Package 'mlmpower'

Analyzes a single mp_data using lme4::lmer

Description

Analyzes a single mp_data based on the data generating model.

Usage

analyze(data, alpha = 0.05, no_lrt = FALSE, ...)

Arguments

Value

A list that with the following named elements:

• estimates: The estimates from fitting the model.

• sig_test: The logical if the estimates were statistically siginificant based on alpha.

• parameters: The mp_parameters extracted from data.

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = 0.1)
)
# Set seed
set.seed(198723)
# Create data set and analyze
model |> generate(5, 50) |> analyze() -> results

Coerce a mp_power to a Data Frame

Description

Outputs mp_power as a data frame.

Usage

## S3 method for class 'mp_power'
as.data.frame(x, row.names = NULL, optional = FALSE, power = TRUE, ...)

Arguments

Value

returns a data frame

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = 0.1)
)
# Set seed
set.seed(19723)
# Create data set and analyze
# Note: Generally Use more than 50 replications
model |> power_analysis(50, 5, 50) -> powersim
# Obtain Results as a data frame
as.data.frame(powersim)

Convert mp_parameters to a list

Description

A wrapper to coerce mp_parameters to a list.

Usage

## S3 method for class 'mp_parameters'
as.list(x, ...)

Arguments

Value

a list

Examples

# Specify model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(
        icc = c(0.1, 0.2),
        within = 0.3
    )
)
# Obtain parameters and convert to a list
model |> summary() |> as.list() -> param_list

Center a data set based on a mp_data

Description

Provides multilevel centering of a mp_data data set.

Usage

center(data, all = FALSE, ...)

Arguments

Details

The ... needs to be the variable's name followed by equals and the centering strategy requested. There are three different strategies available:

• cwc = centering within cluster

• cgm = centering with group mean

• none = no centering

If all is set to TRUE then the default centering will be used unless overwritten by specifying a specific centering strategy.

Value

For ndata = 1 a single data.frame is returned. If a list of data sets are included then they will be contained in a list. Each data.frame has an additional center attribute which denotes the centering strategy used.

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = 0.1)
)
# Set seed
set.seed(198723)

# Create data set with default centering
model |> generate(5, 50) |> center(all = TRUE) -> mydata

# Create data centering X with cwc
model |> generate(5, 50) |> center(X = cwc) -> mydata

# See centering strategy
attr(mydata, 'center')

Description

Creates a list of correlations to be added to a mp_model.

Usage

correlations(within, between, randeff)

Arguments

Details

The default values are random(0.1, 0.3). Currently randeff are required to be zero if more than one random slope is in the model.

Value

A list that corresponds to each correlation value.

See Also

random() fixed()

Examples

(
    outcome('Y')
    + within_predictor('X')
    + effect_size(
        icc = c(0.1, 0.2),
        within = 0.3
    )
    # Defaults
    + correlations(
        within  = random(0.1, 0.3),
        between = random(0.1, 0.3),
        randeff = random(0.1, 0.3)
    )
)

Description

Creates a list of effect sizes to be added to a mp_model.

Returns suggested ICC's for cross-sectional studies (0.05, 0.15, and 0.25).

Returns suggested ICC ranges for longitudinal studies (0.40, 0.50, and 0.60).

Usage

effect_size(icc, within, between, random_slope, product)

cross_sectional()

longitudinal()

Arguments

Value

A list that corresponds to each R2 value.

Examples

# Set ICCs
(
    outcome('Y')
    + within_predictor('X')
    + effect_size(
        icc = c(0.1, 0.2),
        within = 0.3
    )
)

# With cross-sectional ICC
(
    outcome('Y')
    + within_predictor('X')
    + effect_size(
        icc = cross_sectional,
        within = 0.3
    )
)

# With longitudinal ICC
(
    outcome('Y')
    + within_predictor('X')
    + effect_size(
        icc = longitudinal,
        within = 0.3
    )
)

Generates Data Sets Based on a mp_model

Description

Generates data sets based on a mp_model. These data sets will be returned as a data.frame and include the solved parameters as an attribute to the data.frame.

