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> # 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(testCompareR)
>
> test_check("testCompareR")
WARNING:
Zeros exist in contingency table. Tests may return NA/NaN.
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CONTINGENCY TABLES
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True Status - POSITIVE
Test 2
Test 1 Positive Negative
Positive 280 20
Negative 0 100
True Status - NEGATIVE
Test 2
Test 1 Positive Negative
Positive 45 10
Negative 0 145
Gold standard vs. Test 1
Test 1
Gold standard Positive Negative
Positive 300 100
Negative 55 145
Gold standard vs. Test 2
Test 2
Gold standard Positive Negative
Positive 280 120
Negative 45 155
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PREVALENCE (%)
--------------------------------------------------------------------------------
Estimate SE Lower CI Upper CI
Prevalence 66.7 1.9 62.8 70.3
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DIAGNOSTIC ACCURACIES
--------------------------------------------------------------------------------
Test 1 (%)
Estimate SE Lower CI Upper CI
Sensitivity 75.0 2.2 70.5 79.0
Specificity 72.5 3.2 66.0 78.3
Test 2 (%)
Estimate SE Lower CI Upper CI
Sensitivity 70.0 2.3 65.4 74.3
Specificity 77.5 3.0 71.3 82.8
Global Null Hypothesis: Se1 = Se2 & Sp1 = Sp2
Test statistic: 31.57895 Adjusted p value: 4.167158e-07 ***SIGNIFICANT***
Investigating individual differences
Null Hypothesis 1: Se1 = Se2
Test statistic: 18.05 Adjusted p value: 0.0001291072 ***SIGNIFICANT***
Null Hypothesis 2: Sp1 = Sp2
Test statistic: 8.1 Adjusted p value: 0.02213263 ***SIGNIFICANT***
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PREDICTIVE VALUES
--------------------------------------------------------------------------------
Test 1 (%)
Estimate SE Lower CI Upper CI
PPV 84.5 1.9 80.4 87.9
NPV 59.2 3.1 52.9 65.2
Test 2 (%)
Estimate SE Lower CI Upper CI
PPV 86.2 1.9 82.0 89.5
NPV 56.4 3.0 50.5 62.1
Global Null Hypothesis: PPV1 = PPV2 & NPV1 = NPV2
Test statistic: 28.43169 Adjusted p value: 1.340192e-06 ***SIGNIFICANT***
Investigating individual differences
Null Hypothesis 1: PPV1 = PPV2
Test statistic: 4.059529 Adjusted p value: 0.08784551
Null Hypothesis 2: NPV1 = NPV2
Test statistic: 6.343355 Adjusted p value: 0.04712873 ***SIGNIFICANT***
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LIKELIHOOD RATIOS
--------------------------------------------------------------------------------
Test 1 (%)
Estimate SE Lower CI Upper CI
PLR 2.7 0.3 2.2 3.5
NLR 0.3 0.0 0.3 0.4
Test 2 (%)
Estimate SE Lower CI Upper CI
PLR 3.1 0.4 2.4 4.1
NLR 0.4 0.0 0.3 0.5
Global Null Hypothesis: PLR1 = PLR2 & NLR1 = NLR2
Test statistic: 24.2216 Adjusted p value: 5.499788e-06 ***SIGNIFICANT***
Investigating individual differences
Null Hypothesis 1: PLR1 = PLR2
Test statistic: 2.013107 Adjusted p value: 0.08784551
Null Hypothesis 2: NLR1 = NLR2
Test statistic: 2.516314 Adjusted p value: 0.04712873 ***SIGNIFICANT***
WARNING:
Tests have exactly equal performance. Tests may return NA/NaN.
Zeros exist in contingency table. Tests may return NA/NaN.
Youden Index of Test 1 is 0. Tests may return NA/NaN.
Youden Index of Test 2 is 0. Tests may return NA/NaN.
When Youden Index is less than or equal to zero a test returns the
same proportion of positive results irrespective of true status.
This indicates poor test performance.
