knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## Initialize some stuff: library("riskyr") # loads the package op <- par(no.readonly = TRUE)
riskyr is a toolbox for rendering risk literacy more transparent. Its goal is to gain insights into risk-related scenarios with a minimum of hassle and maximum of fun.
This page assumes that you just installed the package and are eager to see what you can do with it. (See the User guide for a more comprehensive introduction.)
How can you use
riskyr? Basically, there are two ways to get started:
Define your own scenario from risk-related information (typically provided in terms of probabilities).
Inspect one of
r length(scenarios) - 1 predefined scenarios to get a glimpse of what types of scenarios are possible.
Either way, you will soon explore some specific risk-related scenario and uncover relationships between its parameters. Please load the package first, if you have not already done so:
library("riskyr") # loads the package
Let's launch your
riskyr-career by creating a ficticious risk scenario that we construct from scratch:^[The data is made-up, but the issue is real. See Dressel and Farid (2018) for a recent study on this issue.]
Imagine you are developing a test to predict if a jailed criminal offender will reoffend after his or her release. Your research yields the following information:
- 45% of 753 jailed offenders in some prison re-offend after they are released (
prev = .45).
- Your test correctly detects those who will re-offend in 98% of the cases (
sens = .98).
- Your test falsely identifies 54% of those who will not re-offend as potential re-offenders. Conversely, this implies that your test correctly identifies 46% of those that will not reoffend (
spec = .46).
John D. is about to get released and is tested. The test predicts that he will reoffend.
What is the probability that John D. will actually reoffend, given his test result?
To answer this question, you could calculate the corresponding probabilities or frequencies (as explained in the user guide). Alternatively, you can use the
riskyr() function to create a
riskyr scenario that you can modify, inspect, and visualize in various ways.
First, we need to translate the numeric information provided in our example into parameter values:
The probability of reoffending provides the prevalence in our population:
prev = .45.
The test's conditional probability of correctly detecting a reoffender provides its sensitivity:
sens = .98.
The test's conditional probability of correctly detecting someone who will not reoffend provides its specificity:
spec = .46.
(This corresponds to a false alarm rate
fart = 1 - spec = .54.)
In addition, the population size of your sample was mentioned to be
N = 753.^[If no population size value
N is specified, a suitable value is provided.]
The following code defines a perfectly valid
riskyr scenario from 3 essential probabilities:
# Create a minimal scenario (from probabilities): my_scenario <- riskyr(prev = .45, sens = .98, spec = .46)
my_scenario from 3 essential probabilities (
fart) and computes a suitable population size
Alternatively, we could create the same minimal scenario from 4 essential frequencies (if they are known). The following code creates the scenario a second time, but now uses the frequencies of
my_scenario to do so:
# Create a minimal scenario (from frequencies): my_scenario_2 <- riskyr(hi = my_scenario$hi, mi = my_scenario$mi, fa = my_scenario$fa, cr = my_scenario$cr)
If this succeeds,
my_scenario_2 contain the same information:
To make various outputs more recognizable, many aspects of a
riskyr scenario can be described by setting optional
scen_lblspecifies a label by which you can recognize the scenario (e.g., "Identifying reoffenders").
popu_lbl specifies the population of interest (e.g., "inmates").
cond_lbl specifies the condition of interest (i.e., "reoffending").
cond_true_lblspecifies a label for the condition being true ("offends again").
cond_false_lbl specifies a label for the condition being false ("does not offend again").
dec_lbl specifies the nature of the decision, prediction, or test ("test result").
dec_pos_lblspecifies a positive decision regarding the condition ("predict to reoffend").
dec_neg_lbl specifies a negative decision regarding the condition ("predict to not reoffend").
cr_lbl specify the four possible combinations of conditions and decisions:
Whereas specifying three essential probabilities is necessary to define a valid
riskyr scenario, providing
N and the other arguments are entirely optional. For illustrative purposes, we create a very well-specified
# Create a scenario with custom labels: my_scenario <- riskyr(scen_lbl = "Identifying reoffenders", popu_lbl = "prison inmates", cond_lbl = "reoffending", cond_true_lbl = "reoffends", cond_false_lbl = "does not reoffend", dec_lbl = "test result", dec_pos_lbl = "predict to\nreoffend", dec_neg_lbl = "predict to\nnot reoffend", hi_lbl = "reoffender found", mi_lbl = "reoffender missed", fa_lbl = "false accusation", cr_lbl = "correct release", prev = .45, # prevalence of being a reoffender. sens = .98, # p( will reoffend | offends again ) spec = .46, # p( will not reoffend | does not offend again ) fart = NA, # p( will reoffend | does not offend gain ) N = 753, # population size scen_src = "(a ficticious example)")
The simple graph has brought more information to the data analyst’s mind than any other device. (...) the meat of the matter can usually be set out in a graph.
