Package: riskyr 0.5.0.9004

riskyr: Rendering Risk Literacy more Transparent

Risk-related information (like the prevalence of conditions, the sensitivity and specificity of diagnostic tests, or the effectiveness of interventions or treatments) can be expressed in terms of frequencies or probabilities. By providing a toolbox of corresponding metrics and representations, 'riskyr' computes, translates, and visualizes risk-related information in a variety of ways. Adopting multiple complementary perspectives provides insights into the interplay between key parameters and renders teaching and training programs on risk literacy more transparent (see <doi:10.3389/fpsyg.2020.567817>, for details).

Authors:Hansjoerg Neth [aut, cre], Felix Gaisbauer [aut], Nico Gradwohl [aut], Wolfgang Gaissmaier [aut]

riskyr_0.5.0.9004.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
riskyr/json (API)

# Install 'riskyr' in R:
install.packages('riskyr', repos = c('https://hneth.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hneth/riskyr/issues

Pkgdown/docs site:https://hneth.github.io

Datasets:
  • 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.
  • df_scenarios - A collection of riskyr scenarios from various sources (as df).
  • 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).

On CRAN:

Conda:

2x2-matrixbayesian-inferencecontingency-tablerepresentationriskrisk-literacyvisualization

7.82 score 19 stars 86 scripts 584 downloads 76 exports 0 dependencies

Last updated from:74cf7484bb. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK140
source / vignettesOK182
linux-release-x86_64OK141
macos-release-arm64OK104
macos-oldrel-arm64OK104
windows-develOK108
windows-releaseOK101
windows-oldrelOK105
wasm-releaseOK144

Exports:accuas_pbas_pccomp_acccomp_accu_freqcomp_accu_probcomp_comp_paircomp_complementcomp_complete_prob_setcomp_errcomp_fartcomp_FDRcomp_FORcomp_freqcomp_freq_freqcomp_freq_probcomp_min_Ncomp_mirtcomp_NPVcomp_popucomp_ppodcomp_PPVcomp_probcomp_prob_freqcomp_prob_probcomp_senscomp_specFFTrees_riskyrfreqinit_numinit_palinit_txtis_complementis_extreme_prob_setis_freqis_integeris_matrixis_percis_probis_suff_prob_setis_valid_prob_pairis_valid_prob_setis_valid_prob_triplenumpalpal_bwpal_bwppal_criskpal_knpal_mbwpal_modpal_orgpal_rgbpal_uniknpal_virplot_areaplot_barplot_criskplot_curveplot_fnetplot_iconsplot_mosaicplot_planeplot_prismplot_tabplot_treepopuprobread_popuriskyrriskyr.guidescenariostxttxt_orgtxt_TFwrite_popu

Dependencies:

riskyr user guide
Motivation: A problem of probabilities | Information provided and asked | Using Bayes' theorem | Using natural frequencies | Using riskyr | Risk vs. uncertainty | Promoting risk perception and communication | A. A fancy calculator | B. Translating between formats | Computing frequencies from probabilities | Computing probabilities from frequencies | Switching back and forth | All at once: Defining a riskyr scenario | C. Visualizing relationships between formats and variables | Icon array | Tree diagram | Area plot | Bar plot | Prism plot | Alternative perspectives | References | Resources | Contact | All riskyr vignettes
Rendered fromA_user_guide.Rmdusingknitr::rmarkdown

Last update: 2025-11-05
Started: 2018-02-12

Confusion matrix and accuracy metrics
Basics | Adopting two perspectives on a population | Example | Accuracy as a third perspective | Avoiding common sources of confusion | Accuracy metrics | A. Specific metrics: Conditional probabilities | B. General metrics: Measures of accuracy | 1. Overall accuracy acc | 2. Weighted accuracy wacc | 3. Matthews correlation coefficient mcc | 4. F1 score | References | Resources | Contact | All riskyr vignettes
Rendered fromC_confusion_matrix.Rmdusingknitr::rmarkdown

Last update: 2025-11-05
Started: 2018-02-12

Data formats
Two representational formats | Frequencies | Definitions | Perspectives: Basic vs. combined frequencies | Relationships among frequencies | Probabilities | Non-conditional vs. conditional probabilities | Relationships among probabilities | Probabilities as ratios between frequencies | Practice | An example | Your tasks | References | Resources | Contact | All riskyr vignettes
Rendered fromB_data_formats.Rmdusingknitr::rmarkdown

