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Type 'q()' to quit R. > library(testthat) > library(SimplyAgree) > > test_check("SimplyAgree") Bland-Altman Limits of Agreement (LoA) of the Ratio (x/y) 95% LoA @ 5% Alpha-Level Log-transformed Nested Data Bias Bias CI Lower LoA Upper LoA LoA CI 1.121 [0.7268, 1.7277] 0.6486 1.936 [0.4303, 2.9177] Coefficient of Variation (%) = 32.1799 MOVER Limits of Agreement (LoA) 95% LoA @ 2.5% Alpha-Level Nested Data Average of Both Methods Bias Bias CI Lower LoA Upper LoA 3.905 0.6195 [-1.6077, 2.8466] -2.231 3.470 5.465 0.7228 [-1.6412, 3.0868] -2.128 3.573 7.395 0.8506 [-1.3945, 3.0958] -2.000 3.701 LoA CI [-9.7791, 11.0181] [-9.6758, 11.1214] [-9.548, 11.2492] SD of Differences = 1.4543 MOVER Limits of Agreement (LoA) of the Ratio (x/y) 95% LoA @ 5% Alpha-Level Log-transformed Nested Data Bias Bias CI Lower LoA Upper LoA LoA CI 1.121 [0.7268, 1.7277] 0.6486 1.936 [0.2315, 5.4244] Coefficient of Variation (%) = 32.1799 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 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 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 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 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 Limit of Agreement = 95% Binomial proportions test and quantile regression for LoA agreement lower.ci upper.ci % within 2.5 0.9444 0.6935 0.9922 Hypothesis Test: don't reject h0 ###- Quantile Limits of Agreement (LoA) -### Estimate Lower CI Upper CI CI Level Lower LoA -1.12 -1.4705 -0.7695 0.90 Bias 0.04 -0.5362 0.6162 0.95 Upper LoA 2.97 2.1954 3.7446 0.90 Limit of Agreement = 95% Binomial proportions test and quantile regression for LoA agreement lower.ci upper.ci % within 2.5 0.9444 0.6935 0.9922 Hypothesis Test: don't reject h0 ###- Quantile Limits of Agreement (LoA) -### Estimate Lower CI Upper CI CI Level Lower LoA @ 3.9 -1.52603 -1.9506 -1.10148 0.90 Lower LoA @ 5.24 -0.58334 -0.7497 -0.41701 0.90 Lower LoA @ 7.4 0.93837 0.6407 1.23608 0.90 Bias @ 3.9 -0.73052 -1.3830 -0.07808 0.95 Bias @ 5.24 -0.07238 -0.8096 0.66486 0.95 Bias @ 7.4 0.99000 -0.9752 2.95519 0.95 Upper LoA @ 3.9 0.52353 -1.9981 3.04516 0.90 Upper LoA @ 5.24 2.27008 1.6152 2.92494 0.90 Upper LoA @ 7.4 5.08940 1.8002 8.37859 0.90 MOVER Limits of Agreement (LoA) 95% LoA @ 2.5% Alpha-Level Data with Replicates Average of Both Methods Bias Bias CI Lower LoA Upper LoA 3.905 -0.3111 [-8.681, 8.0587] -3.341 2.719 5.382 0.6522 [-3.8839, 5.1882] -2.378 3.682 7.395 1.9651 [-7.7328, 11.6631] -1.065 4.995 LoA CI [-11.1274, 10.5051] [-10.1641, 11.4684] [-8.8511, 12.7814] SD of Differences = 1.546 Bland-Altman Limits of Agreement (LoA) of the Ratio (x/y) 95% LoA @ 2.5% Alpha-Level Log-transformed Data with Replicates Bias Bias CI Lower LoA Upper LoA LoA CI 1.119 [0.6373, 1.9636] 0.639 1.958 [0.3961, 3.1593] Coefficient of Variation (%) = 33.0697 MOVER Limits of Agreement (LoA) of the Ratio (x/y) 95% LoA @ 2.5% Alpha-Level Log-transformed Data with Replicates Bias Bias CI Lower LoA Upper LoA LoA CI 1.119 [0.6373, 1.9636] 0.639 1.958 [0.1511, 8.2835] Coefficient of Variation (%) = 33.0697 MOVER Limits of Agreement (LoA) 95% LoA @ 2.5% Alpha-Level Data with Replicates Bias Bias CI Lower LoA Upper LoA LoA CI 0.7152 [-2.2296, 3.66] -2.232 3.662 [-9.7686, 11.199] SD of Differences = 1.5036 Limit of Agreement = 95% Replicate Data Points (true value does not vary) note: hypothesis test likely bogus with proportional bias. Hypothesis Test: don't reject h0 ###- Bland-Altman Limits of Agreement (LoA) -### Estimate Lower CI Upper CI CI Level Bias 0.7046 -1.551 2.9604 0.95 Lower LoA -2.2412 -9.742 -0.4977 0.95 Upper LoA 3.6504 1.907 11.1513 0.95 LoA at average of both measures. Please check plot. 