via U-statistics; may be biased
  Limit of Agreement = 80%
  Nested Data Points (true value may vary)
  
  Hypothesis Test: reject h0
  
  ###- Bland-Altman Limits of Agreement (LoA) -###
            Estimate Lower CI Upper CI CI Level
  Bias        0.7255 -0.09316   1.5442     0.75
  Lower LoA  -1.1484 -2.28235  -0.6037     0.50
  Upper LoA   2.5995  2.05481   3.7334     0.50
  
  ###- Concordance Correlation Coefficient (CCC) -###
  CCC: 0.4454, 75% C.I. [0.3306, 0.5472]
  *Estimated via U-statistics; may be biased
  Limit of Agreement = 80%
  Nested Data Points (true value may vary)
  
  Hypothesis Test: reject h0
  
  ###- Bland-Altman Limits of Agreement (LoA) -###
            Estimate Lower CI Upper CI CI Level
  Bias        0.7255 -0.09316   1.5442     0.75
  Lower LoA  -1.1484 -2.28235  -0.6037     0.50
  Upper LoA   2.5995  2.05481   3.7334     0.50
  
  ###- Concordance Correlation Coefficient (CCC) -###
  CCC: 0.4454, 75% C.I. [0.3306, 0.5472]
  *Estimated via U-statistics; may be biased
  Limit of Agreement = 95%
  Replicate Data Points (true value does not vary)
  
  Hypothesis Test: No Hypothesis Test
  
  ###- Bland-Altman Limits of Agreement (LoA) -###
    Estimate Lower CI Upper CI CI Level
  1   0.7152  -0.6667   2.0971     0.95
  2  -2.2317  -9.7686  -0.4779     0.95
  3   3.6622   1.9084  11.1990     0.95
  
  ###- Concordance Correlation Coefficient* (CCC) -###
  CCC: 0.1069, 95% C.I. [-0.1596, 0.3588]
  *Estimated via U-statistics
  Weighted Deming Regression with 95% C.I.
               coef     bias     se df lower.ci upper.ci       t p.value
  Intercept -0.3251  0.20653 1.9609  8  -4.8470    4.197 -0.1658  0.8724
  Slope      1.0309 -0.02537 0.2189  8   0.5261    1.536  0.1413  0.8911
  Weighted Deming Regression with 95% C.I.
              coef     bias     se df lower.ci upper.ci      t p.value
  Intercept 3.4071 -0.05338 1.7556  2   -4.146   10.961  1.941  0.1918
  Slope     0.2828 -0.01214 0.3859  2   -1.378    1.943 -1.858  0.2042
  95% Limits of Agreement with Parametric Bootstrap 95% Confidence Intervals 
     Average Condition  Measures Estimate Lower CI Upper CI
  1    36.67   23C/5.5      Bias   0.3206  0.08726  0.48915
  2    36.67   23C/5.5 Lower LoA  -0.1665 -0.25819  0.19144
  3    36.67   23C/5.5 Upper LoA   0.8078  0.42496  1.01349
  4    36.67   33C/5.5      Bias   0.2780  0.16884  0.51282
  5    36.67   33C/5.5 Lower LoA  -0.1214 -0.58734  0.22958
  6    36.67   33C/5.5 Upper LoA   0.6775  0.51631  1.07714
  7    36.67   33C/7.5      Bias   0.2812  0.16681  0.53033
  8    36.67   33C/7.5 Lower LoA  -0.1882 -0.41863  0.24767
  9    36.67   33C/7.5 Upper LoA   0.7505  0.57587  1.05208
  10   36.93   23C/5.5      Bias   0.2762  0.08502  0.43684
  11   36.93   23C/5.5 Lower LoA  -0.2109 -0.34938  0.04138
  12   36.93   23C/5.5 Upper LoA   0.7634  0.42271  0.94210
  13   36.93   33C/5.5      Bias   0.2336  0.05602  0.36136
  14   36.93   33C/5.5 Lower LoA  -0.1658 -0.58237  0.08467
  15   36.93   33C/5.5 Upper LoA   0.6331  0.45604  1.06571
  16   36.93   33C/7.5      Bias   0.2368  0.09711  0.46682
  17   36.93   33C/7.5 Lower LoA  -0.2326 -0.44371  0.10502
  18   36.93   33C/7.5 Upper LoA   0.7061  0.47966  1.08284
  19   37.29   23C/5.5      Bias   0.2147 -0.05331  0.50197
  20   37.29   23C/5.5 Lower LoA  -0.2724 -0.56061  0.05707
  21   37.29   23C/5.5 Upper LoA   0.7019  0.31864  0.95481
  22   37.29   33C/5.5      Bias   0.1721 -0.12590  0.30239
  23   37.29   33C/5.5 Lower LoA  -0.2273 -0.58716 -0.07076
  24   37.29   33C/5.5 Upper LoA   0.5715  0.28043  1.09528
  25   37.29   33C/7.5      Bias   0.1752 -0.06191  0.52243
  26   37.29   33C/7.5 Lower LoA  -0.2941 -0.51101  0.10767
  27   37.29   33C/7.5 Upper LoA   0.6446  0.31343  1.12544
  95% Limits of Agreement with Bootstrap 95% Confidence Intervals 
              estimate   lower.ci   upper.ci
  Mean Bias  0.2510000  0.1570124  0.3128609
  Lower LoA -0.1887407 -0.2883997 -0.1073991
  Upper LoA  0.6907407  0.5929600  0.8167491
  
