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The cvasi package is a software library that extends the features of the programming language R by routines for ecotox effect modeling. The routines are intended to be used for scientific purposes as well as in the context of regulatory risk assessments. cvasi implements model equations and default parameters to simulate a set of toxicokinetic-toxicodynamic (TKTD) models. The models are intended to assess the effects of substance exposure on effect endpoints, such as growth and reproduction, for a range of standard test species.
The package offers a standardized framework which can be extended by (almost) any TKTD model that can be implemented in R. Its modeling workflows are designed to be self-explanatory and as intuitive as possible to make modeling approaches more accessible. In addition, the framework’s routines are optimized to reduce the computing time required for extensive risk assessments.
The cvasi package and its routines can be used by anyone with basic to intermediate knowledge of the R programming language. The routines can be used in a procedural fashion, commonly referred to as base R, in which function statements are executed, assigned to a variable, and then passed on to the next function:
library(cvasi)
## Sample base R workflow ##
# Create a scenario object of model GUTS-RED-IT
my_it <- GUTS_RED_IT()
# Set model parameters
my_it <- set_param(my_it, c(kd=1.2, hb=0, alpha=9.2, beta=4.3))
# Print scenario details
my_it
#> 'GUTS-RED-IT' scenario
#> param: kd=1.2, hb=0, alpha=9.2, beta=4.3
#> init : D=0, H=0
#> endpt: L
#> times: none
#> forcs: none
#> expsr: none
#> >> exposure series is empty
A more advanced approach is to use the tidyr syntax (cf. Wickham & Grolemund 2017) which uses verb-like statements to modify data. tidyr syntax can be used to chain functions calls which pass the result of one function on to the next:
## Example 'tidyr' workflow ##
# the pipeline (%>%) symbol passes results to the next statement
GUTS_RED_IT() %>%
set_param(c(kd=1.2, hb=0, alpha=9.2, beta=4.3))
#> 'GUTS-RED-IT' scenario
#> param: kd=1.2, hb=0, alpha=9.2, beta=4.3
#> init : D=0, H=0
#> endpt: L
#> times: none
#> forcs: none
#> expsr: none
#> >> exposure series is empty
Both workflow styles achieve the same result, but tidyr is terser, especially if several operations are performed on the same object. tidyr style is the recommended way to interact with the cvasi package.
The latest development version can be installed from GitHub:
install.packages("remotes", dependencies=TRUE)
remotes::install_github("cvasi-tktd/cvasi", dependencies=TRUE)
The package and its source code is also available on GitHub.
The central concept within the cvasi package is the scenario. It encapsulates all key properties to run a simulation such as initial state and model parameters. The scenario can be thought of as the collection of data and parameters necessary to reproduce a certain study condition or situation. The set of available scenario properties depends on the model type but may include:
Scenario properties can be modified using intuitively named
tidyr verbs: in general, each verb accepts a scenario as an
argument and returns a modified scenario as the result. For instance,
the set_param()
function will update a scenario’s
parameters to new values:
library(cvasi)
# Create a new GUTS-RED-IT scenario and set its model parameters
GUTS_RED_IT() %>%
set_param(c(kd=1.2, hb=0, alpha=9.2, beta=4.3))
#> 'GUTS-RED-IT' scenario
#> param: kd=1.2, hb=0, alpha=9.2, beta=4.3
#> init : D=0, H=0
#> endpt: L
#> times: none
#> forcs: none
#> expsr: none
#> >> exposure series is empty
If a scenario is properly defined, it can be passed to dedicated
functions that, for instance, run a simulation or derive assessment
endpoints. These higher-level functions do not return a scenario object
but a table of e.g. simulation results for that particular scenario. As
an example, simulating the sample scenario minnow_it
will
run a GUTS-RED-IT model using substance-specific
parameters:
# Example GUTS-RED-IT scenario derived from an acute fish toxicity study
# of the fathead minnow and Chlorpyrifos (Geiger et al. 1988)
minnow_it %>%
simulate()
#> time D H S
#> 1 0 0.0000000 0 1.0000000
#> 2 1 0.7075891 0 0.9999854
#> 3 2 0.9144958 0 0.9999558
#> 4 3 0.9749972 0 0.9999417
#> 5 4 0.9926889 0 0.9999370
The table returned by simulate()
contains the value of
each state variable at the requested output time points. In case of the
GUTS-RED-IT model, this comprises the state variables
D
(scaled damage) and H
(cumulative hazard).