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 Bias 0.7152 -0.6667 2.0971 0.95 Lower LoA -2.2317 -9.7686 -0.4779 0.95 Upper LoA 3.6622 1.9084 11.1990 0.95 Limit of Agreement = 95% Replicate Data Points (true value does not vary) Hypothesis Test: don't reject h0 ###- Bland-Altman Limits of Agreement (LoA) -### Estimate Lower CI Upper CI CI Level Bias 0.7152 -0.6667 2.0971 0.95 Lower LoA -2.2317 -7.5482 -0.7295 0.90 Upper LoA 3.6622 2.1599 8.9786 0.90 Limit of Agreement = 80% Replicate Data Points (true value does not vary) Hypothesis Test: reject h0 ###- Bland-Altman Limits of Agreement (LoA) -### Estimate Lower CI Upper CI CI Level Bias 0.7152 -0.09588 1.5263 0.75 Lower LoA -1.2117 -2.31316 -0.6769 0.50 Upper LoA 2.6421 2.10732 3.7436 0.50 Limit of Agreement = 80% Replicate Data Points (true value does not vary) Hypothesis Test: reject h0 ###- Bland-Altman Limits of Agreement (LoA) -### Estimate Lower CI Upper CI CI Level Bias 0.7152 -0.09588 1.5263 0.75 Lower LoA -1.2117 -2.31316 -0.6769 0.50 Upper LoA 2.6421 2.10732 3.7436 0.50 [1] 79.0000000 0.8022956 Weighted Deming Regression with 95% C.I. Call: dem_reg(formula = y ~ x, data = df1, weighted = TRUE, error.ratio = 4, conf.level = 0.95) Coefficients: (Intercept) x -0.3251 1.0309 Weighted Deming Regression with 95% C.I. Call: dem_reg(formula = y ~ x + id, data = reps, id = "id", weighted = TRUE, conf.level = 0.95) Coefficients: (Intercept) x 3.4162 0.2808 Searching for N to achieve 70% power... Testing N = 30... CI: 99.0%, Joint: 100.0% Target power achieved! Searching for N to achieve 99% power... Testing N = 20... CI: 7.0%, Joint: 12.0% Testing N = 30... CI: 8.0%, Joint: 8.0% Searching for N to achieve 60% power... Testing N = 25... CI: 100.0%, Joint: 100.0% Target power achieved! Searching for N to achieve 60% power... Testing N = 25... CI: 100.0%, Joint: 100.0% Target power achieved! 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 0.179362 0.62307 2 36.67 23C/5.5 Lower LoA -0.1665 -0.524443 0.33045 3 36.67 23C/5.5 Upper LoA 0.8078 0.581119 1.05272 4 36.67 33C/5.5 Bias 0.2780 0.134837 0.42243 5 36.67 33C/5.5 Lower LoA -0.1214 -0.427868 0.11787 6 36.67 33C/5.5 Upper LoA 0.6775 0.659564 0.85497 7 36.67 33C/7.5 Bias 0.2812 0.044819 0.56938 8 36.67 33C/7.5 Lower LoA -0.1882 -0.255122 0.20856 9 36.67 33C/7.5 Upper LoA 0.7505 0.312272 1.12957 10 36.93 23C/5.5 Bias 0.2762 0.182737 0.47856 11 36.93 23C/5.5 Lower LoA -0.2109 -0.553161 0.18973 12 36.93 23C/5.5 Upper LoA 0.7634 0.503896 0.99562 13 36.93 33C/5.5 Bias 0.2336 0.133121 0.42297 14 36.93 33C/5.5 Lower LoA -0.1658 -0.420852 0.09898 15 36.93 33C/5.5 Upper LoA 0.6331 0.546052 0.84975 16 36.93 33C/7.5 Bias 0.2368 0.126981 0.47739 17 36.93 33C/7.5 Lower LoA -0.2326 -0.281824 0.12953 18 36.93 33C/7.5 Upper LoA 0.7061 0.404113 1.00616 19 37.29 23C/5.5 Bias 0.2147 0.045646 0.45151 20 37.29 23C/5.5 Lower LoA -0.2724 -0.592925 0.09455 21 37.29 23C/5.5 Upper LoA 0.7019 0.338404 0.95560 22 37.29 33C/5.5 