riskyr
A toolbox for rendering risk literacy more transparent
Starting with a condition (e.g., a disease), a corresponding decision (e.g., a clinical judgment or diagnostic test), and basic probabilities (e.g., the condition's prevalence prev
, and the decision's sensitivity sens
and specificity spec
) we provide a range of functions and metrics to compute, translate, and represent risk-related information (e.g., as probabilities or frequencies for a population of N
individuals). By offering a variety of perspectives on the interplay between key parameters, riskyr
renders teaching and training of risk literacy more transparent.
Solving a problem simply means representing it so as to make the solution transparent. (H.A. Simon)[1]
The issues addressed by riskyr
are less of a computational and more of a representational nature (i.e., concerning the expression in and translation between different formats of information). Whereas people tend to find it difficult to understand and compute information expressed in terms of probabilities, the same information is often easy to understand and compute when expressed in terms of frequencies. But rather than just expressing probabilistic information in terms of frequencies, riskyr
allows translating between formats and illustrates their relationships in a variety of transparent and interactive ways.
Basic assumptions and goals driving the current development of riskyr
include the following:
Effective training in risk literacy requires simple tools and transparent representations.
More specifically, it would be desirable to have a set of (computational and representational) tools that allow various calculations, translations (between formats), and a range of alternative views on the interplay between probabilities and frequencies.
Seeing a variety of visualizations that illustrate how parameters and metrics interact and influence each other facilitates active and explorative learning. It is particularly helpful to view the same or similar relationships from alternative representations or to inspect the change of one parameter as a function of changes in other parameters.
To deliver on these assumptions and goals, we provide a range of computational and representational tools. Importantly, the objects and functions in the riskyr
toolbox are not isolated, but complement, explain, and support each other. All functions and visualizations can be used separately and explored interactively, providing immediate feedback on the effect of changes in parameter values. By providing a variety of customization options, users can explore and design representations of risk-related information that suit their personal goals and needs.
You can install the latest development version of riskyr
from its GitHub repository at https://github.com/hneth/riskyr:
# install.packages("devtools")
devtools::install_github("hneth/riskyr")
riskyr
is designed to address problems like the following:[2]
Screening for hustosis
A new screening device for detecting the clinical condition of hustosis is developed. Its current version is very good, but not yet perfect. It has the following properties: 1. About 4% of the general population suffer from hustosis. 2. If someone suffers from hustosis, there is a chance of 80% that he or she will test positively for the condition. 3. If someone is free from hustosis, there is a chance of 4% that he or she will still test positively for the condition.
Mr. and Ms. Smith have both been screened with this device: - Mr. Smith tested positively (i.e., received a diagnosis of hustosis). - Ms. Smith tested negatively (i.e., was judged to be free of hustosis).
Please answer the following questions: - What is the probability that Mr. Smith actually suffers from hustosis? - What is the probability that Ms. Smith is actually free of hustosis?
The first challenge in solving such problems is in understanding the information provided. The problem description provides three essential probabilities:
prev = .04
.sens = .80
.spec = .04
.The second challenge here lies in understanding the questions that are being asked -- and in realizing that their answers are not simply the decision's sensitivity or specificity values. Instead, we are asked to provide two conditional probabilities:
PPV
).NPV
).One of the best tricks in risk literacy education is to translate probabilistic information into frequencies.[3] To do this, we imagine a representative sample of N = 1000
individuals. Rather than asking about the probabilities for Mr. and Ms. Smith, we could re-frame the questions as:
Assuming a representative sample of 1000 individuals: - What proportion of individuals with a positive test result actually suffer from hustosis? - What proportion of individuals with a negative test result are actually free of hustosis?
riskyr
Here is how riskyr
allows you to view and solve such problems:
library(riskyr) # loads the package
#> Welcome to riskyr!
#> riskyr.guide() opens user guides.
Let us define a new riskyr
scenario (called hustosis
) with the information provided by our problem:
## (1) Create your own scenario: ----------
hustosis <- riskyr(scen.lbl = "Example",
cond.lbl = "hustosis",
dec.lbl = "screening test",
popu.lbl = "representative sample",
N = 1000,
prev = .04, sens = .80, spec = (1 - .05)
)
To obtain a quick overview of key parameter values, we could ask for the summary
of our hustosis
scenario:
summary(hustosis) # summarizes key parameter values
#> Scenario: Example
#>
#> Condition: hustosis
#> Decision: screening test
#> Population: representative sample
#> N = 1000
#> Source: Source information for this scenario
#>
#> Probabilities:
#>
#> Essential probabilities:
#> prev sens mirt spec fart
#> 0.04 0.80 0.20 0.95 0.05
#>
#> Other probabilities:
#> ppod PPV NPV FDR FOR
#> 0.080 0.400 0.991 0.600 0.009
#>
#> Frequencies:
#>
#> by conditions:
#> cond.true cond.false
#> 40 960
#>
#> by decision:
#> dec.pos dec.neg
#> 80 920
#>
#> by correspondence (of decision to condition):
#> dec.cor dec.err
#> 944 56
#>
#> 4 essential (SDT) frequencies:
#> hi mi fa cr
#> 32 8 48 912
#>
#> Accuracy:
#>
#> acc:
#> 0.944
The summary distinguishes between probabilities, frequencies, and accuracy information. In Probabilities
we find the answer to both of our questions when taking into account the information provided above:
The conditional probability that Mr. Smith actually suffers from hustosis given his positive test result is 40% (as PPV = 0.400
).
