function.Mixed_Effects_Regression: Perform Mixed Effects Regression

Description

Performs mixed effects regression analysis using lme4 for mixed-effects linear, logistic, and Poisson regression, mclogit for mixed-effects mutinomial logistic regression, ordinal for mixed-effects ordinal regression, and coxme for mixed-effects Cox regression for binary outcomes. It uses lmerTest and MuMIn for performing stepwise regression. For linear, logistic, and Poisson regression, it chooses the best optimizer using lme4::allFit().

Usage

function.Mixed_Effects_Regression(Predefined_lists, rv)

Value

analysis_outcome: Whether the analysis was performed successfullly
plan: Plan used for analysis
code: Part of code generated for performing the analysis in a standalone version of R
results: Analysis results
results_display: In order to present a single table, multiple results are combined. This results in some numbers stored as text and can cause very wide tables in the shiny output. This issue is fixed wth some modifications to the results table for display purposes.
plots_list: A list of plots generated. Returns "" if no plots are generated.
plots_list_display: In the shiny application, only one figure is displayed. Therefore, a composite image is created from the plots for display purposes. Some analysis functions may return NULL.
selections: Selections made by the user for display.
display_table: Whether the results table should be displayed in the shiny app.
display_plot: Whether the plot should be displayed in the shiny app.

Arguments

Predefined_lists: A list supplied by 'EQUAL-STATS' application
rv: A list supplied by 'EQUAL-STATS' application based on user input