Bias 0.1721 0.002820 0.53180 23 37.29 33C/5.5 Lower LoA -0.2273 -0.429871 0.11674 24 37.29 33C/5.5 Upper LoA 0.5715 0.340632 0.96351 25 37.29 33C/7.5 Bias 0.1752 0.004807 0.36982 26 37.29 33C/7.5 Lower LoA -0.2941 -0.450123 0.05227 27 37.29 33C/7.5 Upper LoA 0.6446 0.428586 0.85544 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): 1.22 Standard Error of Prediction (SEP): 1.9 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): 1.22 Standard Error of Prediction (SEP): 1.9 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. [10.7, 25] Standard Error of Measurement (SEM): 1.01 95% C.I. [0.566, 1.32] Standard Error of the Estimate (SEE): 1.22 95% C.I. [0.65, 1.98] Standard Error of Prediction (SEP): 1.9 95% C.I. [0.967, 3.43] 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): 1.22 Standard Error of Prediction (SEP): 1.9 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 Deming Regression with 95% C.I. Call: dem_reg(formula = Y ~ X, data = ncss_deming1, error.ratio = 4, weighted = FALSE, conf.level = 0.95) Coefficients: (Intercept) X -0.08974 1.00119 Deming Regression with 95% C.I. Call: dem_reg(formula = Y ~ X, data = ncss_deming1, error.ratio = 4, weighted = FALSE, conf.level = 0.95) Coefficients: coef bias se df lower.ci upper.ci t p.value Intercept -0.08974 -0.044938 1.7220 8 -4.0607 3.881 -0.05212 0.9597 Slope 1.00119 0.003529 0.1872 8 0.5696 1.433 0.00638 0.9951 8 degrees of freedom Error variance ratio (lambda): 4.0000 Passing-Bablok (scissors) with 95% C.I. Call: pb_reg(formula = Method2 ~ Method1, data = ncss_pb1) Coefficients: term coef se lower.ci upper.ci df null_value reject_h0 1 Intercept -0.15 0.377175 -0.8457 0.6328 28 0 FALSE 2 Method1 1.00 0.006178 0.9880 1.0122 28 1 FALSE 28 degrees of freedom Error variance ratio (lambda): 1.0000 Deming Regression with 95% C.I. Call: dem_reg(formula = Y ~ X, data = ncss_deming1, error.ratio = 4, weighted = FALSE, conf.level = 0.95) Coefficients: coef bias se df lower.ci upper.ci t p.value Intercept -0.08974 -0.044938 1.7220 8 -4.0607 3.881 -0.05212 0.9597 Slope 1.00119 0.003529 0.1872 8 0.5696 1.433 0.00638 0.9951 8 degrees of freedom Error variance ratio (lambda): 4.0000 Agreement between Measures (Difference: x-y) 95% Prediction Interval with 95% Tolerance Limits Bias Bias CI Prediction Interval Tolerance Limits 0.1908 [0.1462, 0.2355] [-0.1578, 0.5395] [-0.2123, 0.594] Agreement between Measures (Difference: x-y) 95% Prediction Interval with 95% Tolerance Limits Average of Both Methods Bias Bias CI Prediction Interval 36.38 0.2333 [0.1319, 0.3347] [-0.1275, 0.5941] 36.83 0.1901 [0.1453, 0.2348] [-0.1591, 0.5392] 37.23 0.1512 [0.0552, 0.2472] [-0.2081, 0.5105] Tolerance Limits [-0.1844, 0.651] [-0.2141, 0.5943] [-0.2648, 0.5672] Agreement between Measures (Difference: x-y) 95% Prediction Interval with 95% Tolerance Limits Bias Bias CI Prediction Interval Tolerance Limits 0.1908 [0.1191, 0.2625] [-0.2098, 0.5915] [-0.3803, 0.762] Agreement between Measures (Difference: x-y) 95% Prediction Interval with 95% Tolerance Limits Bias Bias CI Prediction Interval Tolerance Limits 0.1907 [0.1284, 0.253] [-0.1828, 0.5642] [-0.2986, 0.68] Agreement between Measures (Difference: x-y) 95% Prediction Interval with 95% Tolerance Limits Bias Bias CI Prediction Interval Tolerance Limits 0.1907 [0.1284, 0.253] [-0.1827, 0.5642] [-0.2986, 