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CONTINGENCY TABLES
--------------------------------------------------------------------------------
True Status - POSITIVE
Test 2
Test 1 Positive Negative
Positive 10 0
Negative 0 390
True Status - NEGATIVE
Test 2
Test 1 Positive Negative
Positive 190 0
Negative 0 10
Gold standard vs. Test 1
Test 1
Gold standard Positive Negative
Positive 10 390
Negative 190 10
Gold standard vs. Test 2
Test 2
Gold standard Positive Negative
Positive 10 390
Negative 190 10
--------------------------------------------------------------------------------
PREVALENCE (%)
--------------------------------------------------------------------------------
Estimate SE Lower CI Upper CI
Prevalence 66.7 1.9 62.8 70.3
--------------------------------------------------------------------------------
DIAGNOSTIC ACCURACIES
--------------------------------------------------------------------------------
Test 1 (%)
Estimate SE Lower CI Upper CI
Sensitivity 2.5 0.8 1.3 4.5
Specificity 5.0 1.5 2.7 8.9
Test 2 (%)
Estimate SE Lower CI Upper CI
Sensitivity 2.5 0.8 1.3 4.5
Specificity 5.0 1.5 2.7 8.9
Global hypothesis testing was not or could not be performed.
This is usually because:
* prevalence is <10% and total number of participants < 100
* tests have identical performance
* there are many zeros in the contingency table
* Youden Index is < 0
Consider the quality of your data and/or tests. Individual tests have been
attempted below.
Investigating individual differences
Null Hypothesis 1: Se1 = Se2
Test statistic: Inf Adjusted p value: 0 ***SIGNIFICANT***
Null Hypothesis 2: Sp1 = Sp2
Test statistic: Inf Adjusted p value: 0 ***SIGNIFICANT***
--------------------------------------------------------------------------------
PREDICTIVE VALUES
--------------------------------------------------------------------------------
Test 1 (%)
Estimate SE Lower CI Upper CI
PPV 5.0 1.5 2.7 8.9
NPV 2.5 0.8 1.3 4.5
Test 2 (%)
Estimate SE Lower CI Upper CI
PPV 5.0 1.5 2.7 8.9
NPV 2.5 0.8 1.3 4.5
Global hypothesis testing was not or could not be performed.
This is usually because:
* tests have identical performance
* there are many zeros in the contingency table
* Youden Index is < 0
Consider the quality of your data and/or tests. Individual tests have been
attempted below.
Investigating individual differences
Null Hypothesis 1: PPV1 = PPV2
Test statistic: NaN Adjusted p value: NaN
NAs or NaNs in individual tests.
This is usually because:
* tests have identical performance
* there are many zeros in the contingency table
* Youden Index is < 0
Consider the quality of your data and/or tests.
Null Hypothesis 2: NPV1 = NPV2
Test statistic: NaN Adjusted p value: NaN
NAs or NaNs in individual tests.
This is usually because:
* tests have identical performance
* there are many zeros in the contingency table
* Youden Index is < 0
Consider the quality of your data and/or tests.
--------------------------------------------------------------------------------
LIKELIHOOD RATIOS
--------------------------------------------------------------------------------
Test 1 (%)
Estimate SE Lower CI Upper CI
PLR 0.0 0 0.0 0.0
NLR 19.5 6 10.9 33.8
Test 2 (%)
Estimate SE Lower CI Upper CI
PLR 0.0 0 0.0 0.0
NLR 19.5 6 10.9 33.8
Global hypothesis testing was not or could not be performed.
This is usually because:
* tests have identical performance
* there are many zeros in the contingency table
* Youden Index is < 0
Consider the quality of your data and/or tests. Individual tests have been
attempted below.
Investigating individual differences
Null Hypothesis 1: PLR1 = PLR2
Test statistic: NaN Adjusted p value: NaN
NAs or NaNs in individual tests.
This is usually because:
* tests have identical performance
* there are many zeros in the contingency table
* Youden Index is < 0
Consider the quality of your data and/or tests.
Null Hypothesis 2: NLR1 = NLR2
Test statistic: NaN Adjusted p value: NaN
NAs or NaNs in individual tests.
This is usually because:
* tests have identical performance
* there are many zeros in the contingency table
* Youden Index is < 0
Consider the quality of your data and/or tests.[ FAIL 0 | WARN 19 | SKIP 0 | PASS 560 ]
[ FAIL 0 | WARN 19 | SKIP 0 | PASS 560 ]
>
> proc.time()
user system elapsed
3.59 0.68 4.29