The conditional probability that Ms. Smith is actually free of hustosis given her negative test result is 99.1% (as NPV = 0.991
).
In case you are surprised by these answers, you are a good candidate for additional instruction in risk literacy. One of the strengths of riskyr
is to analyze and view the scenario from a variety of different perspectives. Here is a quick overview over its different types of visualizations:
## View graphics:
plot(hustosis, plot.type = "tree", by = "dc") # plot a tree diagram (by decision):
This particular tree, which splits the population of N = 1000
individuals into two subgroups by decision (by = "dc"
), actually contains the answer to the second version of our questions:
32/80 = .400
(corresponding to our value of PPV
above).912/920 = .991
(corresponding to our value of NPV
above, except for minimal differences due to rounding).Of course, the frequencies of these ratios were already contained in the hustosis
summary above. But the representation in the form of a tree diagram makes it easier to understand which frequencies are required to answer the question.
plot(hustosis, plot.type = "icons") # plot an icon array:
plot(hustosis, plot.type = "mosaic") # plot a mosaic plot:
plot(hustosis, plot.type = "curve") # plot curves (as a function of prevalence):
plot(hustosis, plot.type = "plane") # plot plane (as a function of sens x spec):
As defining your own scenarios can be cumbersome and the literature is full of existing problems (that study so-called Bayesian reasoning), riskyr
provides a set of -- currently 25) -- pre-defined scenarios (stored in a list scenarios
). Here is an example that shows how you can select and explore them:
Let us assume you want to learn more about the controversy surrounding screening prodecures of prostate-cancer (known as PSA screening). Scenario 21 in our collection of scenarios
is from an article on this topic (Arkes & Gaissmaier, 2012). To select a particular scenario, simply assign it to an R object. For instance, we can assign Scenario 21 to s21
:
## (2) Explore an existing riskyr scenario: ----------
s21 <- scenarios$n21 # assign pre-defined Scenario 21 to s21.
The following commands provide a quick overview of the scenario content in text form:
# Show basic scenario information:
s21$scen.lbl # shows descriptive label:
#> [1] "PSA test 1 (high prev)"
s21$cond.lbl # shows current condition:
#> [1] "prostate cancer"
s21$dec.lbl # shows current decision:
#> [1] "PSA test"
s21$popu.lbl # shows current population:
#> [1] "1000 patients with symptoms diagnostic of prostate cancer taking a PSA test."
s21$scen.apa # shows current source:
#> [1] "Arkes, H. R., & Gaissmaier, W. (2012). Psychological research and the prostate-cancer screening controversy. Psychological Science, 23(6), 547--553."
## View parameters:
summary(s21) # shows key parameter information:
#> Scenario: PSA test 1 (high prev)
#>
#> Condition: prostate cancer
#> Decision: PSA test
#> Population: 1000 patients with symptoms diagnostic of prostate cancer taking a PSA test.
#> N = 1000
#> Source: Arkes & Gaissmaier (2012), p. 550
#>
#> Probabilities:
#>
#> Essential probabilities:
#> prev sens mirt spec fart
#> 0.50 0.21 0.79 0.94 0.06
#>
#> Other probabilities:
#> ppod PPV NPV FDR FOR
#> 0.135 0.778 0.543 0.222 0.457
#>
#> Frequencies:
#>
#> by conditions:
#> cond.true cond.false
#> 500 500
#>
#> by decision:
#> dec.pos dec.neg
#> 135 865
#>
#> by correspondence (of decision to condition):
#> dec.cor dec.err
#> 575 425
#>
#> 4 essential (SDT) frequencies:
#> hi mi fa cr
#> 105 395 30 470
#>
#> Accuracy:
#>
#> acc:
#> 0.575
Generating the following plots will provide you with a quick visual exploration of the scenario:
plot(s21) # plots a network diagram (by default):
plot(s21, plot.type = "icons") # plot an icon array:
plot(s21, plot.type = "mosaic") # plot a mosaic plot:
The following curves show values of conditional probabilities as a function of prevalence:
plot(s21, plot.type = "curve", what = "all") # plot all curves (as a function of prevalence):
The following surface shows the negative predictive value (NPV) as a function of sensitivity and specificity (for a given prevalence):
plot(s21, plot.type = "plane", what = "NPV") # plot plane (as a function of sens x spec):
We hope that these examples succeeded in whetting your appetite for visual exploration. If so, call riskyr.guide()
for viewing the package vignettes and obtaining additional information.