(John W. Tukey)^[Tukey, J.W. (1962). The future of data analysis. (In: The Collected Works of John W. Tukey, Volume 3, p. 457).]
We always can inspect the details of
my_scenario by computing additional metrics and studying their values with
summary(my_scenario). But anyone who regularly works with data knows that graphs can provide key insights faster and in different ways than written summaries and tables. To illustrate this point, we create and inspect some visualizations of our scenario.
A prism plot (or network diagram) shows key frequencies as colored boxes and corresponding probabilities as the edges that connect the boxes. In this particular version, the size of the boxes is fixed. However, we can visualize the relative size of frequencies by using the
area argument and show the names of the frequencies (as provided by our text labels) by adding the
f_lbl = "nam" argument. To save space, we do not show the plots here, but please try and see for yourself:
plot(my_scenario, area = "sq", f_lbl = "nam", p_lbl = "mix") # show frequency names plot(my_scenario, area = "hr", f_lbl = "num", p_lbl = "num") # only numeric labels
The resulting graph maps frequency to the size of square boxes, which makes it easier to distinguish between cases with high and with low frequencies.
my_scenariowith the option
area = "hr". What do you see?
by = "cdac"as another argument to your plotting call. How does the resulting plot relate to the previous ones?
riskyrcreates a plot of
type = "prism"by default. Use
?plot_prismfor the documentation of
plot_prismto learn about and try out additional arguments.
plot(my_scenario, area = "hr") plot(my_scenario, area = "no", by = "cdac") plot(my_scenario, area = "hr", by = "acdc", f_lbl = "nam", p_lbl = "num", f_lwd = .5, col_pal = pal_bw)
An icon array displays the entire population of inmates classified by condition (whether they will reoffend or not) and decisions (our test's predictions). We can plot this display for our scenario by using the
plot function and specifying the
type = "icons":
plot(my_scenario, type = "icons")
From the icon array, we can easily see that roughly half of the inmates reoffend (see the icons in dark green and dark blue). The majority of the reoffenders are classified correctly (shown in dark green rather than dark blue).
But where is John D.? His test result predicted that he would reoffend. Depending on his actual behavior, this means that he will either be classified as a "reoffender found" (if he actually reoffends: dark green icons) or as a "false accusation" (if he does not reoffend: light red icons). As there are a similar number of both types of icons (with some skew towards "reoffenders found"), it appears that his chances of actually reoffending are only slightly higher than chance.
To dig deeper into the dirty details of
my_scenario, let us look at its
The text output (printed in R's console window) provides a brief description of our scenario (i.e., its name, the condition and decision of interest, as well as the type and size of population), followed by a range of numeric parameters (structured into probabilities, frequencies, and overall accuracy).
In the present case, we were interested in a person's conditional probability of reoffending given a positive test result. This metric is also known as the positive predictive value (PPV). Our summary information shows
PPV = 0.598. Thus, based on the information provided, John D.'s probability of reoffending is 59.8\% (quite in line with our visual estimate from the icon array above).
summary(my_scenario, summarize = "prob")
An alternative way to view the our scenario is a frequency tree that splits the population into two subgroups (e.g., by the two possible results of our test) and then classify all members of the population by the possible combinations of decision and actual condition, yielding the same four types of frequencies as identified above (and listed as
cr in the
plot(my_scenario, type = "tree", by = "dc") # plot tree diagram (splitting N by decision)
The frequency tree also shows us how the PPV (shown on the arrow on the lower left) can be computed from
frequencies (shown in the boxes): PPV = (number of offenders found)/(number of people predicted to reoffend) (or
PPV = hi/dec_pos). Numerically, we see that
PPV = 332/556, which amounts to about 60\% (or
1 - 0.403).
The tree also depicts additional information that corresponds to our
summary from above. For instance, if we had wondered about the negative predictive value (NPV) of a negative test result (i.e., the conditional probability of not offending given that the test predicted this), the tree shows this to be
NPV = 190/197 or about 96.4\% (as
NPV = cr/dec_neg). Again, this closely corresponds to our
summary information of
NPV = 0.966.^[The difference between
NPV = 190/197 = 0.964467 (when computing the ratio of frequencies) and
NPV = 0.966 (in the
summary) is due to rounding tree frequencies to integer values. If absolute precision is required, we can plot the frequency tree without rounding by adding an argument
round = FALSE. ]
A good question to ask is: To what extend do the positive and negative predictive values (PPV and NPV) depend on the likelihood of reoffending in our population (i.e., the condition's prevalence)? To answer this, the following code allows to show conditional probabilities (here
NPV) as a function of
prev (and additionally assumes a 5%-uncertainty concerning the exact parameter values):
plot(my_scenario, type = "curve", uc = .05)
As before, we can read off that the current values of
PPV = 59.76% and
NPV = 96,56%, but also see that our 5%-uncertainty implies relatively large fluctuations of the exact numeric values. Importantly, the curves also show that the prevalence value is absolutely crucial for the value of both
NPV. For instance, if
prev dropped further, the
PPV of our test was also considerably lower. In fact, both the PPV and NPV always vary from 0 to 1 depending on the value of
prev, which means that specifying them is actually meaningless when the corresponding value of
prev is not communicated as well. (See the guide on functional perspectives for additional information and options.)