Usage

generate(model, n_within, n_between, ndata = 1, mechanism = NULL)

Arguments

Details

Note that there must only be one global ICC in mp_model.

Use the mechanism argument to specify missing data mechanisms. See mechanisms for predefined missing data mechanisms for the outcome and examples using them. When creating custom mechanisms care needs to be taken because it is considered for advanced usage. This a argument expects a function with the mp_data as the input, and the function should return the modified mp_data. Be careful when using this because it allows you to modify the population parameters, which will be incorrect. You should only induce missing data values on variables. Missing data on the predictors will cause listwise deletion to be used, but missing data on the outcome will be appropriate for MAR-based mechanisms. See examples below for an example that generates MCAR data on the outcome. See parameters to obtain the population parameters from each data set.

Value

For ndata = 1 a single data.frame is returned. The first variable is the cluster identifier labeled ⁠_id⁠. This object is also of class mp_data which means that it was generated based on a specified model. If multiple data sets are requested then they will be contained in a list.

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = 0.1)
)
# Set seed
set.seed(198723)

# Create data set
model |> generate(5, 50) -> mydata

# Induce missing data with built-in function
model |> generate(50, 5, mechanism = MCAR(0.25)) -> mydata_mcar

# Induce missing data with custom function
model |> generate(50, 5, mechanism = \(data) {
    # `data` will be the `mp_data` used
    within(data, {
        # MCAR Process
        Y <- ifelse(runif(NROW(data)) < 0.5, Y, NA)
    })
}) -> mydata_mcar_custom

Description

This function is used to validate if a mp_model is correct. If the model is incorrect an appopriate error message describing while will be supplied

Usage

is_valid(x)

Arguments

Value

Invisibly returns the original model.

Examples

# Create Model
model <- outcome('Y') + within_predictor('X')
# Throws error
tryCatch(
    is_valid(model),
    error = print
)
# Succeeds
is_valid(model + effect_size(icc = 0.1))

Description

Returns which level a variable is observed at in the multilevel model.

Usage

## S3 method for class 'mp_variable'
levels(x)

Arguments

Value

Returns a single integer of the level of observation

Examples

# Returns 1
levels(
    within_predictor(
        'X',
        weight = 1,
        mean = 5,
        sd = 10,
        icc = 0.1
    )
)

Description

Functions to generate data that always follows a specific mechanism in accordance to a single-level model.

Usage

# Generate MCAR data on outcome
MCAR(mis.rate)

# Generate MAR data on outcome due to `cause`
MAR(mis.rate, cause, r2, lower = TRUE)

Arguments

See Also

power_analysis

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = 0.1)
)

# Induce MCAR data on outcome
set.seed(19723)
model |> power_analysis(50, 5, 50, mechanism = MCAR(0.25)) -> powersim_mcar

# Induce MAR data on outcome
set.seed(19723)
model |> power_analysis(
   50, 5, 50,
   mechanism = MAR(0.25, 'X', 0.6)
) -> powersim_mar

Description

mlmpower constructs models by adding different features of the model using the plus sign (+).

Every model requires an outcome and an ICC specified in effect_size to be valid.

model <- outcome('y') + effect_size(icc = 0.1)

Once a model is constructed, we can add additional features to build the model out more. For example, we may want to include a level-1 predictor that is centered within cluster.

model <- model + within_predictor('x', icc = 0.0)

The additions can be chained together to produce the entire model object. For example, the previous two code blocks can be combined into one.

model <- (
    outcome('y')
    + effect_size(icc = 0.1)
    + within_predictor('x', icc = 0.0)
)

Finally, we can also wrap multiple variables into a list and add that. This feature can be useful when programmatically generating a model.

model <- (
    outcome('y')
    + effect_size(icc = 0.1)
    + lapply(1:10, \(i) within_predictor(paste0('x', i), icc = 0.0))
)

For more detailed information see the help vignette by running the following:

vignette('mlmpower')

See Also

Variables effect_size() correlations() random_slope() product()

Description

Specify a random correlation that is uniform between lower and upper

Usage

random(lower, upper)

fixed(value)

Arguments

Value

A mp_corr_func that generates the desired correlation

See Also

correlations()

