Statistical Tools for Evaluation of in Vitro Diagnostic Reagents

Documentation for package ‘ivdtools’ version 0.1.2

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-- A --

arrhenius	arrhenius - Arrhenius accelerated stability analysis
auc	Describe an analysis object
auc.roc	Compute ROC curves and AUC for each evaluation column.

-- B --

bias	Describe an analysis object
bias.mcr	Bias analysis (S3 method) - estimate bias at given medical decision levels
bland_altman	Describe an analysis object
bland_altman.mcr	Bland-Altman analysis (S3 method)
bottle_anova	bottle_anova constructor

-- C --

ci	Describe an analysis object
ci.precision	S3 confidence interval method
coef.fit_equation	Extract coefficients from an equation fit
compare_equation	Fit and compare multiple equations
continuous_to_binary	Convert quantitative columns to binary based on cutoff values
correlation	Describe an analysis object
correlation.mcr	Correlation analysis (S3 method)
counts_to_table	Construct a 2x2 contingency table from TP / FP / TN / FN frequencies (silent construction)
cutoff	Describe an analysis object
cutoff.roc	Optimal Cutoff Analysis (S3 method)

-- D --

describe	Describe an analysis object
describe.fourfold_table	Descriptive Statistics: Raw Data Overview (S3 Method)
describe.mcr	Compute descriptive statistics and store results
describe.roc	Descriptive Statistics (S3 method)
diagnostics	Describe an analysis object
diagnostics.fourfold_table	Diagnostic performance metrics: calculate sensitivity, specificity, likelihood ratios, etc. with confidence intervals for a fourfold_table

-- F --

fit_equation

General-purpose equation fitting

-- I --

ivd_bottle_example	Small deterministic one-way ANOVA example
ivd_mcr_example	Small deterministic method-comparison example
ivd_qualitative_example	Small deterministic qualitative-method example
ivd_roc_example	Small deterministic ROC example

-- K --

kappa	Describe an analysis object
kappa.fourfold_table	Cohen's Kappa / PABAK Agreement Analysis (2x2 table only)

-- L --

list_equation	Print the equation registry
list_sadler	List Sadler precision profile model equations
list_westgard	List Westgard QC rules
lob_lod_loq	Limit of blank, detection, and quantitation (LoB / LoD / LoQ)

-- M --

mcnemar	Describe an analysis object
mcnemar.fourfold_table	McNemar Test (for fourfold_table only)
mcr	mcr constructor
mkt	mkt - Mean Kinetic Temperature
mlr	Describe an analysis object
mlr.roc	Multivariate Logistic Regression (S3 method)

-- N --

normal	Describe an analysis object
normal.precision	S3 normality test method
normal_test	Normality test

-- O --

outlier	Detect outliers in an analysis object
outlier.mcr	Outlier detection (S3 method)
outlier.precision	S3 outlier detection method
outliers_test	Outlier detection

-- P --

plot.fit_equation	Plot an equation fit
plot.mcr	Plot (S3 method) - unified plotting interface
plot.precision	S3 plot method
plot.reference_interval	Plot reference interval results
plot.roc	Plot (S3 method) - ROC Curve
precision	Precision variance component analysis
predict.fit_equation	Predict fitted values or inverse-predict (from y to x)
predict.mcr	Predict (S3 method) - predict based on regression results
predict.roc	Predict (S3 method) - predict from multivariate logistic regression
print.bottle_anova	S3 print method: bottle_anova
print.describe_table	S3 print method for describe_table
print.diagnostics	S3 print method: format 'diagnostics' output (diagnostic performance metrics)
print.fit_equation	Print an equation fit
print.fourfold_table	S3 print method: format a 'fourfold_table' object as a fourfold table
print.kappa_table	S3 print method: format 'kappa_table' output
print.mcnemar_table	S3 print method: format 'mcnemar_table' output
print.mcr	S3 print method
print.mcr_bias	Print method for bias results
print.mcr_bland_altman	Print method for Bland-Altman results
print.mcr_correlation	Print method for correlation results
print.mcr_describe	Print method for describe results
print.mcr_outlier	Print method for outlier results
print.mcr_regression	Print method for regression results
print.precision	Print a precision object overview
print.precision_ci	Print confidence intervals
print.precision_normal	Print normality test results
print.precision_outlier	Print outlier detection results
print.precision_profile	Print precision profile fits
print.precision_vc	Print variance component table
print.reference_interval	Print reference interval analysis results
print.roc	Print a ROC analysis object
print.roc_auc_table	Print method for roc AUC table
print.roc_cutoff_table	Print method for roc cutoff table
print.roc_describe	Print method for roc describe results
print.roc_mlr	Print a multivariate ROC model
print.tukey	S3 print method: tukey
profile	Describe an analysis object
profile.precision	S3 precision profile method

-- Q --

qc_chart

Levey-Jennings QC chart + Westgard rule evaluation

-- R --

raw_to_table	Core function: raw data -> frequency fourfold table (silent construction)
reference_interval	Reference Interval (RI) Analysis
regression	Describe an analysis object
regression.mcr	Regression analysis (S3 method)
replicate_to_mean	Summarize replicate measurements
residuals.fit_equation	Extract residuals from an equation fit
roc	roc constructor

-- S --

sample_size_bland_altman	Sample size and power for Bland-Altman agreement assessment
sample_size_proportion	Single-arm target value test - sample size / significance level / power
sample_size_proportion_ci	Sample size or half-width for a single proportion confidence interval
stability_bias	stability_bias - Node-wise bias analysis across storage conditions
stability_plan	stability_plan - CLSI EP25 Appendix A time-point planning
stability_regression	stability_regression - CLSI EP25 regression-based stability assessment
stability_time	stability_time - Predict time-to-limit from a stability regression
summary.fourfold_table	S3 summary method
summary.mcr	S3 summary method
summary.precision	S3 summary method
summary.roc	Summary (S3 method)

-- T --

tukey	Tukey HSD post-hoc test
tukey.bottle_anova	Tukey HSD post-hoc test (S3 method)

-- V --

variance	Describe an analysis object
variance.precision	S3 variance component estimation method
vc	Describe an analysis object

-- Y --

youden_plot

Youden plot