  Coefficient of Variation (%):  19.1
  Standard Error of Measurement (SEM):  1.01
  Standard Error of the Estimate (SEE):  2.62
  Standard Error of Prediction (SEP):  4.06
  
  Intraclass Correlation Coefficients with  95 % C.I.
             Model         Measures  Type    ICC Lower CI Upper CI
  1 one-way random        Agreement  ICC1 0.1657 -0.09672   0.6434
  2 two-way random        Agreement  ICC2 0.2898  0.04290   0.6911
  3  two-way fixed      Consistency  ICC3 0.7148  0.41183   0.9258
  4 one-way random   Avg. Agreement ICC1k 0.4428 -0.54504   0.8783
  5 two-way random   Avg. Agreement ICC2k 0.6201  0.15204   0.8995
  6  two-way fixed Avg. Consistency ICC3k 0.9093  0.73690   0.9804
  
  
  Coefficient of Variation (%):  19.1
  Standard Error of Measurement (SEM):  1.01
  Standard Error of the Estimate (SEE):  2.62
  Standard Error of Prediction (SEP):  4.06
  
  Intraclass Correlation Coefficients with  95 % C.I.
             Model         Measures  Type    ICC Lower CI Upper CI
  1 one-way random        Agreement  ICC1 0.1657 -0.09672   0.6434
  2 two-way random        Agreement  ICC2 0.2898  0.04290   0.6911
  3  two-way fixed      Consistency  ICC3 0.7148  0.41184   0.9258
  4 one-way random   Avg. Agreement ICC1k 0.4428 -0.54504   0.8783
  5 two-way random   Avg. Agreement ICC2k 0.6201  0.15204   0.8995
  6  two-way fixed Avg. Consistency ICC3k 0.9093  0.73690   0.9804
  
  
  Coefficient of Variation (%): 19.1 95% C.I. [13.1, 27.1]
  Standard Error of Measurement (SEM): 1.01 95% C.I. [0.692, 1.43]
  Standard Error of the Estimate (SEE): 2.62 95% C.I. [1.55, 4.2]
  Standard Error of Prediction (SEP): 4.06 95% C.I. [2.34, 7.75]
  
  Intraclass Correlation Coefficients
             Model         Measures  Type    ICC Lower CI Upper CI
  1 one-way random        Agreement  ICC1 0.1657 -0.09672   0.6434
  2 two-way random        Agreement  ICC2 0.2898  0.04290   0.6911
  3  two-way fixed      Consistency  ICC3 0.7148  0.41184   0.9258
  4 one-way random   Avg. Agreement ICC1k 0.4428 -0.54504   0.8783
  5 two-way random   Avg. Agreement ICC2k 0.6201  0.15204   0.8995
  6  two-way fixed Avg. Consistency ICC3k 0.9093  0.73690   0.9804
  
