R/forestDF.R

In pmur002/metaplot: Meta-analysis Forest Plots

### set up generic function for forestDF
forestDF <- function(object, ...) {
  UseMethod("forestDF")
}

###===================meta=======================###
### metabin
forestDF.metabin <- function(object, study, n.e, event.e,
                             n.c, event.c, effect, se,
                             w.fixed, w.random, mean, lower, upper,
                             e.lower, e.upper, summary = FALSE, ...)
{
  DF <- data.frame(study = study, n.e = n.e, event.e = event.e,
                   n.c = n.c, event.c = event.c, effect = effect,
                   se = se, w.fixed = w.fixed, w.random = w.random,
                   mean = mean, lower = lower, upper = upper,
                   e.lower = e.lower, e.upper = e.upper)

  if (!is.null(object$byvar)) {
    if (summary == FALSE) {
      DF <- cbind(DF, group = object$byvar)
    } else {
      DF <- cbind(DF, group = "")
    }
  }
  DF
}

### metacont
forestDF.metacont <- function(object, study, n.e, mean.e, sd.e, n.c, mean.c,
                              sd.c, effect, se, w.fixed, w.random, mean,
                              lower, upper, summary = FALSE, ...)
{
  DF <-  data.frame(study = study, n.e = n.e, mean.e = mean.e, sd.e = sd.e,
                    n.c = n.c, mean.c = mean.c, sd.c = sd.c, effect = effect,
                    se = se, w.fixed = w.fixed, w.random = w.random,
                    mean = mean, lower = lower, upper = upper)

  if (!is.null(object$byvar)) {
    if (summary == FALSE) {
      DF <- cbind(DF, group = object$byvar)
    } else {
      DF <- cbind(DF, group = "")
    }
  }
  DF
}

###=========================rmeta========================###
### meta.MH
forestDF.meta.MH <- function(object, study, effect, se, rate, lower, upper,
                             ...)
{
  DF <- data.frame(study = study, n.e = NA, event.e = NA, n.c = NA,
                   event.c = NA, effect = effect, se = se, w.fixed = NA,
                   w.random = NA, mean = rate, lower = lower,
                   upper = upper, e.lower = exp(lower), e.upper = exp(upper))
  rownames(DF) <- 1:nrow(DF)
  DF
}

### meta.DSL
forestDF.meta.DSL <- function(object, study, effect, se, rate, lower, upper,
                              ...)
{
  DF <- data.frame(study = study, n.e = NA, event.e = NA, n.c = NA,
                   event.c = NA, effect = effect, se = se, w.fixed = NA,
                   w.random = NA, mean = rate, lower = lower,
                   upper = upper, e.lower = exp(lower), e.upper = exp(upper))

  rownames(DF) <- 1:nrow(DF)
  DF
}

###==========================metafor===========================###
### rma.mh
forestDF.rma.mh <- function(object, study, n.e, event.e, n.c, event.c,
                            w.fixed, effect, se, mean, lower, upper,
                            ...)
{
  DF <- data.frame(study = study, n.e = n.e, event.e = event.e, n.c = n.c,
                   event.c = event.c, effect = effect, se = se,
                   w.fixed = w.fixed, w.random = NA,
                   mean = mean, lower = lower,
                   upper = upper, e.lower = exp(lower), e.upper = exp(upper))
  rownames(DF) <- 1:nrow(DF)
  DF
}

### rma.peto
forestDF.rma.peto <- function(object, study, n.e, event.e, n.c, event.c,
                              w.fixed, effect, se, mean, lower, upper,
                              ...)
{
  DF <- data.frame(study = study, n.e = n.e, event.e = event.e, n.c = n.c,
                   event.c = event.c, effect = effect, se = se,
                   w.fixed = w.fixed, w.random = NA,
                   mean = mean, lower = lower,
                   upper = upper, e.lower = exp(lower), e.upper = exp(upper))
  rownames(DF) <- 1:nrow(DF)
  DF
}

### rma.uni
forestDF.rma.uni <- function(object, study, n.e, event.e, n.c, event.c,
                             w.random, effect, se, mean, lower, upper,
                             ...)
{
  DF <- data.frame(study = study, n.e = n.e, event.e = event.e, n.c = n.c,
                   event.c = event.c, effect = effect, se = se, w.fixed = NA,
                   w.random = w.random, mean = mean, lower = lower,
                   upper = upper, e.lower = exp(lower), e.upper = exp(upper))
  rownames(DF) <- 1:nrow(DF)
  DF
}