Statistical Tools for Evaluation of in Vitro Diagnostic Reagents

Documentation for package ‘ivdtools’ version 0.2.5

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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.
auc_compare	Describe an analysis object
auc_compare.roc	Compare two paired ROC AUCs

-- 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 --

c5_c95	Estimate C5 and C95 from an internal continuous response
ci	Describe an analysis object
ci.precision	S3 confidence interval method
coef.fit_equation	Extract coefficients from an equation fit
commutability	Assess reference-material commutability using four standard approaches
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
dilution_recovery	Calculate dilution recovery

-- F --

fit_equation

General-purpose equation fitting

-- H --

hook_effect

Summarize a high-dose hook-effect experiment

-- I --

interference_dose_response	Analyze an EP07 interference dose-response experiment
interference_paired	Analyze paired-difference interference data
interference_patient	Evaluate interference with patient specimens
interference_replicates	Calculate replicate counts for an EP07 paired-difference experiment
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 --

linearity	Evaluate linearity using straight-line or polynomial regression
linearity_endpoints	Calculate target LOW and HIGH concentrations for verification
linearity_panel	Design a HIGH/LOW linearity panel
linearity_replicates	Calculate replicate counts for a linearity study
list_equation	Print the equation registry
list_sadler	List Sadler precision profile model equations
list_westgard	List Westgard QC rules

-- 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.arrhenius	Plot Arrhenius stability analysis
plot.c5_c95	Plot C5 and C95 results
plot.commutability_result	Plot a commutability assessment
plot.dilution_recovery	Plot dilution-recovery results
plot.fit_equation	Plot an equation fit
plot.hook_effect	Plot a high-dose hook-effect experiment
plot.interference_dose_response	Plot interference dose-response results
plot.interference_paired	Plot paired interference estimates
plot.interference_patient	Plot patient-specimen interference results
plot.linearity	Plot a linearity analysis
plot.mcr	Plot (S3 method) - unified plotting interface
plot.normal_test	Plot normality diagnostics
plot.precision	S3 plot method
plot.qc_chart	Plot a Levey-Jennings QC chart
plot.reference_interval	Plot reference interval results
plot.roc	Plot ROC or cutoff-dependent diagnostic metrics
plot.sensitivity	Plot an analytical-sensitivity analysis
plot.spike_recovery	Plot spike-recovery results
plot.stability_bias	Plot stability bias across storage conditions
plot.stability_regression	Plot a stability regression
plot.stability_time	Plot stability limit-time predictions
plot.uncertainty_budget	Plot an uncertainty budget
plot.uncertainty_propagation	Plot propagated uncertainty
plot.uncertainty_traceability	Plot cumulative uncertainty through a traceability chain
plot.youden_plot	Plot a Youden analysis
precision	Precision variance component analysis
predict.fit_equation	Predict fitted values or inverse-predict (from y to x)
predict.interference_dose_response	Predict from an interference dose-response analysis
predict.mcr	Predict (S3 method) - predict based on regression results
predict.roc	Predict (S3 method) - predict from multivariate logistic regression
print.arrhenius	Print Arrhenius stability-analysis results
print.bottle_anova	S3 print method: bottle_anova
print.c5_c95	Print C5 and C95 estimates
print.commutability_result	Print a commutability assessment
print.compare_equation	Print a multiple-equation comparison
print.cutpoint_split	Print a fixed-cutpoint data split
print.describe_table	S3 print method for describe_table
print.diagnostics	S3 print method: format 'diagnostics' output (diagnostic performance metrics)
print.dilution_recovery	Print dilution-recovery results
print.factor_split	Print a categorical data split
print.fit_equation	Print an equation fit
print.fourfold_table	S3 print method: format a 'fourfold_table' object as a fourfold table
print.hook_effect	Print high-dose hook-effect results
print.interference_dose_response	Print interference dose-response results
print.interference_paired	Print paired interference estimates
print.interference_patient	Print patient-specimen interference results
print.interference_replicates	Print EP07 replicate-count results
print.kappa_table	S3 print method: format 'kappa_table' output
print.linearity	Print a linearity analysis
print.linearity_endpoints	Calculate target LOW and HIGH concentrations for verification
print.linearity_panel	Design a HIGH/LOW linearity panel
print.linearity_replicates	Calculate replicate counts for a linearity study
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.mkt	Print mean kinetic temperature results
print.normal_test	Print a normality test result
print.outliers_test	Print an outlier detection result
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.qc_chart	Print a Levey-Jennings QC chart analysis
print.reference_bias	Print reference-material bias results
print.reference_interval	Print reference interval analysis results
print.roc	Print a ROC analysis object
print.roc_auc_comparison	Print a paired AUC comparison
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.sample_size_bland_altman	Print Bland-Altman sample-size results
print.sample_size_proportion	Print single-proportion target-value sample-size results
print.sample_size_proportion_ci	Print single-proportion confidence-interval sample-size results
print.sensitivity	Print an analytical-sensitivity analysis result
print.sensitivity_design	Print an analytical-sensitivity study design
print.spike_concentration	Print spike-concentration calculations
print.spike_recovery	Print spike-recovery results
print.stability_bias	Print stability-bias results
print.stability_plan	Print a stability study time-point plan
print.stability_regression	Print stability-regression results
print.stability_time	Print stability limit-time predictions
print.tukey	S3 print method: tukey
print.uncertainty_budget	Print a combined uncertainty budget
print.uncertainty_characterization	Print characterization uncertainty results
print.uncertainty_component	Print an uncertainty component
print.uncertainty_homogeneity	Print between-unit homogeneity uncertainty results
print.uncertainty_iqc	Print IQC uncertainty results
print.uncertainty_propagation	Print propagated uncertainty results
print.uncertainty_stability	Print stability uncertainty results
print.uncertainty_traceability	Print traceability-chain uncertainty results
print.youden_plot	Print a Youden plot analysis
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_bias	Estimate bias using reference materials
reference_interval	Reference interval analysis
regression	Describe an analysis object
regression.mcr	Regression analysis (S3 method)
replicate_to_mean	Summarize replicate measurements
report	Describe an analysis object
report.precision	Generate an EP05 precision summary table
residuals.fit_equation	Extract residuals from an equation fit
roc	roc constructor

