R/xtable.R

In AICcmodavg: Model Selection and Multimodel Inference Based on (Q)AIC(c)

##methods for xtable

##aictab
xtable.aictab <- function(x, caption = NULL, label = NULL, align = NULL,
                          digits = NULL, display = NULL, auto = FALSE,
                          nice.names = TRUE, include.AICc = TRUE,
                          include.LL = TRUE, include.Cum.Wt = FALSE, ...) {
 
  ##change to nicer names
  if(nice.names) {
    new.delta <- names(x)[4]
    new.weight <- names(x)[6]
    names(x)[1] <- "Model"
    names(x)[2] <- "K"
    #names(x)[4] <- paste("$\\delta$", unlist(strsplit(new.delta, "_"))[2], collapse = " ") #requires sanitize.text.function( )
    names(x)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
    names(x)[6] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
    names(x)[7] <- "log-Likelihood"
    names(x)[8] <- "Cumulative weight"
  }

  #format to data.frame
  x <- data.frame(x, check.names = FALSE)
  class(x) <- c("xtable","data.frame")
  
  ##with AICc and LL but not Cum.Wt
  if(include.AICc && include.LL && !include.Cum.Wt) {
    x <- x[, c(1:4, 6:7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f"))
  }

  ##with AICc, but not LL and Cum.Wt
  if(include.AICc && !include.LL && !include.Cum.Wt) {
    x <- x[, c(1:4, 6)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
  }

  ##without AICc, but with LL but not Cum.Wt
  if(!include.AICc && include.LL && !include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6:7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
  }

  ##without AICc and LL and Cum.Wt
  if(!include.AICc && !include.LL && !include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f"))
  }

  ##with AICc and LL and Cum.Wt
  if(include.AICc && include.LL && include.Cum.Wt) {
    x <- x[, c(1:4, 6:8)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f","f"))
  }

  ##with AICc, but not LL but with Cum.Wt
  if(include.AICc && !include.LL && include.Cum.Wt) {
    x <- x[, c(1:4, 6, 8)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f"))
  }

  ##without AICc, but with LL and Cum.Wt
  if(!include.AICc && include.LL && include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6:8)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f"))
  }

  ##without AICc and LL but with Cum.Wt
  if(!include.AICc && !include.LL && include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6, 8)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
  }

  caption(x) <- caption
  label(x) <- label
  return(x)
}



##modavg
xtable.modavg <- function(x, caption = NULL, label = NULL, align = NULL,
                          digits = NULL, display = NULL, auto = FALSE,
                          nice.names = TRUE, print.table = FALSE, ...) {

    ##different format for models of class multinom
    if(length(x$Mod.avg.beta) == 1){
        if(print.table) {
            ##extract model selection table
            modavg.table <- data.frame(x$Mod.avg.table[, c(1:4, 6, 8:9)], check.names = FALSE)
            
            ##change to nicer names
            if(nice.names) {
                new.delta <- names(modavg.table)[4]
                new.weight <- names(modavg.table)[5]
                names(modavg.table)[1] <- "Model"
                names(modavg.table)[2] <- "K"
                ##names(x)[4] <- paste("$\\delta$", unlist(strsplit(new.delta, "_"))[2], collapse = " ") #requires sanitize.text.function( )
                names(modavg.table)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
                names(modavg.table)[5] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
                names(modavg.table)[6] <- paste("Beta(", x$Parameter, ")", sep = "")
                names(modavg.table)[7] <- paste("SE(", x$Parameter, ")", sep = "")
            }

            ##format to data.frame
            class(modavg.table) <- c("xtable","data.frame")
            
            align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r","r"))
            digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2,2))
            display(modavg.table) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f","f"))
        }  
    

        ##print model-averaged estimate, unconditional SE, CI
        if(!print.table) {
      
            ##model-averaged estimate                          
            modavg.table <- data.frame(Mod.avg.beta = x$Mod.avg.beta, Uncond.SE = x$Uncond.SE,
                                       Lower.CL = x$Lower.CL, Upper.CL = x$Upper.CL, check.names = FALSE)
            rownames(modavg.table) <- x$Parameter
            
            ##change to nicer names
            if(nice.names) {
                names(modavg.table)[1] <- "Model-averaged beta estimate" 
                names(modavg.table)[2] <- "Unconditional SE"
                names(modavg.table)[3] <- paste(100*x$Conf.level, "%", " lower limit", sep = "")
                names(modavg.table)[4] <- paste(100*x$Conf.level, "%", " upper limit", sep = "")
            }
  