riskyr
originated out of a series of lectures and workshops on risk literacy in spring/summer 2017. The current version (riskyr
0.1.0, as of Feb. 16, 2018) is still under development. Its primary developers and designers are Hansjörg Neth, Felix Gaisbauer, and Nico Gradwohl, who are researchers at the department of Social Psychology and Decision Sciences at the University of Konstanz, Germany.
The riskyr
package is open source software written in R and released under the GPL 2 | GPL 3 licenses.
Please email at [email protected] in case you want to use, adapt, or share this software.
We appreciate your feedback, comments, or questions.
Please report any riskyr
-related issues at https://github.com/hneth/riskyr/issues.
For general inquiries, please email us at [email protected].
To cite riskyr
in derivations and publications use:
riskyr
: A toolbox for rendering risk literacy more transparent.
Social Psychology and Decision Sciences, University of Konstanz, Germany.
Computer software (R package version 0.1.0, Feb. 16, 2018).
Retrieved from https://github.com/hneth/riskyr.A BibTeX entry for LaTeX users is:
@Manual{,
title = {riskyr: A toolbox for rendering risk literacy more transparent},
author = {Hansjörg Neth and Felix Gaisbauer and Nico Gradwohl and Wolfgang Gaissmaier},
year = {2018},
organization = {Social Psychology and Decision Sciences, University of Konstanz},
address = {Konstanz, Germany},
note = {R package (version 0.1.0, Feb. 16, 2018)},
url = {https://github.com/hneth/riskyr},
}
Calling citation("riskyr")
in the package also displays this information.
Arkes, H. R., & Gaissmaier, W. (2012). Psychological research and the prostate-cancer screening controversy. Psychological Science, 23, 547--553.
Gigerenzer, G. (2002). Reckoning with risk: Learning to live with uncertainty. London, UK: Penguin.
Gigerenzer, G. (2014). Risk savvy: How to make good decisions. New York, NY: Penguin.
Gigerenzer, G., Gaissmaier, W., Kurz-Milcke, E., Schwartz, L., & Woloshin, S. (2007). Helping doctors and patients make sense of health statistics. Psychological Science in the Public Interest, 8, 53--96.
Gigerenzer, G., & Hoffrage, U. (1995). How to improve Bayesian reasoning without instruction: Frequency formats. Psychological Review, 102, 684--704.
Hoffrage, U., Gigerenzer, G., Krauss, S., & Martignon, L. (2002). Representation facilitates reasoning: What natural frequencies are and what they are not. Cognition, 84, 343--352.
Hoffrage, U., Krauss, S., Martignon, L., & Gigerenzer, G. (2015). Natural frequencies improve Bayesian reasoning in simple and complex inference tasks. Frontiers in Psychology, 6, 1473.
Hoffrage, U., Lindsey, S., Hertwig, R., & Gigerenzer, G. (2000). Communicating statistical information. Science, 290, 2261--2262.
Kurzenhäuser, S., & Hoffrage, U. (2002). Teaching Bayesian reasoning: An evaluation of a classroom tutorial for medical students. Medical Teacher, 24, 516--521.
Kurz-Milcke, E., Gigerenzer, G., & Martignon, L. (2008). Transparency in risk communication. Annals of the New York Academy of Sciences, 1128, 18--28.
Sedlmeier, P., & Gigerenzer, G. (2001). Teaching Bayesian reasoning in less than two hours. Journal of Experimental Psychology: General, 130, 380--400.
[1] Simon, H.A. (1996). The Sciences of the Artificial (3rd ed.). The MIT Press, Cambridge, MA. (p. 132).
[2] See Gigerenzer (2002, 2014), Gigerenzer and Hoffrage, U. (1995), Gigerenzer et al. (2007), and Hoffrage et al. (2015) for lots of similar problems. Also, Sedlmeier and Gigerenzer (2001) and Kurzenhäuser and Hoffrage (2002) report related training programs.
[3] See Gigerenzer and Hoffrage (1995) and Hoffrage et al. (2000, 2002) on the concept of natural frequencies.
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