Rendering Risk Literacy more Transparent

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Documentation for package ‘riskyr’ version 0.4.0

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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).