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Calculate the expected value of sample information from a decision-analytic model

Source: R/evsi.R
evsi.Rd

Calculate the expected value of sample information from a decision-analytic model

Usage

evsi(
  outputs,
  inputs,
  study = NULL,
  datagen_fn = NULL,
  pars = NULL,
  pars_datagen = NULL,
  n = 100,
  aux_pars = NULL,
  method = NULL,
  likelihood = NULL,
  analysis_fn = NULL,
  analysis_args = NULL,
  model_fn = NULL,
  par_fn = NULL,
  Q = 50,
  npreg_method = "gam",
  nsim = NULL,
  verbose = FALSE,
  check = FALSE,
  ...
)

Arguments

outputs

This could take one of two forms

"net benefit" form: a matrix or data frame of samples from the uncertainty distribution of the expected net benefit. The number of rows should equal the number of samples, and the number of columns should equal the number of decision options.

"cost-effectiveness analysis" form: a list with the following named components:

"c": a matrix or data frame of samples from the distribution of costs. There should be one column for each decision option.

"e": a matrix or data frame of samples from the distribution of effects, likewise.

"k": a vector of willingness-to-pay values.

Objects of class "bcea", as created by the BCEA package, are in this "cost-effectiveness analysis" format, therefore they may be supplied as the outputs argument.

Users of heemod can create an object of this form, given an object produced by run_psa (obj, say), with import_heemod_outputs.

If outputs is a matrix or data frame, it is assumed to be of "net benefit" form. Otherwise if it is a list, it is assumed to be of "cost effectiveness analysis" form.

inputs

Matrix or data frame of samples from the uncertainty distribution of the input parameters of the decision model. The number of columns should equal the number of parameters, and the columns should be named. This should have the same number of rows as there are samples in outputs, and each row of the samples in outputs should give the model output evaluated at the corresponding parameters.

Users of heemod can create an object of this form, given an object produced by run_psa (obj, say), with import_heemod_inputs.

study

Name of one of the built-in study types supported by this package for EVSI calculation. If this is supplied, then the columns of inputs that correspond to the parameters governing the study data should be identified in pars.

Current built-in studies are

"binary" A study with a binary outcome observed on one sample of individuals. Requires one parameter: the probability of the outcome. The sample size is specifed in the n argument to evsi(), and the binomially-distributed outcome is named X1.

"trial_binary" Two-arm trial with a binary outcome. Requires two parameters: the probability of the outcome in arm 1 and 2 respectively. The sample size is the same in each arm, specifed in the n argument to evsi(), and the binomial outcomes are named X1 and X2 respectively.

"normal_known" A study of a normally-distributed outcome, with a known standard deviation, on one sample of individuals. Likewise the sample size is specified in the n argument to evsi(). The standard deviation defaults to 1, and can be changed by specifying sd as a component of the aux_pars argument, e.g. evsi(..., aux_pars=list(sd=2)).

Either study or datagen_fn should be supplied to evsi().

For the EVSI calculation methods where explicit Bayesian analyses of the simulated data are performed, the prior parameters for these built-in studies are supplied in the analysis_args argument to evsi(). These assume Beta priors for probabilities, and Normal priors for the mean of a normal outcome.

datagen_fn

If the proposed study is not one of the built-in types supported, it can be specified in this argument as an R function to sample predicted data from the study. This function should have the following specification:

  1. the function's first argument should be a data frame of parameter simulations, with one row per simulation and one column per parameter. The parameters in this data frame must all be found in inputs, but need not necessarily be in the same order or include all of them.

  2. the function should return a data frame.

  3. the returned data frame should have number of rows equal to the number of parameter simulations in inputs.

  4. if inputs is considered as a sample from the posterior, then datagen_fn(inputs) returns a corresponding sample from the posterior predictive distribution, which includes two sources of uncertainty: (a) uncertainty about the parameters and (b) sampling variation in observed data given fixed parameter values.

  5. the function can optionally have more than one argument. If so, these additional arguments should be given default values in the definition of datagen_fn. If there is an argument called n, then it is interpreted as the sample size for the proposed study.

pars

Character vector identifying which parameters are learned from the proposed study. This is required for the moment matching and importance sampling methods, and these should be columns of inputs. This is not required for the nonparametric regression methods.

pars_datagen

Character vector identifying which columns of inputs are the parameters required to generate data from the proposed study. These should be columns of inputs.

If pars_datagen is not supplied, then it is assumed to be the same as pars. Note that these can be different. Even if the study data are generated by a particular parameter, when analysing the data we could choose to ignore the information that the data provides about that parameter.

n

Sample size of future study, or vector of alternative sample sizes. This is understood by the built-in study designs. For studies specified by the user with datagen_fn, if datagen_fn has an argument n, then this is interpreted as the sample size. However if calling evsi for a user-specified design where datagen_fn does not have an n argument, then any n argument supplied to evsi will be ignored.

Currently this shortcut is not supported if more than one quantity is required to describe the sample size, for example, trials with unbalanced arms. In that case, you will have to hard-code the required sample sizes into datagen_fn.

For the nonparametric regression and importance sampling methods, the computation is simply repeated for each sample size supplied here.

The moment matching method uses a regression model to estimate the dependency of the EVSI on the sample size, hence to enable EVSI to be calculated efficiently for any number of sample sizes (Heath et al. 2019).

aux_pars

A list of additional fixed arguments to supply to the function to generate the data, whether that is a built-in study design or user-defined function supplied in datagen_fn. For example, evsi(..., aux_pars = list(sd=2)) defines the fixed standard deviation in the "normal_known" model.

method

Character string indicating the calculation method. Defaults to "gam".