Author

Kurinchi Gurusamy

References

https://sites.google.com/view/equal-group/home

Examples

Run this code

# Create simulated data ####
data <- cbind.data.frame(
  `Subject ID` = c(
    "S0001", "S0002", "S0003", "S0004", "S0005",
    "S0006", "S0007", "S0008", "S0009", "S0010",
    "S0011", "S0012", "S0013", "S0014", "S0015",
    "S0016", "S0017", "S0018", "S0019", "S0020",
    "S0021", "S0022", "S0023", "S0024", "S0025",
    "S0026", "S0027", "S0028", "S0029", "S0030"),
  `Centre` = c(
    "C_0001", "C_0002", "C_0002", "C_0002", "C_0002",
    "C_0001", "C_0001", "C_0003", "C_0001", "C_0003",
    "C_0001", "C_0002", "C_0002", "C_0001", "C_0003",
    "C_0002", "C_0002", "C_0003", "C_0001", "C_0002",
    "C_0002", "C_0002", "C_0002", "C_0003", "C_0002",
    "C_0001", "C_0003", "C_0001", "C_0001", "C_0001"),
  `Treatment` = c(
    "Intensive rehabilitation", "Intensive rehabilitation", "Standard rehabilitation",
    "Intensive rehabilitation", "Intensive rehabilitation", "Intensive rehabilitation",
    "Intensive rehabilitation", "Intensive rehabilitation", "Intensive rehabilitation",
    "Standard rehabilitation", "Intensive rehabilitation", "Standard rehabilitation",
    "Standard rehabilitation", "Intensive rehabilitation", "Intensive rehabilitation",
    "Intensive rehabilitation", "Standard rehabilitation", "Standard rehabilitation",
    "Intensive rehabilitation", "Standard rehabilitation", "Intensive rehabilitation",
    "Intensive rehabilitation", "Standard rehabilitation", "Intensive rehabilitation",
    "Intensive rehabilitation", "Standard rehabilitation", "Standard rehabilitation",
    "Intensive rehabilitation", "Standard rehabilitation", "Intensive rehabilitation"),
  `Obesity status` = c(
    "Obese", "Non-obese", "Obese", "Non-obese", "Non-obese",
    "Obese", "Obese", "Obese", "Non-obese", "Obese",
    "Non-obese", "Non-obese", "Obese", "Non-obese", "Obese",
    "Obese", "Non-obese", "Obese", "Obese", "Obese",
    "Non-obese", "Non-obese", "Non-obese", "Obese", "Obese",
    "Non-obese", "Obese", "Obese", "Obese", "Obese"),
  `Unable to walk independently at 6 weeks` = c(
    "unable", "able", "able", "unable", "able",
    "able", "unable", "unable", "unable", "unable",
    "able", "unable", "able", "unable", "unable",
    "able", "unable", "unable", "unable", "unable",
    "able", "able", "able", "able", "unable",
    "able", "able", "unable", "able", "unable"),
  `Mobility score at 6 months` = c(
    86, 65.1, 48, 99.8, 73.4, 70, 74.7, 36.5, 64.6, 85.4,
    41.7, 60.1, 73.3, 42.4, 55.3, 47.3, 85.9, 63, 64.6, 101.8,
    108.1, 72.3, 96.4, 87.5, 66.2, 92.9, 47.7, 55.8, 56.4, 133.8),
  `Pain at 6 weeks` = c(
    "3_severe", "1_mild", "1_mild", "2_moderate", "1_mild",
    "1_mild", "2_moderate", "2_moderate", "1_mild", "3_severe",
    "1_mild", "2_moderate", "1_mild", "3_severe", "3_severe",
    "1_mild", "2_moderate", "3_severe", "2_moderate", "2_moderate",
    "1_mild", "1_mild", "1_mild", "1_mild", "2_moderate",
    "1_mild", "1_mild", "2_moderate", "1_mild", "2_moderate"),
  `Number of falls within 6 months` = c(
    3, 2, 3, 2, 2, 1, 4, 2, 2, 5,
    3, 2, 2, 2, 5, 3, 2, 2, 3, 4,
    3, 1, 2, 2, 2, 7, 2, 1, 1, 8),
  `Mobility score at 12 months` = c(
    90, 69.1, 52, 103.8, 77.4, 74, 78.7, 40.5, 68.6, 89.4,
    45.7, 64.1, 77.3, 46.4, 59.3, 51.3, 89.9, 67, 68.6, 105.8,
    112.1, 76.3, 100.4, 91.5, 70.2, 96.9, 51.7, 59.8, 60.4, 137.8) ,
  `Admission to care home` = c(
    "Not admitted", "Not admitted", "Admitted", "Not admitted", "Admitted",
    "Admitted", "Not admitted", "Admitted", "Admitted", "Not admitted",
    "Admitted", "Admitted", "Not admitted", "Not admitted", "Not admitted",
    "Not admitted", "Admitted", "Admitted", "Not admitted", "Not admitted",
    "Not admitted", "Admitted", "Not admitted", "Admitted", "Admitted",
    "Admitted", "Admitted", "Admitted", "Admitted", "Not admitted"),
  `Follow-up` = c(
    10, 8, 8, 8, 12, 12, 11, 10, 8, 7,
    8, 6, 9, 6, 9, 8, 10, 8, 11, 9,
    6, 9, 12, 9, 8, 11, 12, 9, 10, 11)
)
# Simulate lists provided by EQUAL-STATS
Predefined_lists <- list(
  main_menu = c(
    'Calculate summary measures',
    'Create plots',
    'Check distribution',
    'Compare sample mean versus population mean',
    'Compare groups/variables (independent samples)',
    'Compare groups/variables (paired samples or repeated measures)',
    'Find the correlation (quantitative variables)',
    'Calculate measurement error',
    'Find the diagnostic accuracy (primary data)',
    'Perform sample size and power calculations (primary data)',
    'Perform survival analysis',
    'Perform regression analysis',
    'Analyse time series',
    'Perform mixed-effects regression',
    'Perform multivariate regression',
    'Generate hypothesis',
    'Perform sample size and power calculations (effect size approach)',
    'Make correct conclusions (effect size approach)',
    'Find the diagnostic accuracy (tabulated data)'
  ),
  menu_short = c(
    'Summary_Measures',
    'Create_Plots',
    'Check_Distribution',
    'Compare_Sample_Pop_Means',
    'Compare_Groups',
    'Repeated_Measures',
    'Correlation',
    'Measurement_Error',
    'Diagnostic_Accuracy_Primary',
    'Sample_Size_Calculations_Primary',
    'Survival_Analysis',
    'Regression_Analysis',
    'Time_Series',
    'Mixed_Effects_Regression',
    'Multivariate_Regression',
    'Generate_Hypothesis',
    'Sample_Size_Calculations_Effect_size',
    'Make_Conclusions_Effect_size',
    'Diagnostic_Accuracy_Tables'
  )
)
entry <- list()
entry <- lapply(1:15, function(x) entry[[x]] <- '')
rv <- list(
  StorageFolder = tempdir(),
  first_menu_choice = NA,
  second_menu_choice = NA,
  entry = entry,
  import_data = NULL,
  same_row_different_row = NA,
  submit_button_to_appear = FALSE,
  summary_measures_choices = c("EQUAL-STATS choice", "Total observations",
  "Missing observations", "Available observations"),
  analysis_outcome = list(),
  code = list(),
  plan = list(),
  results = list(),
  plots_list = list(),
  reports = list()
)
# Store the data in a folder
data_file_path = paste0(tempdir(), "/data.csv")
write.csv(data, file = data_file_path, row.names = FALSE, na = "")
# Load the necessary packages and functions ####
library(stringr)
library(DescTools)
library(lme4)
library(MuMIn)
library(ggplot2)
library(ggcorrplot)
library(cowplot)
rv$import_data <- function.read_data(data_file_path)
# Update choices ####
rv$first_menu_choice <- "Mixed_Effects_Regression"
rv$second_menu_choice <- "Logistic regression"
rv$entry[[1]] <- "Unable to walk independently at 6 weeks"
rv$entry[[2]] <- ""
rv$entry[[3]] <- "Centre"
rv$entry[[4]] <- "Treatment"
rv$entry[[5]] <- ""
rv$entry[[6]] <- ""
rv$entry[[7]] <- ""
rv$entry[[8]] <- "No"
# Final function ####
Results <- function.Mixed_Effects_Regression(Predefined_lists, rv)

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