Effect levels, effect profiles, and dose-response graphs can be derived
in a similar manner. Please refer to EFSA PPR Panel (2018) or the
package help for more information on GUTS-RED type models:
A scenario is created by first calling a constructor function that is dedicated to a particular model. The cvasi package supports multiple TKTD models, for instance:
GUTS_RED_SD()
GUTS_RED_IT()
Lemna_Schmitt()
, published by Schmitt et al.
(2013)Lemna_SETAC()
, published by Klein et al.
(2021)Myrio()
, an adaption of Klein et al. (2021) to
Myriophyllum at Tier 2CAlgae_Weber()
, published by Weber et al.
(2012)Algae_TKTD()
, based on Weber et al. (2012),
but with scaled damageAlgae_Simple()
, simplified growth model without
external forcing variablesDEB_abj()
, the abj model with type M
accelerationDEBtox()
, as implemented in the DEBtox2019
module of BYOMThe listed functions create objects that will carry all data and settings to fully describe a scenario. In case of a GUTS-RED-IT scenario, one needs to provide at least the four model parameters and an exposure time-series to fully define a scenario:
# Define an exposure time-series
myexposure <- data.frame(time=c(0, 1, 1.01, 5),
conc=c(10, 10, 0, 0))
# Create and parameterize a scenario
GUTS_RED_IT() %>%
set_param(c(kd=1.2, hb=0, alpha=9.2, beta=4.3)) %>%
set_exposure(myexposure) -> myscenario
One can examine the main scenario properties by passing the scenario to the console like in the next example. The console will print the model name, model parameters (param), initial state (init), enabled effect endpoints (endpt), output times (times), environmental forcings (forcs), and exposure series (expsr). Depending on model type, the scenario may carry additional properties that are not necessarily displayed in the console output.
# Print information about the scenario
myscenario
#> 'GUTS-RED-IT' scenario
#> param: kd=1.2, hb=0, alpha=9.2, beta=4.3
#> init : D=0, H=0
#> endpt: L
#> times: [0,5] n=4, regular
#> forcs: none
#> expsr: none
#> time conc
#> 1 0.00 10
#> 2 1.00 10
#> 3 1.01 0
#> 4 5.00 0
Several set_*()
verbs are available to modify scenario
properties, such as:
set_tag()
, to assign a custom tag to identify the
scenarioset_init()
, to set the initial stateset_param()
, to modify model parametersset_times()
, to define output time pointsset_forcings()
, to set environmental factors
(i.e. forcings)set_exposure()
, to set an exposure time-seriesset_endpoints()
, to enable/disable assessment
endpointsset_transfer()
, to define transfer intervals of
Lemna frondsset_moa()
, to select a model’s mode of actionset_window()
, to control moving exposure windowsPlease note that set_exposure()
will, by default, use
the exposure series’ time points also as output time points. If this
behavior is undesired, it can be disabled by setting the argument
reset_times=FALSE
:
# Update the exposure time-series but keep former output time points
myscenario %>%
set_exposure(no_exposure(), reset_times=FALSE)
#> 'GUTS-RED-IT' scenario
#> param: kd=1.2, hb=0, alpha=9.2, beta=4.3
#> init : D=0, H=0
#> endpt: L
#> times: [0,5] n=4, regular
#> forcs: none
#> expsr: no exposure
#> time conc
#> 1 0 0
Note that times
still has the original four elements
although the assigned exposure series has only a single entry. Output
time points can be explicitly set with set_times()
. For
deriving effect endpoints, the simulated time frame can be split up into
moving exposure windows of a certain length using
set_window()
. A more complex scenario setup may look like
the following workflow:
# Selected model parameters
myparam <- c(p_M=3211, v=0.023, k_J=0.63)
# Initial body length L
myinit <- c(L=0.02)
# Constant non-zero exposure
myexposure <- data.frame(time=0, conc=1.72)
DEB_abj() %>%
set_param(myparam) %>%
set_init(myinit) %>%
set_exposure(myexposure) %>%
set_times(0:10) %>% # Output times 0,1,2,...,10
set_mode_of_action(4) %>% # Method of Action #4 to be activated
set_window(length=3) # Using moving exposure windows of length 3 days
#> 'DEB_abj' scenario
#> param: p_M=3211, v=0.023, k_J=0.63, MoA=4
#> init : L=0.02, E=0, H=0, R=0, cV=0, Lmax=0
#> endpt: L, R
#> times: [0,10] n=11, regular
#> forcs: none
#> expsr: none
#> time conc
#> 1 0 1.72
After a scenario is fully set up, it can be passed to
simulate()
to return model results:
# Example scenario of the Lemna TKTD model
metsulfuron %>%
set_times(0:7) %>%
simulate()
#> time BM E M_int C_int FrondNo
#> 1 0 50.00000 1 0.0000 0.0000000 500000.0
#> 2 1 52.15858 1 223.0745 0.2560989 521585.8
#> 3 2 52.43495 1 369.6344 0.4221192 524349.5