  
  Coefficient of Variation (%):  19.1
  Standard Error of Measurement (SEM):  1.01
  Standard Error of the Estimate (SEE):  2.62
  Standard Error of Prediction (SEP):  4.06
  
  Intraclass Correlation Coefficients with  95 % C.I.
             Model         Measures  Type    ICC Lower CI Upper CI
  1 one-way random        Agreement  ICC1 0.1657 -0.09672   0.6434
  2 two-way random        Agreement  ICC2 0.2898  0.04290   0.6911
  3  two-way fixed      Consistency  ICC3 0.7148  0.41184   0.9258
  4 one-way random   Avg. Agreement ICC1k 0.4428 -0.54504   0.8783
  5 two-way random   Avg. Agreement ICC2k 0.6201  0.15204   0.8995
  6  two-way fixed Avg. Consistency ICC3k 0.9093  0.73690   0.9804
  
  Limit of Agreement = 95%
  
  ###- Shieh Results -###
  Exact 90% C.I.  [-2.6418, 3.5184]
  Hypothesis Test: don't reject h0
  
  ###- Bland-Altman Limits of Agreement (LoA) -###
            Estimate Lower CI Upper CI CI Level
  Bias        0.4383  -0.1669    1.044     0.95
  Lower LoA  -1.9470  -2.6296   -1.264     0.90
  Upper LoA   2.8237   2.1411    3.506     0.90
  
  ###- Concordance Correlation Coefficient (CCC) -###
  CCC: 0.4791, 95% C.I. [0.1276, 0.7237]
  [ FAIL 4 | WARN 9 | SKIP 0 | PASS 62 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-agree_nest.R:106:3'): examples from Zou ────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ggeffects'
  Backtrace:
      ▆
   1. ├─base::plot(nest_test3, type = 1, smooth_method = "gam") at test-agree_nest.R:106:3
   2. ├─SimplyAgree:::plot.simple_agree(nest_test3, type = 1, smooth_method = "gam")
   3. │ └─SimplyAgree:::simple_ba_plot(...)
   4. │   └─base::as.data.frame(ggeffects::ggemmeans(gam1, "mean"))
   5. └─base::loadNamespace(x)
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base (local) withOneRestart(expr, restarts[[1L]])
   8.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-agree_np.R:24:5'): Simple Use Run Through ──────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ggeffects'
  Backtrace:
      ▆
   1. ├─base::plot(agree1, smooth_method = "gam") at test-agree_np.R:24:5
   2. ├─SimplyAgree:::plot.simple_agree(agree1, smooth_method = "gam")
   3. │ └─SimplyAgree:::simple_ba_plot(...)
   4. │   └─base::as.data.frame(ggeffects::ggemmeans(gam1, "mean"))
   5. └─base::loadNamespace(x)
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base (local) withOneRestart(expr, restarts[[1L]])
   8.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-agree_reps.R:70:3'): examples from Zou ─────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ggeffects'
  Backtrace:
      ▆
   1. ├─base::plot(reps_test, type = 1, smooth_method = "gam") at test-agree_reps.R:70:3
   2. ├─SimplyAgree:::plot.simple_agree(reps_test, type = 1, smooth_method = "gam")
   3. │ └─SimplyAgree:::simple_ba_plot(...)
   4. │   └─base::as.data.frame(ggeffects::ggemmeans(gam1, "mean"))
   5. └─base::loadNamespace(x)
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base (local) withOneRestart(expr, restarts[[1L]])
   8.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_agree_test.R:72:3'): Simple Use Run Through ────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ggeffects'
  Backtrace:
      ▆
   1. ├─base::plot(agree1, type = 1, smooth_method = "gam") at test_agree_test.R:72:3
   2. ├─SimplyAgree:::plot.simple_agree(agree1, type = 1, smooth_method = "gam")
   3. │ └─SimplyAgree:::simple_ba_plot(...)
   4. │   └─base::as.data.frame(ggeffects::ggemmeans(gam1, "mean"))
   5. └─base::loadNamespace(x)
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base (local) withOneRestart(expr, restarts[[1L]])
   8.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 4 | WARN 9 | SKIP 0 | PASS 62 ]
  Error: Test failures
  Execution halted