InitializationCreating riskyr scenarios and corresponding parameter collections. |
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Convert from FFTrees to riskyr objects. |
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Plot a riskyr scenario. |
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Print summary information of a riskyr scenario. |
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Create a riskyr scenario. |
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Opens the riskyr package guides |
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Summarize a riskyr scenario. |
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A collection of riskyr scenarios from various sources (as df). |
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A collection of riskyr scenarios from various sources (as list). |
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Initialize basic numeric variables. |
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Initialize basic color information. |
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Initialize basic text elements. |
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List current values of basic numeric variables. |
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A table of cases (in the current population). |
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Read population data (from df) into a riskyr scenario (description). |
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List current values of scenario color palette. |
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Alternative color palette for black-and-white (greyscale) graphs. |
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Alternative color palette for black-and-white graphs (for printing purposes). |
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Color palette for cumulative risk curve. |
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Alternative color palette for kn. |
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Modern and reduced color palette (in green/blue/bw). |
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Modern color palette (in green/blue/orange). |
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Original color palette. |
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Alternative color palette for graphs (with RGB colors). |
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Alternative color palette for unikn. |
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Alternative color palette using viridis colors. |
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Basic text elements. |
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Alternative text labels (TP, FN, FP, TN). |
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List of original values of text elements. |
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VisualizationFunctions for creating graphical representations of riskyr scenarios. |
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Plot a frequency box object. |
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Plot a riskyr scenario. |
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Plot an area diagram of probabilities or frequencies. |
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Plot bar charts of population frequencies. |
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Plot a cumulative risk curve. |
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Plot curves of selected values (e.g., PPV or NPV) as a function of prevalence. |
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Plot frequency net diagram of frequencies and probabilities. |
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Plot an icon array of a population. |
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Plot a mosaic plot of population frequencies. |
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Plot a plane of selected values (e.g., PPV or NPV) as a function of sensitivity and specificity. |
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Plot prism diagram of frequencies and probabilities. |
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Plot a 2 x 2 contingency table of population frequencies. |
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Plot a tree diagram of frequencies and probabilities. |
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ProbabilitiesLists and objects representing probability information. |
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List current probability information. |
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The prevalence (baseline probability) of a condition. |
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The sensitivity (or hit rate) of a decision process or diagnostic procedure. |
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The miss rate of a decision process or diagnostic procedure. |
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The specificity of a decision process or diagnostic procedure. |
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The false alarm rate (or false positive rate) of a decision process or diagnostic procedure. |
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The proportion (or baseline) of a positive decision (aka. bias). |
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The positive predictive value of a decision process or diagnostic procedure. |
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The negative predictive value of a decision process or diagnostic procedure. |
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The false detection rate of a decision process or diagnostic procedure. |
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The false omission rate (FOR) of a decision process or diagnostic procedure. |
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Accuracy (acc) is the probability of a correct decision. |
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A list containing current accuracy information. |
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Error rate (err) as the probability of an incorrect decision. |
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FrequenciesLists and objects representing frequencies (i.e., various subsets of a population). |
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List current frequency information. |
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Number of individuals in the population. |
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Number of individuals for which the condition is false. |
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Number of individuals for which the condition is true. |
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Number of individuals for which the decision is correct. |
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Number of individuals for which the decision is erroneous. |
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Number of individuals for which the decision is negative. |
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Number of individuals for which the decision is positive. |
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Frequency of hits or true positives (TP). |
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Frequency of misses or false negatives (FN). |
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Frequency of false alarms or false positives (FP). |
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Frequency of correct rejections or true negatives (TN). |
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Computation and conversionComputing parameters and translating between representational formats and data/descriptions. |
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Compute a decision's false detection rate (FDR) from probabilities. |
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Compute a decision's false omission rate (FOR) from probabilities. |
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Compute a decision's negative predictive value (NPV) from probabilities. |
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Compute a decision's positive predictive value (PPV) from probabilities. |
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Compute overall accuracy (acc) from probabilities. |
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Compute accuracy metrics of current classification results. |
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Compute exact accuracy metrics based on probabilities. |
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Compute a probability's (missing) complement and return both. |
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Compute a probability's complement probability. |
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Compute a complete set of probabilities from valid probability inputs. |
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Compute overall error rate (err) from probabilities. |
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Compute a decision's false alarm rate from its specificity. |
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Compute frequencies from (3 essential) probabilities. |
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Compute frequencies from (4 essential) frequencies. |
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Compute frequencies from (3 essential) probabilities. |
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Compute a suitable minimum population size value N. |
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Compute a decision's miss rate from its sensitivity. |
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Compute a population table (data) from frequencies (description). |
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Compute the proportion of positive decisions (ppod) from probabilities. |
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Compute the condition's prevalence (baseline probability) from frequencies. |
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Compute probabilities from (3 essential) probabilities. |
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Compute probabilities from (4 essential) frequencies. |
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Compute probabilities from (3 essential) probabilities. |
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Compute a decision's sensitivity from its miss rate. |
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Compute a decision's specificity from its false alarm rate. |
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Read population data (from df) into a riskyr scenario (description). |
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Write a population table (data) from a riskyr scenario (description). |
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DatasetsData used in examples and illustrations. |
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A collection of riskyr scenarios from various sources (as df). |
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Cumulative risk of breast cancer in women with the BRCA1 mutation. |
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Cumulative risk of breast cancer in women with the BRCA1 mutation. |
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Cumulative risk of ovarian cancer in women with the BRCA1 mutation. |
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Cumulative risk of breast cancer in women with the BRCA2 mutation. |
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Cumulative risk of breast cancer in women with the BRCA2 mutation. |
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Cumulative risk of ovarian cancer in women with the BRCA2 mutation. |
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Cumulative risk curve A (main/transfer task A). |
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Cumulative risk curve B (main/transfer task B). |
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Cumulative risk curve I (introductory task). |
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Validation and formattingVerifying and displaying representational formats. |
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Verify that two numbers are complements. |
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Verify that a set of probabilities describes an extreme case. |
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Verify that input is a frequency (positive integer value). |
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Test for inters (i.e., whole numbers). |
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Verify a 2x2 matrix as a numeric contingency table. |
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Verify that input is a percentage (numeric value from 0 to 100). |
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Verify that input is a probability (numeric value from 0 to 1). |
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Verify a sufficient set of probability inputs. |
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Verify that a pair of probability inputs can be a pair of complementary probabilities. |
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Verify that a set of probability inputs is valid. |
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Verify that a triple of essential probability inputs is valid. |
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Display a percentage as a (numeric and rounded) probability. |
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Display a probability as a (numeric and rounded) percentage. |
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ExtensionsExtensions and links to other packages. |
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Convert from FFTrees to riskyr objects. |