#> 4 3 52.33917 1 463.0261 0.5297392 523391.7
#> 5 4 52.17923 1 521.8927 0.5989176 521792.3
#> 6 5 52.00016 1 558.6268 0.6432808 520001.6
#> 7 6 51.81403 1 581.2187 0.6717006 518140.3
#> 8 7 51.63740 1 474.0716 0.5497473 516374.0
simulate()
returns the model state for each output time
point. In this example, it returns results for the period from zero to
seven with an equi-distant time step length of one. The temporal
resolution of results can be increased by specifying additional output
times:
# Same simulation period, but with a smaller step length of 0.1
metsulfuron %>%
set_times(seq(0, 7, 0.1)) %>%
simulate() %>%
tail()
#> time BM E M_int C_int FrondNo
#> 66 6.5 51.72111 1 556.4478 0.6442288 517211.1
#> 67 6.6 51.70319 1 544.1623 0.6302236 517031.9
#> 68 6.7 51.68570 1 529.6855 0.6136648 516857.0
#> 69 6.8 51.66877 1 513.1159 0.5946630 516687.7
#> 70 6.9 51.65259 1 494.5480 0.5733237 516525.9
#> 71 7.0 51.63740 1 474.0716 0.5497473 516374.0
The resulting table now contains ten times as many rows because we decreased the step length by a factor of ten but simulated the same period. The temporal resolution of simulations can have an influence on results, i.e. the numerical values of the returned variables. These differences usually originate from small numerical errors introduced by the solver of the model’s Ordinary Differential Equations. Generally, parameters such as the step-length in time can have influence on the precision of simulation results.
There are several ways to increase the precision of simulation
results without modifying a scenario’s output times. One option is to
decrease the solver’s maximum step length in time by setting the
optional argument hmax
. The smaller hmax
, the
more precise the results:
# Original simulation period, but with a maximum solver step length of hmax=0.01
metsulfuron %>%
set_times(0:7) %>%
simulate(hmax=0.01)
#> time BM E M_int C_int FrondNo
#> 1 0 50.00000 1 0.0000 0.0000000 500000.0
#> 2 1 52.15858 1 223.0745 0.2560989 521585.8
#> 3 2 52.43495 1 369.6344 0.4221192 524349.5
#> 4 3 52.33917 1 463.0261 0.5297392 523391.7
#> 5 4 52.17923 1 521.8927 0.5989176 521792.3
#> 6 5 52.00016 1 558.6268 0.6432808 520001.6
#> 7 6 51.81403 1 581.2187 0.6717006 518140.3
#> 8 7 51.63740 1 474.0716 0.5497473 516374.0
Although very effective, reducing hmax
to small values
may lead to inefficiently long runtimes of simulations. If numerical
precision is an issue, it is advisable to also test other solver
settings such as absolute and relative error tolerances
(atol
and rtol
) or to switch to another solver
method. Numerical precision and stability is a complex and advanced
topic, please refer to the manual of simulate()
for
additional information:
Simulation results are the basis for deriving assessment endpoints such as effect levels and effect profiles. The cvasi package implements routines to derive these endpoints efficiently independent of the actual model that is being assessed. Hence, if a model is available within the package framework, it can be used to derive assessment endpoints. As an example, the following statement derives effect levels for a sample GUTS-RED-IT scenario:
# GUTS-RED-IT scenario of the fathead minnow and chlorpyrifos
minnow_it %>% effect()
#> # A tibble: 1 × 4
#> scenario L L.dat.start L.dat.end
#> <list> <dbl> <dbl> <dbl>
#> 1 <GutsRdIt> 0.0000630 0 4
The lethality endpoint L
has a value of
6.3e-5
which means that lethality has only marginally
increased by 0.0063% compared to a control scenario without exposure to
the contaminant. The columns L.dat.start
and
L.dat.end
denote the period for which the effect level was
observed. In case of GUTS-RED models, this usually refers to
the whole simulation period. For certain assessments it may be necessary
to evaluate all exposure periods of a certain length within the original
series separately. This approach is referred to as a moving exposure
window:
# Setting up a custom scenario with a total simulation period of 14 days and
# an exposure window length of 7 to assess a trapezoidal exposure pattern
americamysis %>%
set_window(7) %>%
set_exposure(data.frame(t=c(0,3,4,7,8), c=c(0,0,3,3,0))) %>%
set_times(0:14) -> mydeb
# Derive maximum effect level of all exposure windows
mydeb %>% effect()
#> # A tibble: 1 × 7
#> scenario L L.dat.start L.dat.end R R.dat.start R.dat.end
#> <list> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 <DebAbj> 0.0521 2 9 0 0 7
The americamysis
scenario provides two effect endpoints:
structural length (L
) and reproduction (R
).
