R/time_lnVR.R

In minter: Effect Sizes for Meta-Analysis of Interactions from Factorial Experiments

#' Log of Variability Ratio: Interaction Between Treatment and Time
#'
#' @param data Data frame containing the variables used.
#' @param col_names Vector of two strings to name the output columns for the effect size and its sampling variance. Default is 'yi' and 'vi'.
#' @param append Logical. Append the results to \code{data}. Default is TRUE
#' @param t0_Ctrl_sd Standard deviation from the control group at time 0
#' @param t1_Ctrl_sd Standard deviation from the control group at time 1
#' @param Ctrl_n Sample size of the control group
#' @param Ctrl_cor Number or numeric vector. Correlation between the means of the control group at t0 and t1
#' @param t0_Exp_sd Standard deviation from the experimental group at time 0
#' @param t1_Exp_sd Standard deviation from the experimental group at time 1
#' @param Exp_n Sample size of the experimental group
#' @param Exp_cor Number or numeric vector. Correlation between the means of the experimental group at t0 and t1
#'
#' @inherit lnRR_ind return
#'
#' @author Facundo Decunta - fdecunta@agro.uba.ar
#'
#' @references 
#'   Shinichi Nakagawa and Daniel Noble, personal communication.
#'
#' @examples
#' data <- data.frame(
#'   study_id = 1:2,
#'   pre_control_sd = c(2.1, 2.4),
#'   post_control_sd = c(2.2, 2.5),
#'   control_n = c(24, 19),
#'   pre_invaded_sd = c(2.0, 2.3),
#'   post_invaded_sd = c(4.1, 4.6),
#'   invaded_n = c(21, 22)
#' )
#' 
#' result <- time_lnVR(
#'   data = data,
#'   t0_Ctrl_sd = "pre_control_sd", t1_Ctrl_sd = "post_control_sd",
#'   Ctrl_n = "control_n", Ctrl_cor = 0.6,
#'   t0_Exp_sd = "pre_invaded_sd", t1_Exp_sd = "post_invaded_sd",
#'   Exp_n = "invaded_n", Exp_cor = 0.4
#' )
#'
#' @export
time_lnVR <- function(
  data,
  col_names = c("yi", "vi"),
  append = TRUE,
  t0_Ctrl_sd,
  t1_Ctrl_sd,
  Ctrl_n,
  Ctrl_cor,
  t0_Exp_sd,
  t1_Exp_sd,
  Exp_n,
  Exp_cor
) {
  .assert_args(col_names, append, data)
  .assert_cor_value(Ctrl_cor, data)
  .assert_cor_value(Exp_cor, data)

  call_args <- as.list(match.call())[-1]

  time_lnvr_func <- ".time_interaction_lnVR"
  time_lnvr_args <-.get_columns(call_args[.time_lnVR_requirements], data)

  time_lnvr_args$Ctrl_cor <- Ctrl_cor
  time_lnvr_args$Exp_cor <- Exp_cor

  df <- .compute_and_format(
    data = data,
    effsize_func = time_lnvr_func,
    effsize_args = time_lnvr_args,
    col_names = col_names,
    append = append
  )

  return(df)
}


.time_lnVR_requirements <- c(
   "t0_Ctrl_sd",
   "t1_Ctrl_sd",
   "Ctrl_n",
   "t0_Exp_sd",
   "t1_Exp_sd",
   "Exp_n"
)


#' Log of Variability Ratio: Interaction Between Experimental Treatment and Time
#'
#' @param t0_Ctrl_sd Standard deviation from the control group at time 0
#' @param t1_Ctrl_sd Standard deviation from the control group at time 1
#' @param Ctrl_n Sample size of the control group
#' @param Ctrl_cor Correlation between the means of the control group at t0 and t1
#' @param t0_Exp_sd Standard deviation from the experimental group at time 0
#' @param t1_Exp_sd Standard deviation from the experimental group at time 1
#' @param Exp_n Sample size of the experimental group
#' @param Exp_cor Correlation between the means of the experimental group at t0 and t1
#'
#' @keywords internal
.time_interaction_lnVR <- function(
   t0_Ctrl_sd,
   t1_Ctrl_sd,
   Ctrl_n,
   Ctrl_cor,
   t0_Exp_sd,
   t1_Exp_sd,
   Exp_n,
   Exp_cor
) {
  lnVR <- log((t1_Exp_sd / t1_Ctrl_sd) / (t0_Exp_sd / t0_Ctrl_sd))
  
  lnVRv <- ((1 - Exp_cor^2) / (Exp_n - 1)) +
        ((1 - Ctrl_cor^2) / (Ctrl_n - 1)) 

  return(data.frame(lnVR, lnVRv))
}