# Rendering Risk Literacy more Transparent

## Documentation for package ‘riskyr’ version 0.4.0

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

## Help Pages

A B C D E F H I M N P R S T W

## -- A --

acc | Accuracy (acc) is the probability of a correct decision.
accu | A list containing current accuracy information.
accurate | Accuracy (acc) is the probability of a correct decision.
alpha | The false alarm rate (or false positive rate) of a decision process or diagnostic procedure.
as_pb | Display a percentage as a (numeric and rounded) probability.
as_pc | Display a probability as a (numeric and rounded) percentage.

## -- B --

baserate_cond_true | The prevalence (baseline probability) of a condition.
baserate_dec_pos | The proportion (or baseline) of a positive decision (aka. bias).
beta | The miss rate of a decision process or diagnostic procedure.
bias | The proportion (or baseline) of a positive decision (aka. bias).
BRCA1 | Cumulative risk of breast cancer in women with the BRCA1 mutation.
BRCA1_mam | Cumulative risk of breast cancer in women with the BRCA1 mutation.
BRCA1_ova | Cumulative risk of ovarian cancer in women with the BRCA1 mutation.
BRCA2 | Cumulative risk of breast cancer in women with the BRCA2 mutation.
BRCA2_mam | Cumulative risk of breast cancer in women with the BRCA2 mutation.
BRCA2_ova | Cumulative risk of ovarian cancer in women with the BRCA2 mutation.

## -- C --

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_complement | Compute a probability's complement probability.
comp_complete_prob_set | Compute a complete set of probabilities from valid probability inputs.
comp_comp_pair | Compute a probability's (missing) complement and return both.
comp_err | Compute overall error rate (err) from probabilities.
comp_fart | Compute a decision's false alarm rate from its specificity.
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_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_NPV | Compute a decision's negative predictive value (NPV) from probabilities.
comp_popu | Compute a population table (data) from frequencies (description).
comp_ppod | Compute the proportion of positive decisions (ppod) from probabilities.
comp_PPV | Compute a decision's positive predictive value (PPV) 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.
cond_false | Number of individuals for which the condition is false.
cond_true | Number of individuals for which the condition is true.
correct | Accuracy (acc) is the probability of a correct decision.
cr | Frequency of correct rejections or true negatives (TN).

## -- D --

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

## -- E --

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

## -- F --

fa | Frequency of false alarms or false positives (FP).
fallout | The false alarm rate (or false positive rate) of a decision process or diagnostic procedure.
fart | The false alarm rate (or false positive rate) of a decision process or diagnostic procedure.
FDR | The false detection rate of a decision process or diagnostic procedure.
FFTrees_riskyr | Convert from FFTrees to riskyr objects.
FN | Frequency of misses or false negatives (FN).
FNR | The miss rate of a decision process or diagnostic procedure.
FOR | The false omission rate (FOR) of a decision process or diagnostic procedure.
FP | Frequency of false alarms or false positives (FP).
FPR | The false alarm rate (or false positive rate) of a decision process or diagnostic procedure.
freq | List current frequency information.

## -- H --

hi | Frequency of hits or true positives (TP).
HR | The sensitivity (or hit rate) of a decision process or diagnostic procedure.

## -- I --

init_num | Initialize basic numeric variables.
init_pal | Initialize basic color information.
init_txt | Initialize basic text elements.
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_integer | Test for inters (i.e., whole numbers).
is_matrix | Verify a 2x2 matrix as a numeric contingency table.
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.

## -- M --

mi | Frequency of misses or false negatives (FN).
mirt | The miss rate of a decision process or diagnostic procedure.

## -- N --

N | Number of individuals in the population.
NPV | The negative predictive value of a decision process or diagnostic procedure.
num | List current values of basic numeric variables.

## -- P --

pal | List current values of scenario color palette.
pal_bw | Alternative color palette for black-and-white (greyscale) graphs.
pal_bwp | Alternative color palette for black-and-white graphs (for printing purposes).
pal_crisk | Color palette for cumulative risk curve.
pal_kn | Alternative color palette for 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_unikn | Alternative color palette for unikn.
pal_vir | Alternative color palette using viridis colors.
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_crisk | Plot a cumulative risk curve.
plot_curve | Plot curves of selected values (e.g., PPV or NPV) as a function of prevalence.
plot_fnet | Plot frequency net 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.
popu | A table of cases (in the current population).
power | The sensitivity (or hit rate) of a decision process or diagnostic procedure.
ppod | The proportion (or baseline) of a positive decision (aka. bias).
PPV | The positive predictive value of a decision process or diagnostic procedure.
PR | The proportion (or baseline) of a positive decision (aka. bias).
precision | The positive predictive value of a decision process or diagnostic procedure.
prev | The prevalence (baseline probability) of a condition.
print.summary.riskyr | Print summary information of a riskyr scenario.
prob | List current probability information.

## -- R --

read_popu | Read population data (from df) into a riskyr scenario (description).
recall | The sensitivity (or hit rate) of a decision process or diagnostic procedure.
riskyr | Create a riskyr scenario.
riskyr.guide | Opens the riskyr package guides

## -- S --

scenarios | A collection of riskyr scenarios from various sources (as list).
sens | The sensitivity (or hit rate) of a decision process or diagnostic procedure.
spec | The specificity of a decision process or diagnostic procedure.
summary.riskyr | Summarize a riskyr scenario.

## -- T --

TN | Frequency of correct rejections or true negatives (TN).
TNR | The specificity of a decision process or diagnostic procedure.
TP | Frequency of hits or true positives (TP).
TPR | The sensitivity (or hit rate) of a decision process or diagnostic procedure.
txt | Basic text elements.
txt_org | List of original values of text elements.
txt_TF | Alternative text labels (TP, FN, FP, TN).
type-I-errors | Frequency of false alarms or false positives (FP).
type-II-errors | Frequency of misses or false negatives (FN).
t_A | Cumulative risk curve A (main/transfer task A).
t_B | Cumulative risk curve B (main/transfer task B).
t_I | Cumulative risk curve I (introductory task).

## -- W --

write_popu | Write a population table (data) from a riskyr scenario (description).