Exposure to the simulated toxicant results at maximum in a 5.21%
decrease in body length compared to control scenarios. The maximum
effect was observed in the exposure window starting at time
2.0
and ending at 9.0
, cf. columns
L.dat.start
and L.dat.end
. The toxicant had no
effect on reproduction due to the simulation being too short for
reproduction to occur.
Scenarios can also be assessed regarding to so-called effect
profiles, or EPx values for short. An EPx value
quantifies the multiplication factor that is necessary to produce an
effect level of x% for that particular scenario. As an example, an
EP50 of 17.0
would mean that the scenario’s
exposure series needs to be multiplied by a factor of 17 to observe a
50% effect. The function epx()
can derive effect profiles
efficiently with arbitrary precision:
# Restrict assessed endpoints to structural length (L)
mydeb %>%
set_endpoints("L") %>%
epx()
#> # A tibble: 1 × 3
#> scenario L.EP10 L.EP50
#> <list> <dbl> <dbl>
#> 1 <DebAbj> 1.16 1.71
In this example, a factor of 1.16
resulted in 10% effect
on structural length and a factor of 1.71
in 50% effect.
epx()
provides means to control the precision of derived
EPx values, the range of tested multiplication factors, factor
cutoff thresholds, and debugging capabilities. To examine how a
particular EPx value was derived, simply set the argument
verbose=TRUE
:
# Examine how the EP20 value is derived
minnow_it %>% epx(level=20, verbose=TRUE)
#> epx: screening multiplication factors
#> start: 10
#> L.EP20: 1 <<<
#> L.EP20: 5.5
#> L.EP20: 7.75
#> L.EP20: 6.625
#> L.EP20: 7.1875
#> L.EP20: 6.90625
#> L.EP20: 6.765625
#> L.EP20: 6.8359375
#> L.EP20: 6.80078125
#> # A tibble: 1 × 2
#> scenario L.EP20
#> <list> <dbl>
#> 1 <GutsRdIt> 6.80
In this example, the algorithm of epx()
first tests a
multiplication factor of 10
and then continues testing
additional factors using a binary search algorithm until a factor is
found that causes 20% effect.
Please note: Depending on model and chosen parameters, it may be impossible to calculate EPx values (for selected effect levels), because the model or organism cannot reach the required state. As an example: If the simulated period of a DEB_abj scenario is too short, reproduction cannot occur. Therefore, effects on reproduction will always be zero independent of the exposure level. Consequently, EPx values for the reproduction endpoint will not be available.
Input data for the cvasi package relies on common R data structures and imposes only minimal requirements to set up scenarios:
data.frame
with exactly two numerical columns: The
first column for time, the second for the series’ value. The column
names are irrelevant but sensible names may help documenting the data.
Constant values can be represented by time-series with only a single row
or entry.Therefore, it should be possible to apply the package’s routines on existing datasets with minimal effort. Please refer to Wickham and Grolemund (2017) on how to implement plain and consistent processes to import and transform data using tidyr syntax.
cvasi does support loading data from common sources, such as the exposure model TOXSWA, to ease data processing. Notable file formats and data structures that are supported are exposure time-series from the model FOCUS TOXSWA, as well as fitted GUTS-RED model parameter sets from morse.