0.68] Agreement between Measures (Difference: x-y) 95% Prediction Interval with 95% Tolerance Limits Condition Bias Bias CI Prediction Interval Tolerance Limits AM 0.1581 [0.0786, 0.2377] [-0.2164, 0.5327] [-0.3403, 0.6565] PM 0.2233 [0.1438, 0.3028] [-0.1513, 0.5979] [-0.2751, 0.7217] Agreement between Measures (Difference: x-y) 95% Prediction Interval with 95% Tolerance Limits Condition Bias Bias CI Prediction Interval Tolerance Limits AM 0.1537 [0.0595, 0.2478] [-0.2919, 0.5993] [-0.3513, 0.642] PM 0.2280 [0.1342, 0.3218] [-0.3162, 0.7722] [-0.3557, 0.8522] Agreement between Measures (Ratio: x/y) 95% Prediction Interval with 95% Tolerance Limits Average of Both Methods Bias Bias CI Prediction Interval 36.38 1.005 [1.0014, 1.0082] [0.9943, 1.0153] 36.83 1.005 [1.003, 1.0074] [0.9935, 1.0171] 37.23 1.006 [1.0024, 1.0089] [0.9952, 1.0161] Tolerance Limits [0.9921, 1.0176] [0.9877, 1.0231] [0.9928, 1.0185] Sympercent Difference between Methods (s%) 95% Prediction Interval with 95% Tolerance Limits Average of Both Methods Bias Bias CI Prediction Interval 36.38 0.4745 [0.1362, 0.8128] [-0.5679, 1.5169] 36.83 0.5194 [0.3011, 0.7377] [-0.654, 1.6928] 37.23 0.5598 [0.2359, 0.8837] [-0.4811, 1.6007] Tolerance Limits [-0.7957, 1.7447] [-1.2419, 2.2807] [-0.7182, 1.8378] Agreement between Measures (Ratio: x/y) 95% Prediction Interval with 95% Tolerance Limits Condition Average of Both Methods Bias Bias CI Prediction Interval AM 36.38 1.007 [1.0035, 1.0096] [0.9955, 1.0176] PM 36.38 1.010 [1.0062, 1.0139] [0.9989, 1.0213] AM 36.83 1.003 [1.001, 1.0057] [0.992, 1.0149] PM 36.83 1.007 [1.0047, 1.0091] [0.9927, 1.0213] AM 37.23 1.001 [0.9967, 1.0045] [0.9895, 1.0117] PM 37.23 1.004 [1.0015, 1.0066] [0.9929, 1.0153] Tolerance Limits [0.9931, 1.0201] [0.9969, 1.0234] [0.9882, 1.0188] [0.9836, 1.0308] [0.9876, 1.0137] [0.9897, 1.0186] Agreement between Measures (Ratio: x/y) 95% Prediction Interval with 95% Tolerance Limits Condition Average of Both Methods Bias Bias CI Prediction Interval AM 36.38 1.007 [1.0035, 1.0096] [0.9955, 1.0176] PM 36.38 1.010 [1.0062, 1.0139] [0.9989, 1.0213] AM 36.83 1.003 [1.001, 1.0057] [0.992, 1.0149] PM 36.83 1.007 [1.0047, 1.0091] [0.9927, 1.0213] AM 37.23 1.001 [0.9967, 1.0045] [0.9895, 1.0117] PM 37.23 1.004 [1.0015, 1.0066] [0.9929, 1.0153] Tolerance Limits [0.9929, 1.0206] [0.9958, 1.0253] [0.9897, 1.0174] [0.9917, 1.0218] [0.9854, 1.0156] [0.9899, 1.018] Agreement between Measures (Ratio: x/y) 95% Prediction Interval with 95% Tolerance Limits Average of Both Methods Bias Bias CI Prediction Interval 36.38 1.005 [1.0014, 1.0082] [0.9943, 1.0153] 36.83 1.005 [1.003, 1.0074] [0.9935, 1.0171] 37.23 1.006 [1.0024, 1.0089] [0.9952, 1.0161] Tolerance Limits [0.9903, 1.0181] [0.9918, 1.0193] [0.9928, 1.02] 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 -2.8162 -1.078 0.90 Upper LoA 2.8237 1.9545 3.693 0.90 ###- Concordance Correlation Coefficient (CCC) -### CCC: 0.4791, 95% C.I. [0.1276, 0.7237] [ FAIL 0 | WARN 2 | SKIP 6 | PASS 701 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On CRAN (6): 'test-deming_power.R:300:3', 'test-deming_power.R:318:3', 'test-deming_power.R:354:3', 'test-deming_power.R:375:3', 'test-deming_power.R:411:3', 'test-deming_power.R:439:3' [ FAIL 0 | WARN 2 | SKIP 6 | PASS 701 ] > > proc.time() user system elapsed 165.25 3.60 168.95