R/xPairwise.R

In cwendorf/EASIalt: easiOrigin

# easiOrigin
## Pairwise Comparisons

### Confidence Intervals

.ciPairwise <- function(x, ...) {
  UseMethod(".ciPairwise")
}

.ciPairwise.default <- function(frame, conf.level = .95, ...) {
  data <- data.frame(frame)
  nr <- dim(data)[2]
  rn <- colnames(data)
  ncomp <- (nr) * (nr - 1) / 2
  results <- data.frame(matrix(ncol = 5, nrow = ncomp))
  colnames(results) <- c("Diff", "SE", "df", "LL", "UL")
  comp <- 1
  for (i in 1:(nr - 1)) {
    for (j in (i + 1):nr) {
      rownames(results)[comp] <- paste(rn[i], "v", rn[j])
      varx <- get(rn[i])
      vary <- get(rn[j])
      object <- t.test(varx, vary, paired = TRUE, conf.level = conf.level)
      results[comp, ] <- .ciDifference(object, ...)
      comp <- comp + 1
    }
  }
  results
}

.ciPairwise.formula <- function(formula, ...) {
  varx <- eval(formula[[3]])
  vary <- eval(formula[[2]])
  nr <- nlevels(varx)
  rn <- levels(varx)
  ncomp <- (nr) * (nr - 1) / 2
  results <- data.frame(matrix(ncol = 5, nrow = ncomp))
  colnames(results) <- c("Diff", "SE", "df", "LL", "UL")
  comp <- 1
  for (i in 1:(nr - 1)) {
    for (j in (i + 1):nr) {
      rownames(results)[comp] <- paste(rn[i], "v", rn[j])
      Comparison <- factor(varx, c(rn[i], rn[j]))
      object <- t.test(vary ~ Comparison, ...)
      results[comp, ] <- .ciDifference(object, ...)
      comp <- comp + 1
    }
  }
  results
}

ciPairwise <- function(..., conf.level = .95, main = NULL, digits = 3) {
  results <- .ciPairwise(..., conf.level = conf.level)
  if (is.null(main)) {
    main <- "Confidence Intervals for the Pairwise Comparisons"
  }
  .formatList(list(results), main = main, digits = digits)
}

### Null Hypothesis Significance Tests

.nhstPairwise <- function(x, ...) {
  UseMethod(".nhstPairwise")
}

.nhstPairwise.default <- function(frame, conf.level = .95, mu = 0, ...) {
  data <- data.frame(frame)
  nr <- dim(data)[2]
  rn <- colnames(data)
  ncomp <- (nr) * (nr - 1) / 2
  results <- data.frame(matrix(ncol = 5, nrow = ncomp))
  colnames(results) <- c("Diff", "SE", "t", "df", "p")
  comp <- 1
  for (i in 1:(nr - 1)) {
    for (j in (i + 1):nr) {
      rownames(results)[comp] <- paste(rn[i], "v", rn[j])
      varx <- get(rn[i])
      vary <- get(rn[j])
      object <- t.test(varx, vary, paired = TRUE, conf.level = conf.level, mu = mu)
      results[comp, ] <- .nhstDifference(object, ...)
      comp <- comp + 1
    }
  }
  results
}

.nhstPairwise.formula <- function(formula, ...) {
  varx <- eval(formula[[3]])
  vary <- eval(formula[[2]])
  nr <- nlevels(varx)
  rn <- levels(varx)
  ncomp <- (nr) * (nr - 1) / 2
  results <- data.frame(matrix(ncol = 5, nrow = ncomp))
  colnames(results) <- c("Diff", "SE", "t", "df", "p")
  comp <- 1
  for (i in 1:(nr - 1)) {
    for (j in (i + 1):nr) {
      rownames(results)[comp] <- paste(rn[i], "v", rn[j])
      Comparison <- factor(varx, c(rn[i], rn[j]))
      object <- t.test(vary ~ Comparison, ...)
      results[comp, ] <- .nhstDifference(object, ...)
      comp <- comp + 1
    }
  }
  results
}

nhstPairwise <- function(..., main = NULL, digits = 3) {
  results <- .nhstPairwise(...)
  if (is.null(main)) {
    main <- "Hypothesis Tests for the Pairwise Comparisons"
  }
  .formatList(list(results), main = main, digits = digits)
}

### Confidence Interval Plots

graphPairwise <- function(x, ...) {
  UseMethod("graphPairwise")
}

graphPairwise.default <- function(frame, main = NULL, ylab = "Mean Difference", xlab = "", mu = NULL, rope = NULL, conf.level = .95, values = TRUE, ylim = NULL, digits = 3, pch = 17, col = "black", ...) {
  results <- .ciPairwise(frame, conf.level = conf.level)[, c("Diff", "LL", "UL")]
  if (is.null(main)) {
    main <- "Confidence Intervals for the Pairwise Comparisons"
  }
  .cipMain(results, main = main, ylab = ylab, xlab = xlab, mu = mu, rope = rope, values = values, ylim = ylim, digits = digits, connect = FALSE, pch = pch, col = col)
}

graphPairwise.formula <- function(formula, main = NULL, ylab = "Mean Difference", xlab = "", mu = NULL, rope = NULL, conf.level = .95, values = TRUE, ylim = NULL, digits = 3, pch = 17, col = "black", ...) {
  results <- .ciPairwise(formula, conf.level = conf.level)[, c("Diff", "LL", "UL")]
  if (is.null(main)) {
    main <- "Confidence Interval for the Pairwise Comparisons"
  }
  .cipMain(results, main = main, ylab = ylab, xlab = xlab, mu = mu, rope = rope, values = values, ylim = ylim, digits = digits, connect = FALSE, pch = pch, col = col)
}