sim_pow_glm_nested3: Power simulation for nested designs

Description Usage Arguments Details See Also

View source: R/pow_sim_glm.r

Description

Takes simulation conditions as input, exports power.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
sim_pow_glm_nested3(fixed, random, random3, fixed_param,
  random_param = list(), random_param3 = list(), cov_param, k, n, p,
  data_str, cor_vars = NULL, fact_vars = list(NULL),
  unbal = list(level2 = FALSE, level3 = FALSE),
  unbal_design = list(level2 = NULL, level3 = NULL), contrasts = NULL,
  outcome_type, cross_class_params = NULL, knot_args = list(NULL),
  missing = FALSE, missing_args = list(NULL), pow_param = NULL,
  alpha, pow_dist = c("z", "t"), pow_tail = c(1, 2),
  lme4_fit_mod = NULL, lme4_fit_family, general_mod = NULL,
  general_extract = NULL, ...)

Arguments

fixed

One sided formula for fixed effects in the simulation. To suppress intercept add -1 to formula.

random

One sided formula for random effects in the simulation. Must be a subset of fixed.

random3

One sided formula for random effects at third level in the simulation. Must be a subset of fixed (and likely of random).

fixed_param

Fixed effect parameter values (i.e. beta weights). Must be same length as fixed.

random_param

A list of named elements that must contain:

  • random_var: variance of random parameters,

  • rand_gen: Name of simulation function for random effects.

Optional elements are:

  • ther: Theorectial mean and variance from rand_gen,

  • ther_sim: Simulate mean/variance for standardization purposes,

  • cor_vars: Correlation between random effects,

  • ...: Additional parameters needed for rand_gen function.

random_param3

A list of named elements that must contain:

  • random_var: variance of random parameters,

  • rand_gen: Name of simulation function for random effects.

Optional elements are:

  • ther: Theorectial mean and variance from rand_gen,

  • ther_sim: Simulate mean/variance for standardization purposes,

  • cor_vars: Correlation between random effects,

  • ...: Additional parameters needed for rand_gen function.

cov_param

List of arguments to pass to the continuous generating function, must be the same order as the variables specified in fixed. This list does not include intercept, time, factors, or interactions. Required arguments include:

  • dist_fun: This is a quoted R distribution function.

  • var_type: This is the level of variable to generate. Must be 'level1', 'level2', or 'level3'. Must be same order as fixed formula above.

Optional arguments to the distribution functions are in a nested list, see the examples or vignettes for example code.

k

Number of third level clusters.

n

Cluster sample size.

p

Within cluster sample size.

data_str

Type of data. Must be "cross", "long", or "single".

cor_vars

A vector of correlations between variables.

fact_vars

A nested list of factor, categorical, or ordinal variable specification, each list must include:

  • numlevels = Number of levels for ordinal or factor variables.

  • var_type = Must be 'level1', 'level2', or 'level3'.

Optional arguments include:

  • replace

  • prob

  • value.labels

See also sample for use of these optional arguments.

unbal

A named TRUE/FALSE list specifying whether unbalanced simulation design is desired. The named elements must be: "level2" or "level3" representing unbalanced simulation for level two and three respectively. Default is FALSE, indicating balanced sample sizes at both levels.

unbal_design

When unbal = TRUE, this specifies the design for unbalanced simulation in one of two ways. It can represent the minimum and maximum sample size within a cluster via a named list. This will be drawn from a random uniform distribution with min and max specified. Secondly, the actual sample sizes within each cluster can be specified. This takes the form of a vector that must have the same length as the level two or three sample size. These are specified as a named list in which level two sample size is controlled via "level2" and level three sample size is controlled via "level3".

contrasts

An optional list that specifies the contrasts to be used for factor variables (i.e. those variables with .f or .c). See contrasts for more detail.

outcome_type

A vector specifying the type of outcome, must be either logistic or poisson. Logitstic outcome will be 0/1 and poisson outcome will be counts.

cross_class_params

A list of named parameters when cross classified data structures are desired. Must include the following arguments:

  • num_ids: The number of cross classified clusters. These are in addition to the typical cluster ids

  • random_param: This argument is a list of arguments passed to sim_rand_eff. These must include:

    • random_var: The variance of the cross classified random effect

    • rand_gen: The random generating function used to generate the cross classified random effect.

    Optional elements are:

    • ther: Theorectial mean and variance from rand_gen,

    • ther_sim: Simulate mean/variance for standardization purposes,

    • cor_vars: Correlation between random effects,

    • ...: Additional parameters needed for rand_gen function.

knot_args

A nested list of named knot arguments. See sim_knot for more details. Arguments must include:

  • var

  • knot_locations

missing

TRUE/FALSE flag indicating whether missing data should be simulated.

missing_args

Additional missing arguments to pass to the missing_data function. See missing_data for examples.

pow_param

Name of variable to calculate power for, must be a name from fixed.

alpha

What should the per test alpha rate be used for the hypothesis testing.

pow_dist

Which distribution should be used when testing hypothesis test, z or t?

pow_tail

One-tailed or two-tailed test?

lme4_fit_mod

Valid lme4 formula syntax to be used for model fitting.

lme4_fit_family

Valid lme4 family specification passed to glmer.

general_mod

Valid model syntax. This syntax can be from any R package. By default, broom is used to extract model result information. Note, package must be defined or loaded prior to running the sim_pow function.

general_extract

A valid function to extract model results if general_mod argument is used. This argument is primarily used if extracting model results is not possibly using the broom package. If this is left NULL (default), broom is used to collect model results.

...

Not currently used.

Details

Power function to compute power for a regression term for the generalized linear mixed model. This function would need to be replicated to make any statement about power. Use sim_pow_glm as a convenient wrapper for this.

See Also

sim_pow_glm for a wrapper to replicate.


simglm documentation built on Jan. 24, 2019, 1:04 a.m.