-- S --

sample_size_bland_altman	Sample size for Bland-Altman agreement assessment
sample_size_proportion	Sample size for a single-proportion target-value test
sample_size_proportion_ci	Sample size for a single-proportion confidence interval
sensitivity_design	Summarize an analytical-sensitivity study design
sensitivity_lob	Establish a limit of blank
sensitivity_lod	Establish a limit of detection
sensitivity_loq	Establish a limit of quantitation
sensitivity_verify	Verify an LoB, LoD, or LoQ claim
spike_concentration	Calculate the concentration of a spiked sample
spike_recovery	Calculate spike recovery against a solvent control
split_by_cutpoints	Split a data frame at fixed numeric cutpoints
split_by_factors	Split a data frame by the levels of one categorical variable
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.commutability_result	Summarize a commutability assessment
summary.fourfold_table	S3 summary method
summary.mcr	S3 summary method
summary.precision	S3 summary method
summary.roc	Summary (S3 method)

-- T --

tukey	Describe an analysis object
tukey.bottle_anova	Tukey HSD post-hoc test (S3 method)

-- U --

uncertainty_characterization	Estimate uncertainty from interlaboratory characterization
uncertainty_combine	Combine standard uncertainty components
uncertainty_homogeneity	Estimate the between-unit homogeneity uncertainty of a reference material
uncertainty_iqc	Estimate top-down uncertainty from internal quality-control data
uncertainty_propagate	Propagate uncertainty through a general measurement model
uncertainty_stability	Estimate long-term stability uncertainty
uncertainty_traceability	Accumulate uncertainty along a metrological traceability chain
uncertainty_type_a	Estimate a Type A uncertainty component
uncertainty_type_b	Estimate a Type B uncertainty component

-- V --

variance	Describe an analysis object
variance.precision	S3 variance component estimation method
vc	Describe an analysis object
vc.precision	Backward-compatible alias for variance.precision

-- Y --

youden_plot

Youden plot