power_calc: Power Calculations

Description Usage Arguments Value Examples

View source: R/assess_performance.R

Description

Calculates the expected power of an environmental epidemiology time series analysis based on simulated datasets. This function uses the simulation provided by eesim to simulate multiple environmental epidemiology datasets under different scenarios (e.g., total days in study, size of association between exposure and outcome, or baseline average daily count of the outcome in the study) and estimates the power of a specified analysis to detect the hypothesized association.

Usage

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power_calc(varying, values, n_reps, custom_model, central, exposure_type,
  n = NULL, sd = NULL, exposure_trend = "no trend", exposure_amp = NULL,
  average_outcome = NULL, outcome_trend = "no trend", outcome_amp = NULL,
  rr = NULL, start.date = "2000-01-01", cust_exp_func = NULL,
  cust_exp_args = NULL, cust_base_func = NULL, cust_lambda_func = NULL,
  cust_base_args = NULL, cust_lambda_args = NULL,
  custom_model_args = NULL, plot = FALSE)

Arguments

varying

A character string specifying the parameter to be varied. Choices are 'n' (which varies the number of days in each dataset of simulated data), 'rr' (which varies the relative rate per unit increase in exposure that is used to simulate the data), or 'average_outcome' (which varies the average value of the outcomes in each dataset). For whichever of these three values is not set to vary in this argument, the user must specify a constant value to this function through the n, rr, or average_outcome arguments.

values

A numeric vector with the values you would like to test for the varying parameters. For example, values = c(1.05, 1.10, 1.15) would produce power estimates for the four specified values of relative risk if the user has specified varying = 'rr'.

n_reps

An integer specifying the number of datasets to simulate (e.g., n_reps = 1000 would simulate one thousand time series datasets with the specified characteristics, which can be used for a power analysis or to investigate the performance of a proposed model).

custom_model

The object name of an R function that defines the code that will be used to fit the model. This object name should not be in quotations. See Details for more.

central

A numeric value specifying the mean probability of exposure (for binary data) or the mean exposure value (for continuous data).

exposure_type

A character string specifying the type of exposure. Choices are "binary" or "continuous".

n

An integer specifying the number of days to simulate (e.g., n = 365 would simulate a dataset with a year's worth of data).

sd

A non-negative numeric value giving the standard deviation of the exposure values from the exposure trend line (not the total standard deviation of the exposure values).

exposure_trend

A character string specifying a seasonal and / or long-term trend for expected mean exposure. See the vignette for eesim for examples of each option. The shapes are based on those used in Bateson and Schwartz (1999). For trends with a seasonal component, the amplitude of the seasonal trend can be customized using the exposure\_amp argument. For trends with a long-term pattern, the slope of the long-term trend can be set using the exposure\_slope argument. If using the "monthly" option for a binary exposure, you must input a numeric vector of length 12 for the central argument that gives the probability of exposure for each month, starting in January and ending in December. Options for continuous exposure are:

  • "no trend": No trend, either seasonal or long-term (default).

  • "cos1": A seasonal trend only.

  • "cos2": A seasonal trend with variable amplitude across years.

  • "cos3": A seasonal trend with steadily decreasing amplitude over time.

  • "linear": A linear long-term trend with no seasonal trend.

  • "curvilinear": A curved long-term trend with no seasonal trend.

  • "cos1linear": A seasonal trend plus a linear long-term trend.

Options for binary exposure are:

  • "no trend": No trend, either seasonal or long-term (default).

  • "cos1": A seasonal trend only.

  • "cos2": A seasonal trend with variable amplitude across years.

  • "cos3": A seasonal trend with steadily decreasing amplitude over time.

  • "linear": A linear long-term trend with no seasonal trend.

  • "monthly": Uses a user-specified probability of exposure for each month.

exposure_amp

A numeric value specifying the amplitude of the exposure trend. Must be between -1 and 1 for continuous exposure or between -0.5 and 0.5 for binary exposure. Positive values will simulate a pattern with higher values at the time of the year of the start of the dataset (typically January) and lowest values six months following that (typically July). Negative values can be used to simulate a trend with lower values at the time of year of the start of the dataset and higher values in the opposite season.

average_outcome

A non-negative numeric value specifying the average daily outcome count.

outcome_trend

A character string specifying the seasonal trend in health outcomes. Options are the same as for continuous exposure data.

outcome_amp

A numeric value specifying the amplitude of the outcome trend. Must be between -1 and 1.

rr

A non-negative numeric value specifying the relative risk (i.e., the relative risk per unit increase in the exposure).

start.date

A date of the format "yyyy-mm-dd" from which to begin simulating daily exposures

cust_exp_func

An R object name specifying the name of a custom trend function to generate exposure data

cust_exp_args

A list of arguments and their values for the user-specified custom exposure function.

cust_base_func

A R object name specifying a user-made custom function for baseline trend.

cust_lambda_func

An R object name specifying a user-made custom function for relating baseline, relative risk, and exposure

cust_base_args

A list of arguments and their values used in the user-specified custom baseline function

cust_lambda_args

A list of arguments and their values used in the user-specified custom lambda function

custom_model_args

A list of arguments and their values for a custom model. These arguments are passed through to the function specified with custom_model.

plot

"TRUE" or "FALSE" for whether to produce a plot

Value

Data frame with the values of the varying parameter and the estimated power for each. If the plot argument is set to TRUE, it also returns a power curve plot as a side effect. Because these estimates are based on simulations, there will be some random variation in estimates of power. Estimates will be more stable if a higher value is used for n_reps, although this will increase the time it takes the function to run.

Examples

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# Calculate power for studies that vary in the total length of the study period
# (between one and twenty-one years of data) for the association between a continuous
# exposure with a seasonal trend (mean = 100, sd from seasonal baseline = 10) and a count
# outcome (e.g., daily number of deaths, mean daily value across the study period of 22).
# The alternative hypothesis is that there is a relative rate of the outcome of 1.001 for
# every one-unit increase in exposure. The null hypothesis is that there is no association
# between the exposure and the outcome. The model used to test for an association is a
# case-crossover model
## Not run: 
pow <- power_calc(varying = "n", values = floor(365.25 * seq(1, 21, by = 5)), n_reps = 20,
           central = 100, sd = 10, rr = 1.001, exposure_type = "continuous",
           exposure_trend = "cos1", exposure_amp = .6, average_outcome = 22,
           outcome_trend = "no trend", outcome_amp = .6,
           custom_model = spline_mod, plot = TRUE)

## End(Not run)

eesim documentation built on June 4, 2017, 1:03 a.m.