tm_a_gee.md
In teal.modules.clinical: 'teal' Modules for Standard Clinical Outputs

template_a_gee t_gee_cov table works as expected with default input

Code
  res
Output
  $model
  {
      model_fit <- tern.gee::fit_gee(vars = tern.gee::vars_gee(response = as.vector("AVAL"), 
          covariates = as.vector(NULL), id = as.vector("USUBJID"), 
          arm = as.vector("ARMCD"), visit = as.vector("AVISIT")), 
          data = ANL, regression = "logistic", cor_struct = "unstructured")
  }

  $table
  {
      table <- tern.gee::as.rtable(model_fit, type = "cov")
      subtitles(table) <- NULL
      main_footer(table) <- NULL
  }

template_a_gee t_gee_coef table works as expected with default input

Code
  res
Output
  $model
  {
      model_fit <- tern.gee::fit_gee(vars = tern.gee::vars_gee(response = as.vector("AVAL"), 
          covariates = as.vector(NULL), id = as.vector("USUBJID"), 
          arm = as.vector("ARMCD"), visit = as.vector("AVISIT")), 
          data = ANL, regression = "logistic", cor_struct = "unstructured")
  }

  $table
  {
      table <- tern.gee::as.rtable(data.frame(Coefficient = model_fit$coefficients))
      subtitles(table) <- NULL
      main_footer(table) <- NULL
  }

template_a_gee works as expected with non-default reference arm

Code
  res
Output
  $model
  {
      model_fit <- tern.gee::fit_gee(vars = tern.gee::vars_gee(response = as.vector("AVAL"), 
          covariates = as.vector(NULL), id = as.vector("USUBJID"), 
          arm = as.vector("ARMCD"), visit = as.vector("AVISIT")), 
          data = ANL, regression = "logistic", cor_struct = "unstructured")
  }

  $table
  {
      lsmeans_fit_model <- tern.gee::lsmeans(model_fit, 0.95)
      table <- rtables::basic_table(show_colcounts = TRUE) %>% 
          rtables::split_cols_by(var = "ARM", ref_group = model_fit$ref_level) %>% 
          tern.gee::summarize_gee_logistic() %>% rtables::build_table(df = lsmeans_fit_model, 
          alt_counts_df = ANL_ADSL)
      subtitles(table) <- NULL
      main_footer(table) <- NULL
  }

template_a_gee works as expected when arm is not considered in the model

Code
  res
Output
  $model
  {
      model_fit <- tern.gee::fit_gee(vars = tern.gee::vars_gee(response = as.vector("AVAL"), 
          covariates = as.vector(NULL), id = as.vector("USUBJID"), 
          arm = as.vector(NULL), visit = as.vector("AVISIT")), 
          data = ANL, regression = "logistic", cor_struct = "unstructured")
  }

  $table
  {
      lsmeans_fit_model <- tern.gee::lsmeans(model_fit, 0.95)
      table <- rtables::basic_table(show_colcounts = TRUE) %>% 
          rtables::split_cols_by(var = "ARM", ref_group = model_fit$ref_level) %>% 
          tern.gee::summarize_gee_logistic() %>% rtables::build_table(df = lsmeans_fit_model, 
          alt_counts_df = ANL_ADSL)
      subtitles(table) <- NULL
      main_footer(table) <- NULL
  }