R: Statistical Tools for Evaluation of in Vitro Diagnostic Reagents

# Statistical Tools for Evaluation of in Vitro Diagnostic Reagents

## Documentation for package ‘ivdtools’ version 0.1.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D F I K L M N O P Q R S T V Y

## -- 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