Having illustrated how we can create a scenario from scratch and begin to inspect it in a few ways, we can now turn towards loading scenarios that are contained in the
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
r length(scenarios)) -- pre-defined scenarios (stored in a list
scenarios). The following table provides a first overview of the scenarios available, including their relevant condition, their population size
N, and basic probability information:
library(knitr) scen_table <- df_scenarios[, c("scen_lbl", "cond_lbl", "N", "prev", "sens", "spec", "fart")] scen_table[, -c(1:2)] <- round(scen_table[, -c(1:2)], 3) names(scen_table) <- c("Scenario", "Condition", "N", "prev", "sens", "spec", "fart") knitr::kable(scen_table)
In the following, we show you can select and explore these scenarios.
Let us assume you want to learn more about the controversy surrounding screening procedures 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 10 (i.e.,
scenarios$n10) to an object
s10 <- scenarios$n10 # assign pre-defined Scenario 10 to s10.
As each scenario is stored as a list, different aspects of a scenario can be printed by their element names:
# Show basic scenario information: s10$scen_lbl # shows descriptive label: s10$cond_lbl # shows current condition: s10$dec_lbl # shows current decision: s10$popu_lbl # shows current population: s10$scen_apa # shows current source:
A description of the scenario can be printed by calling
As explained above, an overview of the main parameters of a scenario is provided by
summary(s10) # summarizes key scenario information:
Note that -- in this particular population -- the prevalence for the condition (
r s10$cond_lbl) is assumed to be relatively high (with a value of
To eyeball basic scenario information, we can visualize it in many different ways. To save space, we do not show the plots here, but please try and see for yourself:
plot(s10, type = "tab") # plot 2x2 table plot(s10, type = "icons", cex_lbl = .75) # plot an icon array plot(s10, type = "prism", area = "sq") # plot a network/prism diagram plot(s10, type = "area") # plot an area plot plot(s10, type = "bar", dir = 2) # plot a bar chart
These initial inspections reveal that the overall accuracy of the decision considered (
r s10$scen_lbl) is not great: There are almost as many cases of incorrect classifications (shown in blue) as correct ones (shown in green). In fact, both the summary and the icon array note that the overall accuracy of the test is at 57.5%. Given that green squares signal correct classifications and blue squares signal incorrect classifications, it is immediately obvious that our main issue with accuracy here consists in so-called misses: Patients with cancer that remain undetected (marked with "
r s10$mi_lbl" and denoted by icons in lighter blue).
Next, we could another prism diagram, to further illuminate the interplay between probabilities and frequencies in this scenario:
plot(s10, by = "cddc", # perspective: upper half by condition, lower half by decision area = "hr", # frequency boxes as horizontal rectangles (scaled to N) p_lbl = "num") # probability labels: numeric only
This variant of the prism plot shows how the probability values of key condition and decision parameters split the assumed population of
N = 1000 patients into subgroups that correspond to 9 frequencies (also listed in the summary). Calling the same command with the optional argument
p_lbl = "nam" would print the probability names, rather than their values (see also the options
p_lbl = "min" and
"mix".) The middle row of boxes shows the four essential frequencies (of hits
mi, false alarms
fa, and correct rejections
cr) in colors corresponding to the icon array above. Setting
area = "hr" in our
plot command switched the default display (of rectangular boxes) to a version in which the frequency boxes at each level of the network are shown as horizontal rectangles (hence
hr) and the box widths are scaled to add up to the population width
N on each level. Thus, the relative width of each box illustrates the frequency of corresponding cases, making it easy to spot locations and paths with few or many cases.
A fact that was not so obvious in the icon array -- but shown in the lower half of the prism plot -- is that the current scenario yields mostly negative decisions (865 out of 1000, or 86.5%). Of those negative decisions, 470 (or 54.34%) are correct (see
cr shown in light green) and 395 (or 45.66%) are incorrect (see
mi shown in dark red). The ratio
cr/dec_neg = 470/865 = 54.34% indicates the negative predictive value (
NPV) of the test.
Can you find the current positive predictive value (
PPV) in the diagram? (Hint: Its value marks an arrow between two boxes, but is also shown on the margin and was contained in the summary above.)