Examples

# Create Model with random and fixed correlations
(
    outcome('Y')
    + within_predictor('X')
    + between_predictor('Z')
    + effect_size(icc = 0.1)
    # Defaults
    + correlations(
        within  = random(0.1, 0.3),
        between = fixed(0.2)
    )
)

Description

An S3 class that contains an base::environment with the following objects:

• r2: The population proportion of variance explained

• phi_b: The population predictor covariance matrix for between

• phi_p: The population within cluster covariance matrix for products

• phi_w: The population predictor covariance matrix for within

• mean_Z: The population mean for level-2 predictors

• mean_X: The population mean for level-1 predictors

• var_e: The population within residual variance

• tau: The population level-2 covariance matrix

• gammas: The regression coefficients

• mean_Y: The population mean of the outcome

See Also

parameters

Obtain mp_parameters from objects

Description

A generic function to obtain mp_parameters from defined models and data sets.

Usage

parameters(object)

## S3 method for class 'mp_model'
parameters(object)

## S3 method for class 'mp_data'
parameters(object)

## S3 method for class 'mp_power'
parameters(object)

Arguments

Details

Currently object can be:

• mp_model

• mp_data

• mp_power

If using on a mp_model and the model has random correlations then the average is used.

Value

A mp_parameters object

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = 0.1)
)

# Create data set and obtain population parameters
model |> parameters()
# Set seed
set.seed(198723)
# Create data set and obtain population parameters
model |> generate(5, 50) |> parameters()
# Set seed
set.seed(198723)
# Create data set and obtain population parameters
model |> power_analysis(50, 5, 50) |> parameters()

Conduct a Power Analysis Based on mp_model

Description

This function will construct a multilevel power analysis via a Monte Carlo Simulation based on a constructed mp_model.

Usage

power_analysis(model, replications, n_within, n_between, ...)

Arguments

Details

Specifying multiple n_within and n_between will produce a full factorial simulation design.

Specify a mechanism argument to pass down to the generate function. See the details of generate for more information about specifying missing data mechanisms. See mechanisms for predefined missing data mechanisms.

Specify an analyze argument to use custom analysis functions. These functions should map onto analyze's structure, but can allow for things like specifying multiple imputations etc. This is considered an advance usage that requires extreme care and caution.

Value

A mp_power object that contains the results. See print.mp_power for more information. The object has the following slots:

• sim: The information about the simulation

• power: The power power results per condition.

• estimates: The simulation summaries of the parameter estimates per condition.

• mean_parameters: The average population parameter per condition.

See Also

generate()

mechanisms

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = 0.1)
)
# Set seed
set.seed(19723)
# Create data set and analyze
# Note: Generally Use more than 50 replications
model |> power_analysis(50, 5, 50)

# Induce missing data on outcome with built in mechanisms
set.seed(19723)
model |> power_analysis(50, 5, 50, mechanism = MCAR(0.25)) -> powersim_mcar

Prints a mp_correlations

Description

Prints a mp_correlations in a human readable format.

Usage

## S3 method for class 'mp_correlations'
print(x, ...)

Arguments

Value

Invisibly returns the original variable.

Examples

model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(
        icc = c(0.1, 0.2),
        within = 0.3
    )
)
# Print correlations only
print(model$corrs)

Prints a mp_effsize

Description

Prints a mp_effsize in a human readable format.

Usage

## S3 method for class 'mp_effsize'
print(x, ...)

Arguments

Value

Invisibly returns the original variable.

Examples

model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(
        icc = c(0.1, 0.2),
        within = 0.3
    )
)
# Print effect size only
print(model$effect_size)

Prints a mp_model

Description

Prints a mp_variable in a human readable format.

Usage

## S3 method for class 'mp_model'
print(x, ...)

Arguments

Value

Invisibly returns the original variable.

Examples

print(
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = cross_sectional)
)

Prints a mp_parameters

Description

Prints a mp_parameters in a human readable format.

Usage

## S3 method for class 'mp_parameters'
print(x, ...)

Arguments

Value

Invisibly returns the original variable.

