## Initialization

Creating riskyr scenarios and corresponding collections of parameters.

plot(<riskyr>)

Plot a riskyr scenario.

print(<summary.riskyr>)

Print summary information of a riskyr scenario.

riskyr()

Create a riskyr scenario.

riskyr.guide()

Opens the riskyr package guides

summary(<riskyr>)

Summarize a riskyr scenario.

df_scenarios

A collection of riskyr scenarios from various sources (as df).

scenarios

A collection of riskyr scenarios from various sources (as list).

init_num()

Initialize basic numeric variables.

init_pal()

Initialize basic color information.

init_txt()

Initialize basic text elements.

num

List current values of basic numeric variables.

popu

A population table based on current frequencies.

read_popu()

Read a population (given as data frame) into a riskyr scenario.

pal

List current values of scenario color palette.

pal_bw

Alternative color palette for black-and-white graphs.

pal_kn

Alternative color palette for uni.kn.

pal_mbw

Modern and reduced color palette (in green/blue/bw).

pal_mod

Modern color palette (in green/blue/orange).

pal_org

Original color palette.

pal_rgb

Alternative color palette for graphs (with RGB colors).

pal_vir

Alternative color palette using viridis colors.

txt

Basic text elements.

txt_TF

Alternative text labels (TP, FN, FP, TN).

txt_org

List of original values of text elements.

## Visualization

Functions for creating graphical representations of riskyr scenarios.

plot(<box>)

Plot a frequency box object.

plot(<riskyr>)

Plot a riskyr scenario.

plot_area()

Plot an area diagram of probabilities or frequencies.

plot_bar()

Plot bar charts of population frequencies.

plot_curve()

Plot curves of selected values (e.g., PPV or NPV) as a function of prevalence.

plot_fnet()

Plot a network diagram of frequencies and probabilities.

plot_icons()

Plot an icon array of a population.

plot_mosaic()

Plot a mosaic plot of population frequencies.

plot_plane()

Plot a plane of selected values (e.g., PPV or NPV) as a function of sensitivity and specificity.

plot_prism()

Plot prism diagram of frequencies and probabilities.

plot_tab()

Plot a 2 x 2 contingency table of population frequencies.

plot_tree()

Plot a tree diagram of frequencies and probabilities.

## Probabilities

Lists and objects representing probability information.

prob

List current probability information.

prev

The prevalence (baseline probability) of a condition.

sens

The sensitivity (or hit rate) of a decision process or diagnostic procedure.

mirt

The miss rate of a decision process or diagnostic procedure.

spec

The specificity of a decision process or diagnostic procedure.

fart

The false alarm rate (or false positive rate) of a decision process or diagnostic procedure.

ppod

The proportion (or baseline) of a positive decision.

PPV

The positive predictive value of a decision process or diagnostic procedure.

NPV

The negative predictive value of a decision process or diagnostic procedure.

FDR

The false detection rate of a decision process or diagnostic procedure.

FOR

The false omission rate (FOR) of a decision process or diagnostic procedure.

acc

Accuracy (acc) is the probability of a correct decision.

accu

A list containing current accuracy information.

err

Error rate (err) as the probability of an incorrect decision.

## Frequencies

Lists and objects representing frequencies (i.e., various subsets of a population).

freq

List current frequency information.

N

Number of individuals in the population.

cond_false

Number of individuals for which the condition is false.

cond_true

Number of individuals for which the condition is true.

dec_cor

Number of individuals for which the decision is correct.

dec_err

Number of individuals for which the decision is erroneous.

dec_neg

Number of individuals for which the decision is negative.

dec_pos

Number of individuals for which the decision is positive.

hi

Frequency of hits or true positives (TP).

mi

Frequency of misses or false negatives (FN).

fa

Frequency of false alarms or false positives (FP).

cr

Frequency of correct rejections or true negatives (TN).

## Computation and translation

Computing parameters and translating between representational formats.

comp_FDR()

Compute a decision's false detection rate (FDR) from probabilities.

comp_FOR()

Compute a decision's false omission rate (FOR) from probabilities.

comp_NPV()

Compute a decision's negative predictive value (NPV) from probabilities.

comp_PPV()

Compute a decision's positive predictive value (PPV) from probabilities.

comp_acc()

Compute overall accuracy (acc) from probabilities.

comp_accu_freq()

Compute accuracy metrics of current classification results.

comp_accu_prob()

Compute exact accuracy metrics based on probabilities.

comp_comp_pair()

Compute a probability's (missing) complement and return both.

comp_complement()

Compute a probability's complement probability.

comp_complete_prob_set()

Compute a complete set of probabilities from valid probability inputs.

comp_err()

Compute overall error rate (err) from probabilities.

comp_fart()

Compute a decision's false alarm rate from its specificity.

comp_freq()

Compute frequencies from (3 essential) probabilities.

comp_freq_freq()

Compute frequencies from (4 essential) frequencies.

comp_freq_prob()

Compute frequencies from (3 essential) probabilities.

comp_min_N()

Compute a suitable minimum population size value N.

comp_mirt()

Compute a decision's miss rate from its sensitivity.

comp_popu()

Compute a population table from frequencies.

comp_ppod()

Compute the proportion of positive decisions (ppod) from probabilities.

comp_prev()

Compute the condition's prevalence (baseline probability) from frequencies.

comp_prob()

Compute probabilities from (3 essential) probabilities.

comp_prob_freq()

Compute probabilities from (4 essential) frequencies.

comp_prob_prob()

Compute probabilities from (3 essential) probabilities.

comp_sens()

Compute a decision's sensitivity from its miss rate.

comp_spec()

Compute a decision's specificity from its false alarm rate.

## Validation and formatting

Verifying and displaying representational formats.

is_complement()

Verify that two numbers are complements.

is_extreme_prob_set()

Verify that a set of probabilities describes an extreme case.

is_freq()

Verify that input is a frequency (positive integer value).

is_perc()

Verify that input is a percentage (numeric value from 0 to 100).

is_prob()

Verify that input is a probability (numeric value from 0 to 1).

is_suff_prob_set()

Verify a sufficient set of probability inputs.

is_valid_prob_pair()

Verify that a pair of probability inputs can be a pair of complementary probabilities.

is_valid_prob_set()

Verify that a set of probability inputs is valid.

is_valid_prob_triple()

Verify that a triple of essential probability inputs is valid.

as_pb()

Display a percentage as a (numeric and rounded) probability.

as_pc()

Display a probability as a (numeric and rounded) percentage.