Re-create the prism plot of
s10 from different perspectives (e.g.,
by = "cdac") and different area settings (e.g.,
area = "sq", see "?plot_prism" for the options available). For instance, what would the following commands plot:
plot(s10, by = "cdac", area = "sq") plot(s10, by = "ac", area = "hr")
One way to further understand the relations between basic probabilities -- like the prevalence
prev, which does not depend on our decision, but only on the environmental probability of the condition (here: "
r s10$cond_lbl") -- and probabilities conditional on both the condition and on features of the decision (like
NPV) is to plot the latter as a function of the former. Calling
type = "curve" does this for us. To save space, we do not show the plots here, but please try and see for yourself:
plot(s10, type = "curve", what = "all", # plot "all" available curves uc = .05) # with a 5%-uncertainty range
The additional argument
what = "all" instructed
riskyr to provide us with additional curves, corresponding to the percentage of positive decisions (
ppod) and overall accuracy (
acc). Just like
NPV, the values of these metrics crucially depend on the value of the current prevalence (shown on the x-axis) and on our current range of uncertainty (shown as shaded polygons around the curves). Interestingly, the curves of
acc appear to be linear, even though the
riskyr function plots them in exactly the same way as
NPV. Would you have predicted this without seeing it?
accintersects the curve of
PPVat the point at the same point as the curve of
While the curves shown for
NPV so far illustrate their dependence on the prevalence (
prev), we can also ask:
How do these conditional probabilities vary as a function of the decisions sensitivity (
sens) and specificity (
To provide a visual answer to this question, we plot them as 3D planes (i.e., as functions of both
spec, for a given value of
prev) with the following commands:^[The
par() commands before and after the calls to
plot in this example are not needed if you re-create the plots for yourself. They only set and reset the R plotting space to allow plotting both planes next to each other.]
# opar <- par(no.readonly = TRUE) # save plot settings. # par(mfrow = c(1, 2)) # 1 row with 2 plots:
## Plot plane of PPV and NPV as functions of sens and spec (for given prev): plot(s10, type = "plane", what = "PPV", cex_lbl = .7) # PPV by sens x spec (fixed prev) plot(s10, type = "plane", what = "NPV", cex_lbl = .7) # NPV by sens x spec (fixed prev)
# par(op) # reset plot settings.
This comparison shows that the curves of
NPV (created by
type = "curve" above) were only two out of an infinite number of possible intersections of two planes (created by
type = "plane" here). Consequently, the current values of
NPV (shown as yellow points on the planes) crucially depend on the condition's prevalence (
prev), the decision's sensitivity (
sens), and the decision's specificity (
In retrospect, these dependencies make it clear why it is so hard to provide an answer to the seemingly simple question: What's the probability of having some condition when testing positive or negative for it? While
riskyr cannot simplify this issue, we hope that you are convinced that it helps to compute, transform, and see some relationships that are not immediately obvious from the mathematical definitions of the underlying concepts. If you feel that this improves your understanding, we came a little closer to our goal of rendering risk literacy more transparent.
scenarioscontains a version of the same situation that assumes a different population (with a lower prevalence value for the same condition). Inspect and explore the consequence of this change by following the same steps for
Here are the first steps:
# Select Scenario 9: s9 <- scenarios$n9 # assign pre-defined Scenario 9 to s9. # Basic scenario information: s9$scen_lbl # shows descriptive label: s9$popu_lbl # shows current population:
Now re-do the plots (for
s10 above) -- and note the changes between
Importantly, the properties of the test are identical for both scenarios -- only the population (i.e., its prevalence for the condition) has changed.
This introduction should suffice to get you started with using
Have fun by exploring the provided scenarios and creating your own examples!
Arkes, H. R., & Gaissmaier, W. (2012). Psychological research and the prostate-cancer screening controversy. Psychological Science, 23, 547--553.
Dressel, J., & Farid, H. (2018). The accuracy, fairness, and limits of predicting recidivism. Science Advances, 4, eaao5580.
The following resources and versions are currently available:
Type: | Version: | URL: |
riskyr (R package): | Release version | https://CRAN.R-project.org/package=riskyr |
\ | Development version | https://github.com/hneth/riskyr |
riskyrApp (R Shiny code): | Online version | http://riskyr.org |
\ | Development version | https://github.com/hneth/riskyrApp |
C. Online documentation: | Release version | https://hneth.github.io/riskyr |
\ | Development version | https://hneth.github.io/riskyr/dev |
We appreciate your feedback, comments, or questions.
Please report any
riskyr-related issues at https://github.com/hneth/riskyr/issues.
Email us at email@example.com if you want to modify or share this software.
| Nr. | Vignette | Content |
| ---: |:---------|:-----------| | A. | User guide | Motivation and general instructions | | B. | Data formats | Data formats: Frequencies and probabilities | | C. | Confusion matrix | Confusion matrix and accuracy metrics | | D. | Functional perspectives | Adopting functional perspectives | | E. | Quick start primer | Quick start primer |
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