In general, all models require parameter values specific to the simulated species and substance. Some scenario types contain default values for selected model parameters as recommended by model authors. Scenarios providing default values include:
Lemna_Schmitt()
and derived models are parameterized
according to Schmitt et al. (2013)Lemna_SETAC()
, Myrio()
, and derived models
are parameterized as recommended by Klein et al. (2021)In addition, some models require values for environmental factors such as temperature and nutrient concentrations. These values or time-series are specific to a certain scenario and must be chosen accordingly.
Parameters of TKTD sub-models are substance-specific and are usually
obtained by fitting model parameters to observed data. The
cvasi package supports this process with the function
calibrate()
which uses a frequentist approach for parameter
fitting. However, parameters can also be derived by other means.
Generally, the user is responsible for choosing model parameters and the
package does not impose any restrictions in this regard.
The package function calibrate()
supports the following
operation modes:
Parameter fitting builds upon the R function
stats::optim()
and it exposes full control over the fitting
process. In this context, a dataset is represented by a calibration
set object which consists of a scenario, observed data, and an
optional weighting term. Please refer to the Modeling Howto for a description of the
fitting process using calibrate()
.
As an alternative for GUTS-RED type models, model parameters can also be obtained using the morse package. It uses a Bayesian approach for parameter fitting.
The cvasi package does not use or define any custom file
formats for model outputs but strictly relies on common R data
structures. Simulation results and assessment endpoints are returned in
tabular formats which can easily be serialized to common file formats
such as .csv
or Microsoft Excel files for further
processing and data storage.
The following subsections will describe in detail the return values of common package routines for simulating and assessing scenarios.
The return value of simulate()
is a
data.frame
containing the value of each state variable at
each requested output time. The first column represents time,
followed by columns for each state variable:
## Display selected scenario properties
metsulfuron@times # Output times
#> [1] 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
metsulfuron@init # Initial state
#> BM E M_int
#> 50 1 0
## Simulate the sample scenario
metsulfuron %>% simulate()
#> time BM E M_int C_int FrondNo
#> 1 0 50.00000 1 0.00000 0.00000000 500000.0
#> 2 1 52.15858 1 223.07447 0.25609887 521585.8
#> 3 2 52.43495 1 369.63440 0.42211917 524349.5
#> 4 3 52.33917 1 463.02605 0.52973924 523391.7
#> 5 4 52.17923 1 521.89269 0.59891761 521792.3
#> 6 5 52.00016 1 558.62681 0.64328081 520001.6
#> 7 6 51.81403 1 581.21867 0.67170059 518140.3
#> 8 7 51.63740 1 474.07158 0.54974731 516374.0
#> 9 8 51.61806 1 301.84519 0.35015964 516180.6
#> 10 9 52.32264 1 192.18727 0.21994721 523226.4
#> 11 10 54.34850 1 122.36718 0.13482205 543485.0
#> 12 11 57.08426 1 77.91217 0.08172830 570842.6
#> 13 12 59.99459 1 49.60731 0.04951275 599945.9
#> 14 13 62.96113 1 31.58537 0.03003980 629611.3
#> 15 14 65.95879 1 20.11066 0.01825733 659587.9
The model state in the first row is, by definition, equal to the
initial state of the scenario. The simulation result may contain
additional columns that are derived variables or intermediate model
variables. In case of the metsulfuron
scenario, the
internal toxicant concentration (C_int
) was derived from
BM
, M_int
, and model parameters. The number of
fronds (FrondNo
) was derived from BM
and model
parameters. Additional outputs such as C_int
and
FrondNo
are included in results for user convenience and to
support model understanding. Additional outputs can be disabled by
setting the optional argument nout=0
:
metsulfuron %>%
simulate(nout=0) %>%
head(5)
#> time BM E M_int
#> 1 0 50.00000 1 0.0000
#> 2 1 52.15858 1 223.0745
#> 3 2 52.43495 1 369.6344
#> 4 3 52.33917 1 463.0261
#> 5 4 52.17923 1 521.8927
Intermediate model variables can be enabled in the same manner:
metsulfuron %>%
simulate(nout=8) %>%
head(5)
#> time BM E M_int C_int FrondNo C_int_u BM_fresh k_phot_eff