Last update: 2025-11-05
Started: 2018-02-12

Adopting functional perspectives
Functions | Curves as a function of prevalence | Planes as a function of sensitivity and specificity (given a prevalence) | Resources | Contact | All riskyr vignettes
Rendered fromD_functional_perspectives.Rmdusingknitr::rmarkdown

Last update: 2025-11-05
Started: 2018-02-13

Quick start primer on using riskyr
Getting started | Defining a scenario | Example | Necessary scenario information | Optional scenario information | Viewing scenario information | Prism plot | Practice | Icon array | Alternative perspectives | Using existing scenarios | 1. Selecting a scenario | 2. Printing scenario information | 3. Visualizing frequencies and probabilities | 4. Visualizing probabilistic relationships | Conclusion | References | Resources | Contact | All riskyr vignettes
Rendered fromE_riskyr_primer.Rmdusingknitr::rmarkdown

Last update: 2025-11-05
Started: 2018-02-14

Readme and manuals

Help Manual

Help pageTopics
Accuracy (acc) is the probability of a correct decision.acc accurate correct
A list containing current accuracy information.accu
Display a percentage as a (numeric and rounded) probability.as_pb
Display a probability as a (numeric and rounded) percentage.as_pc
Cumulative risk of breast cancer in women with the BRCA1 mutation.BRCA1
Cumulative risk of breast cancer in women with the BRCA1 mutation.BRCA1_mam
Cumulative risk of ovarian cancer in women with the BRCA1 mutation.BRCA1_ova
Cumulative risk of breast cancer in women with the BRCA2 mutation.BRCA2
Cumulative risk of breast cancer in women with the BRCA2 mutation.BRCA2_mam
Cumulative risk of ovarian cancer in women with the BRCA2 mutation.BRCA2_ova
Compute overall accuracy (acc) from probabilities.comp_acc
Compute accuracy metrics of current classification results.comp_accu_freq
Compute exact accuracy metrics based on probabilities.comp_accu_prob
Compute a probability's (missing) complement and return both.comp_comp_pair
Compute a probability's complement probability.comp_complement
Compute a complete set of probabilities from valid probability inputs.comp_complete_prob_set
Compute overall error rate (err) from probabilities.comp_err
Compute a decision's false alarm rate from its specificity.comp_fart
Compute a decision's false detection rate (FDR) from probabilities.comp_FDR
Compute a decision's false omission rate (FOR) from probabilities.comp_FOR
Compute frequencies from (3 essential) probabilities.comp_freq
Compute frequencies from (4 essential) frequencies.comp_freq_freq
Compute frequencies from (3 essential) probabilities.comp_freq_prob
Compute a suitable minimum population size value N.comp_min_N
Compute a decision's miss rate from its sensitivity.comp_mirt
Compute a decision's negative predictive value (NPV) from probabilities.comp_NPV
Compute a population table (data) from frequencies (description).comp_popu
Compute the proportion of positive decisions (ppod) from probabilities.comp_ppod
Compute a decision's positive predictive value (PPV) from probabilities.comp_PPV
Compute the condition's prevalence (baseline probability) from frequencies.comp_prev
Compute probabilities from (3 essential) probabilities.comp_prob
Compute probabilities from (4 essential) frequencies.comp_prob_freq
Compute probabilities from (3 essential) probabilities.comp_prob_prob
Compute a decision's sensitivity from its miss rate.comp_sens
Compute a decision's specificity from its false alarm rate.comp_spec
Number of individuals for which the condition is false.cond_false
Number of individuals for which the condition is true.cond_true
Frequency of correct rejections or true negatives (TN).cr TN
Number of individuals for which the decision is correct.dec_cor
Number of individuals for which the decision is erroneous.dec_err
Number of individuals for which the decision is negative.dec_neg
Number of individuals for which the decision is positive.dec_pos
A collection of riskyr scenarios from various sources (as df).df_scenarios
Error rate (err) as the probability of an incorrect decision.err
Frequency of false alarms or false positives (FP).fa FP type-I-errors
The false alarm rate (or false positive rate) of a decision process or diagnostic procedure.alpha fallout fart FPR