All the nonparametric regression methods supported for evppi, that is "gam","gp","earth","inla", can also be used for EVSI calculation by regressing on a summary statistic of the predicted data (Strong et al 2015).

"is" for importance sampling (Menzies 2016)

"mm" for moment matching (Heath et al 2018)

Note that the "is" and "mm" methods are used in conjunction with nonparametric regression, and the gam_formula argument can be supplied to evsi to specify this regression - see evppi for documentation of this argument.

likelihood

Likelihood function, required (and only required) for the importance sampling method when a study design other than one of the built-in ones is used. This should have two arguments, named as follows:

Y: a one-row data frame of predicted data. Columns are defined by different outcomes in the data, with names matching the names of the data frame returned by datagen_fn.

inputs. a data frame of simulated parameter values. Columns should correspond to different variables in inputs. The column names should all be found in the names of inputs, though they do not have to be in the same order, or include everything in inputs. The number or rows should be the same as the number of rows in inputs.

The function should return a vector whose length matches the number of rows of the parameters data frame given as the second argument. Each element of the vector gives the likelihood of the corresponding set of parameters, given the data in the first argument. An example is given in the vignette.

The likelihood can optionally have a n argument, which is interpreted as the sample size of the study. If the n argument to evsi is used then this is passed to the likelihood function. Conversely any n argument to evsi will be ignored by a likelihood function that does not have its own n argument.

Note the definition of the likelihood should agree with the definition of datagen_fn to define a consistent sampling distribution for the data. No automatic check is performed for this.

analysis_fn

Function which fits a Bayesian model to the generated data. Required for method="mm" if a study design other than one of the built-in ones is used. This should be a function that takes the following arguments:

data: A data frame with names matching the output of datagen_fn

args: A list with constants required in the Bayesian analysis, e.g. prior parameters, or options for the analysis, e.g. number of MCMC simulations. The component of this list called n is assumed to contain the sample size of the study.

pars Names of the parameters whose posterior is being sampled.

The function should return a data frame with names matching pars, containing a sample from the posterior distribution of the parameters given data supplied through data.

analysis_fn is required to have all three of these arguments, but you do not need to use any elements of args or pars in the body of analysis_fn. Instead, sample sizes, prior parameters, MCMC options and parameter names can alternatively be hard-coded inside analysis_fn. Passing these through the function arguments (via the analysis_args argument to evsi) is only necessary if we want to use the same analysis_fn to do EVSI calculations with different sample sizes or other settings.

analysis_args

List of arguments required for the Bayesian analysis of the predicted data, e.g. definitions of the prior and options to control sampling. Only used in method="mm". This is required if the study design is one of the built-in ones specified in study. If a custom design is specifed through analysis_fn, then any constants needed in analysis_fn can either be supplied in analysis_args, or hard-coded in analysis_fn itself.

For the built-in designs, the lists should have the following named components. An optional component niter in each case defines the posterior sample size (default 1000).

study="binary": a and b: Beta shape parameters

study="trial_binary": a1 and b1: Beta shape parameters for the prior for the first arm, a2 and b2: Beta shape parameters for the prior for the second arm.

study="normal_known": prior_mean, prior_sd (mean and standard deviation deviation of the Normal prior) and sampling_sd (SD of an individual-level normal observation, so that the sampling SD of the mean outcome over the study is sampling_sd/sqrt(n).

model_fn

Function which evaluates the decision-analytic model, given parameter values. Required for method="mm". See evppi_mc for full documentation of the required specification of this function.

par_fn

Function to simulate values from the uncertainty distributions of parameters needed by the decision-analytic model. Should take one argument and return a data frame with one row for each simulated value, and one column for each parameter. See evppi_mc for full specification.

Q

Number of quantiles to use in method="mm".

npreg_method

Method to use to calculate the EVPPI, for those methods that require it. This is passed to evppi as the method argument.

nsim

Number of simulations from the model to use for calculating EVPPI. The first nsim rows of the objects in inputs and outputs are used.

verbose

If TRUE, then messages are printed describing each step of the calculation, if the method supplies these. Can be useful to see the progress of slow calculations.

check

If TRUE, then extra information about the estimation is saved inside the object that this function returns. This currently only applies to the regression-based methods "gam" and "earth" where the fitted regression model objects are saved. This allows use of the check_regression function, which produces some diagnostic checks of the regression models.

...

Other arguments understood by specific methods, e.g. gam_formula and other controlling options (see evppi) can be passed to the nonparametric regression used inside the moment matching method.

Value

A data frame with a column pars, indicating the parameter(s), and a column evsi, giving the corresponding EVPPI. If the EVSI for multiple sample sizes was requested, then the sample size is returned in the column n, and if outputs is of "cost-effectiveness analysis" form, so that there is one EVPPI per willingness-to-pay value, then a column k identifies the willingness-to-pay.

Details

See the package overview / Get Started vignette for some examples of using this function.

References

Strong, M., Oakley, J. E., Brennan, A., & Breeze, P. (2015). Estimating the expected value of sample information using the probabilistic sensitivity analysis sample: a fast, nonparametric regression-based method. Medical Decision Making, 35(5), 570-583.

Menzies, N. A. (2016). An efficient estimator for the expected value of sample information. Medical Decision Making, 36(3), 308-320.

Heath, A., Manolopoulou, I., & Baio, G. (2018). Efficient Monte Carlo estimation of the expected value of sample information using moment matching. Medical Decision Making, 38(2), 163-173.

Heath, A., Manolopoulou, I., & Baio, G. (2019). Estimating the expected value of sample information across different sample sizes using moment matching and nonlinear regression. Medical Decision Making, 39(4), 347-359.