#> 1 0 50.00000 1 0.0000 0.0000000 500000.0 0.0000000 835.0000 0.07548561
#> 2 1 52.15858 1 223.0745 0.2560989 521585.8 0.3414652 871.0482 0.03746128
#> 3 2 52.43495 1 369.6344 0.4221192 524349.5 0.5628256 875.6636 0.01993781
#> 4 3 52.33917 1 463.0261 0.5297392 523391.7 0.7063190 874.0641 0.01760496
#> 5 4 52.17923 1 521.8927 0.5989176 521792.3 0.7985568 871.3931 0.01699676
#> k_resp_eff f_Eff P_up_eff
#> 1 0.02030631 1.0000000 0.0054
#> 2 0.02030631 0.5049205 0.0054
#> 3 0.02030631 0.2693322 0.0054
#> 4 0.02030631 0.2376344 0.0054
#> 5 0.02030631 0.2291285 0.0054
The return value of effect()
is a
data.frame
containing the effect level of each selected
endpoint. The first column, scenario
, contains the original
scenario which was the basis of the assessment. Followed by the effect
level and the exposure window in which the maximum effect was
observed:
metsulfuron %>%
set_times(0:7) %>% # restrict scenario to the period [0,7]
effect()
#> # A tibble: 1 × 7
#> scenario BM BM.dat.start BM.dat.end r r.dat.start r.dat.end
#> <list> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 <LmnSchmS> 0.268 0 7 0.906 0 7
Effect levels are reported as a fraction relative to a control
scenario. Effects can be converted to percentages by multiplying the
value with 100
(%). For scenarios with moving exposure
windows disabled, the reported window will cover the entire simulation
period. If multiple windows result in identical maximum effect levels,
the first matching window will be reported. The table’s content can be
reduced to endpoints only by setting the argument
ep_only=TRUE
.
effect()
can also be instructed to return the effect
levels of all assessed exposure windows by setting the argument
max_only=FALSE
:
metsulfuron %>%
set_window(length=7, interval=1) %>% # enable moving exposure windows
effect(max_only=FALSE) # return effects of all windows
#> # A tibble: 8 × 5
#> scenario BM r dat.start dat.end
#> <list> <dbl> <dbl> <dbl> <dbl>
#> 1 <LmnSchmS> 2.68e- 1 9.06e- 1 0 7
#> 2 <LmnSchmS> 2.65e- 1 8.95e- 1 1 8
#> 3 <LmnSchmS> 2.48e- 1 8.29e- 1 2 9
#> 4 <LmnSchmS> 2.05e- 1 6.69e- 1 3 10
#> 5 <LmnSchmS> 1.47e- 1 4.63e- 1 4 11
#> 6 <LmnSchmS> 7.39e- 2 2.23e- 1 5 12
#> 7 <LmnSchmS> 3.15e- 3 9.18e- 3 6 13
#> 8 <LmnSchmS> -6.66e-16 -1.78e-15 7 14
In few cases, effect()
may report spurious non-zero
effect levels that are very close to zero. These can either be avoided
by increasing the numerical precision of simulations or by setting a
marginal effect threshold which instructs effect()
to zero
any effect below that threshold. A warning will be shown if a marginal
effect threshold greater than 1% is chosen. Applying a threshold of 1%
to the previous example results in zeroing the effect in the last and
second to last exposure window but leaving the remaining results
unchanged:
metsulfuron %>%
set_window(length=7, interval=1) %>% # enable moving exposure windows
effect(max_only=FALSE, marginal_effect=0.01) # return effects of all windows
#> # A tibble: 8 × 5
#> scenario BM r dat.start dat.end
#> <list> <dbl> <dbl> <dbl> <dbl>
#> 1 <LmnSchmS> 0.268 0.906 0 7
#> 2 <LmnSchmS> 0.265 0.895 1 8
#> 3 <LmnSchmS> 0.248 0.829 2 9
#> 4 <LmnSchmS> 0.205 0.669 3 10
#> 5 <LmnSchmS> 0.147 0.463 4 11
#> 6 <LmnSchmS> 0.0739 0.223 5 12
#> 7 <LmnSchmS> 0 0 6 13
#> 8 <LmnSchmS> 0 0 7 14
The return value of epx()
is a data.frame
containing the effect profile (EPx) of each selected endpoint
and effect level. The first column, scenario
, contains the
original scenario which was the basis of the assessment. Followed by the
derived effect profiles, i.e. the multiplication factors to achieve x%
effect:
metsulfuron %>% epx()
#> Warning in epx(.): Some scenarios have failed (n=1), result will include NAs
#> ** multiplication factor out of range: BM.EP50 > 1e+30
#> # A tibble: 1 × 6
#> scenario BM.EP10 r.EP10 BM.EP50 r.EP50 error
#> <list> <dbl> <dbl> <dbl> <dbl> <chr>
#> 1 <LmnSchmS> 0.395 0.325 NA 0.880 " multiplication factor out of range…
For the sample metsulfuron
scenario, a factor of
0.395
would need to be applied to the exposure series to
achieve an effect level of 10% on biomass (BM). An effect level
of 50% on biomass is unattainable with the tested factors ranging from
1e-30
to 1e30
which is demonstrated by the
warning message and the NA
value for
BM.EP50
.