The false detection rate of a decision process or diagnostic procedure.FDR
Convert from FFTrees to riskyr objects.FFTrees_riskyr
The false omission rate (FOR) of a decision process or diagnostic procedure.FOR
List current frequency information.freq
Frequency of hits or true positives (TP).hi TP
Initialize basic numeric variables.init_num
Initialize basic color information.init_pal
Initialize basic text elements.init_txt
Verify that two numbers are complements.is_complement
Verify that a set of probabilities describes an extreme case.is_extreme_prob_set
Verify that input is a frequency (positive integer value).is_freq
Test for inters (i.e., whole numbers).is_integer
Verify a 2x2 matrix as a numeric contingency table.is_matrix
Verify that input is a percentage (numeric value from 0 to 100).is_perc
Verify that input is a probability (numeric value from 0 to 1).is_prob
Verify a sufficient set of probability inputs.is_suff_prob_set
Verify that a pair of probability inputs can be a pair of complementary probabilities.is_valid_prob_pair
Verify that a set of probability inputs is valid.is_valid_prob_set
Verify that a triple of essential probability inputs is valid.is_valid_prob_triple
Frequency of misses or false negatives (FN).FN mi type-II-errors
The miss rate of a decision process or diagnostic procedure.beta FNR mirt
Number of individuals in the population.N
The negative predictive value of a decision process or diagnostic procedure.NPV
List current values of basic numeric variables.num
List current values of scenario color palette.pal
Alternative color palette for black-and-white (greyscale) graphs.pal_bw
Alternative color palette for black-and-white graphs (for printing purposes).pal_bwp
Color palette for cumulative risk curve.pal_crisk
Alternative color palette for kn.pal_kn
Modern and reduced color palette (in green/blue/bw).pal_mbw
Modern color palette (in green/blue/orange).pal_mod
Original color palette.pal_org
Alternative color palette for graphs (with RGB colors).pal_rgb
Alternative color palette for unikn.pal_unikn
Alternative color palette using viridis colors.pal_vir
Plot an area diagram of probabilities or frequencies.plot_area
Plot bar charts of population frequencies.plot_bar
Plot cumulative risk dynamics (as bar chart)plot_cbar
Plot a cumulative risk curve.plot_crisk
Plot curves of selected values (e.g., PPV or NPV) as a function of prevalence.plot_curve
Plot frequency net diagram of frequencies and probabilities.plot_fnet
Plot an icon array of a population.plot_icons
Plot a mosaic plot of population frequencies.plot_mosaic
Plot a plane of selected values (e.g., PPV or NPV) as a function of sensitivity and specificity.plot_plane
Plot prism diagram of frequencies and probabilities.plot_prism
Plot a 2 x 2 contingency table of population frequencies.plot_tab
Plot a tree diagram of frequencies and probabilities.plot_tree
Plot a frequency box objectplot.box
Plot a riskyr scenario.plot.riskyr
A table of cases (in the current population).popu
The proportion (or baseline) of a positive decision (aka. bias).baserate_dec_pos bias ppod PR
The positive predictive value of a decision process or diagnostic procedure.PPV precision
The prevalence (baseline probability) of a condition.baserate_cond_true prev
Print summary information of a riskyr scenario.print.summary.riskyr
List current probability information.prob
Read population data (from df) into a riskyr scenario (description).read_popu
Create a riskyr scenario.riskyr
Opens the riskyr package guidesriskyr.guide
A collection of riskyr scenarios from various sources (as list).scenarios
The sensitivity (or hit rate) of a decision process or diagnostic procedure.HR power recall sens TPR
The specificity of a decision process or diagnostic procedure.spec TNR
Summarize a riskyr scenario.summary.riskyr
Cumulative risk curve A (main/transfer task A).t_A
Cumulative risk curve B (main/transfer task B).t_B
Cumulative risk curve I (introductory task).t_I
Basic text elements.txt
List of original values of text elements.txt_org
Alternative text labels (TP, FN, FP, TN).txt_TF
Write a population table (data) from a riskyr scenario (description).write_popu