Examples

print(
    summary(
        outcome('Y')
        + within_predictor('X')
        + effect_size(icc = cross_sectional)
    )
)

Prints a mp_power

Description

Prints a mp_power in a human readable format.

Usage

## S3 method for class 'mp_power'
print(x, ...)

Arguments

Value

Invisibly returns the original variable.

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = 0.1)
)
# Set seed
set.seed(19723)
# Create data set and analyze
# Note: Generally Use more than 50 replications
model |> power_analysis(50, 5, 50) -> powersim
# Print results
print(powersim)

Prints a mp_variable

Description

Prints a mp_variable in a human readable format.

Usage

## S3 method for class 'mp_variable'
print(x, ...)

Arguments

Value

Invisibly returns the original variable.

Examples

print(
    within_predictor(
        'X',
        weight = 1,
        mean = 5,
        sd = 10,
        icc = 0.1
    )
)

Description

Creates a product term between two variables that can be added to a mp_model.

Usage

product(name1, name2, weight = 1)

Arguments

Details

Currently the product term is only limited to cross-level interactions between a level-1 centered within cluster variable (icc = 0) and level-2 variable.

Value

A mp_action that can be added to a mp_model.

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X', icc = 0.0)
    + between_predictor('Z')
)
# Add random slope to the model
model + product('X', 'Z')

Description

Creates a random slope that can be added to a mp_model.

Usage

random_slope(name, weight = 1)

Arguments

Value

A mp_action that can be added to a mp_model.

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(
        icc = 0.1,
        within = 0.1,
        random_slope = 0.03
    )
)
# Add random slope to the model
model + random_slope('X')

Subset a mp_model by Global ICC

Description

Subsets a mp_model with multiple ICC values specified in effect_size into a model with only the single ICC value.

Usage

## S3 method for class 'mp_model'
subset(x, icc, ...)

Arguments

Value

A new mp_model with only the subset ICC

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = cross_sectional)
)
# Obtain Model with only 0.15 ICC
model |> subset(icc = 0.15)

Obtain the Parameter Summaries for A mp_model

Description

Provide the summarized parameter estimates for a mp_model, including the variance explained break downs.

Usage

## S3 method for class 'mp_model'
summary(object, ...)

Arguments

Value

A mp_parameters object that contains the population parameters based on the model. If random correlations are used the average correlation is used to compute the parameters. If multiple ICC's are specified then a named base::list is returned containing the parameter value for each ICC value.

Examples

summary(
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = cross_sectional)
)

Summarizes a mp_power

Description

Summarizes a mp_power in a human readable format. This is a simple wrapper for print.mp_power.

Usage

## S3 method for class 'mp_power'
summary(object, ...)

Arguments

Value

Invisibly returns the original variable.

Examples

# Create Model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(icc = 0.1)
)
# Set seed
set.seed(19723)
# Create data set and analyze
# Note: Generally Use more than 50 replications
model |> power_analysis(50, 5, 50) -> powersim
# Summarizes results
summary(powersim)

Convert mp_data to a stats::formula to be used for lme4::lmer

Description

Produces the formula including the centering functions based on a data set generated with generate.

Usage

to_formula(data, nested = FALSE)

Arguments

Value

a stats::formula

Examples

# Specify model
model <- (
    outcome('Y')
    + within_predictor('X')
    + effect_size(
        icc = 0.2,
        within = 0.3
    )
)
# Set seed
set.seed(198723)
# Create formula based on data set
model |> generate(5, 50) |> to_formula()

Description

These functions are the building blocks used to create the multilevel model and are used to specify the names, properties, and variable types.

Usage

outcome(name, mean = 10, sd = 5, icc = NULL)

within_predictor(name, weight = 1, mean = 0, sd = 1, icc = NULL)

within_time_predictor(name, values, weight = 1)

between_predictor(name, weight = 1, mean = 0, sd = 1)

between_binary_predictor(name, proportion = 0.5, weight = 1)

Arguments

Details

Note that specifying an icc = 0 in within_predictor() will result in a centered within cluster (CWC) predictor.

See vignettes for more details.

vignette(package = 'mlmpower')

Value

Returns a mp_variable object based on the variable's type.