The table’s content can be reduced to endpoints only by setting the
argument ep_only=TRUE
. The range of tested factors can be
controlled by setting the arguments min_factor
and
max_factor
. Multiplication factors exceeding this range
will raise a warning and NA
will be returned for that
EPx. Finding multiplication factors can be cut short if a
certain margin of safety is reached by using the argument
factor_cutoff
: if the algorithm identifies that an
EPx greater or equal to factor_cutoff
is required,
then factor_cutoff
is reported as the result. This approach
may be used to save computational resources for long running models if
the exact EPx value above the cutoff is not of interest.
The precision of EPx values is controlled by the argument
effect_tolerance
and is given as the upper absolute error
threshold of effects that is deemed acceptable. The default value of
0.001
ensures that a derived EPx will result in an
effect of x% ± 0.1. Decreasing the effect_tolerance
will
result in additional model iterations and longer runtime.
The algorithm’s inner workings can be examined by setting the
argument verbose=TRUE
:
metsulfuron %>%
set_endpoints("BM") %>%
epx(verbose=TRUE)
#> epx: screening multiplication factors
#> start: 10
#> BM.EP10: 1 <<<
#> BM.EP10: 0.1 <<<
#> BM.EP10: 0.55
#> BM.EP10: 0.325
#> BM.EP10: 0.4375
#> BM.EP10: 0.38125
#> BM.EP10: 0.409375
#> BM.EP10: 0.3953125
#> BM.EP50: 100 >>>
#> BM.EP50: 1000 >>>
#> BM.EP50: 10000 >>>
#> BM.EP50: 1e+05 >>>
#> BM.EP50: 1e+06 >>>
#> BM.EP50: 1e+07 >>>
#> BM.EP50: 1e+08 >>>
#> BM.EP50: 1e+09 >>>
#> BM.EP50: 1e+10 >>>
#> BM.EP50: 1e+11 >>>
#> BM.EP50: 1e+12 >>>
#> BM.EP50: 1e+13 >>>
#> BM.EP50: 1e+14 >>>
#> BM.EP50: 1e+15 >>>
#> BM.EP50: 1e+16 >>>
#> BM.EP50: 1e+17 >>>
#> BM.EP50: 1e+18 >>>
#> BM.EP50: 1e+19 >>>
#> BM.EP50: 1e+20 >>>
#> BM.EP50: 1e+21 >>>
#> BM.EP50: 1e+22 >>>
#> BM.EP50: 1e+23 >>>
#> BM.EP50: 1e+24 >>>
#> BM.EP50: 1e+25 >>>
#> BM.EP50: 1e+26 >>>
#> BM.EP50: 1e+27 >>>
#> BM.EP50: 1e+28 >>>
#> BM.EP50: 1e+29 >>>
#> BM.EP50: 1e+30 >>>
#> BM.EP50: 1e+31 >>>
#> Warning in epx(., verbose = TRUE): Some scenarios have failed (n=1), result will include NAs
#> ** multiplication factor out of range: BM.EP50 > 1e+30
#> # A tibble: 1 × 4
#> scenario BM.EP10 BM.EP50 error
#> <list> <dbl> <dbl> <chr>
#> 1 <LmnSchmS> 0.395 NA " multiplication factor out of range: BM.EP50 > 1e…
In this example, the binary search finds a BM.EP10
with
acceptable precision in less than ten iterations. For the
BM.EP50
, the algorithm re-uses the knowledge gained from
previously performed calculations but is ultimately unable to find a
suitable multiplication factor within the allowed range of
multiplication factors.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.