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Calculate the expected value of sample information for an estimation problem

Source: R/evsivar.R
evsivar.Rd

Calculate the expected value of sample information for an estimation problem. This computes the expected reduction in variance in some quantity of interest from a study of a certain design that informs the parameters of interest.

Usage

evsivar(
  outputs,
  inputs,
  study = NULL,
  datagen_fn = NULL,
  pars = NULL,
  n = 100,
  aux_pars = NULL,
  method = NULL,
  nsim = NULL,
  verbose = TRUE,
  ...
)

Arguments

outputs

a vector of values for the quantity of interest, sampled from the uncertainty distribution of this quantity that is induced by the uncertainty about the parameters.

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.

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

See evsi, only nonparametric regression methods are currently supported in evsivar.

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.

...

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 EVSI. If there are EVSI estimates for multiple sample sizes, the sample size is returned in the column n.

References

Jackson, C., Presanis, A., Conti, S., & De Angelis, D. (2019). Value of information: Sensitivity analysis and research design in Bayesian evidence synthesis. Journal of the American Statistical Association, 114(528), 1436-1449.