            ##format to data.frame
            class(modavg.table) <- c("xtable","data.frame")

            align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
            digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,2,2,2,2))
            display(modavg.table) <- switch(1+is.null(display), display, c("s","f","f","f","f"))
        }
    }

    if(length(x$Mod.avg.beta) > 1){
        if(print.table) {
            ##extract model selection table
            modavg.table <- data.frame(x$Mod.avg.table[, c(1:4, 6)], check.names = FALSE)
            
            ##change to nicer names
            if(nice.names) {
                new.delta <- names(modavg.table)[4]
                new.weight <- names(modavg.table)[5]
                names(modavg.table)[1] <- "Model"
                names(modavg.table)[2] <- "K"
                ##names(x)[4] <- paste("$\\delta$", unlist(strsplit(new.delta, "_"))[2], collapse = " ") #requires sanitize.text.function( )
                names(modavg.table)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
                names(modavg.table)[5] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
                ##names(modavg.table)[6] <- paste("Beta(", x$Parameter, ")", sep = "")
                ##names(modavg.table)[7] <- paste("SE(", x$Parameter, ")", sep = "")
            }

            ##format to data.frame
            class(modavg.table) <- c("xtable","data.frame")
            
            align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
            digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
            display(modavg.table) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
        }
    

        ##print model-averaged estimate, unconditional SE, CI
        if(!print.table) {
      
            ##model-averaged estimate                          
            modavg.table <- data.frame(Mod.avg.beta = x$Mod.avg.beta, Uncond.SE = x$Uncond.SE,
                                       Lower.CL = x$Lower.CL, Upper.CL = x$Upper.CL, check.names = FALSE)
            rownames(modavg.table) <- names(x$Mod.avg.beta)
            
            ##change to nicer names
            if(nice.names) {
                names(modavg.table)[1] <- "Model-averaged beta estimate" 
                names(modavg.table)[2] <- "Unconditional SE"
                names(modavg.table)[3] <- paste(100*x$Conf.level, "%", " lower limit", sep = "")
                names(modavg.table)[4] <- paste(100*x$Conf.level, "%", " upper limit", sep = "")
            }
  
            ##format to data.frame
            class(modavg.table) <- c("xtable","data.frame")

            align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
            digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,2,2,2,2))
            display(modavg.table) <- switch(1+is.null(display), display, c("s","f","f","f","f"))
        }

    }
    
        
  caption(modavg.table) <- caption
  label(modavg.table) <- label
  return(modavg.table)
}



##modavgShrink
xtable.modavgShrink <- function(x, caption = NULL, label = NULL, align = NULL,
                                digits = NULL, display = NULL, auto = FALSE, 
                                nice.names = TRUE, print.table = FALSE, ...) {

  if(print.table) {
    ##extract model selection table
    modavg.table <- data.frame(x$Mod.avg.table[, c(1:4, 6, 8:9)], check.names = FALSE)

    ##change to nicer names
    if(nice.names) {
      new.delta <- names(modavg.table)[4]
      new.weight <- names(modavg.table)[5]
      names(modavg.table)[1] <- "Model"
      names(modavg.table)[2] <- "K"
      ##names(x)[4] <- paste("$\\delta$", unlist(strsplit(new.delta, "_"))[2], collapse = " ") #requires sanitize.text.function( )
      names(modavg.table)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
      names(modavg.table)[5] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
      names(modavg.table)[6] <- paste("Beta(", x$Parameter, ")", sep = "")
      names(modavg.table)[7] <- paste("SE(", x$Parameter, ")", sep = "")
    }

    ##format to data.frame
    class(modavg.table) <- c("xtable","data.frame")

    align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r","r"))
    digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2,2))
    display(modavg.table) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f","f"))
  }  


  ##print model-averaged estimate, unconditional SE, CI
  if(!print.table) {
      
    ##model-averaged estimate                          
    modavg.table <- data.frame(Mod.avg.beta = x$Mod.avg.beta, Uncond.SE = x$Uncond.SE,
                               Lower.CL = x$Lower.CL, Upper.CL = x$Upper.CL, check.names = FALSE)
    rownames(modavg.table) <- x$Parameter
    
    ##change to nicer names
    if(nice.names) {
      names(modavg.table)[1] <- "Model-averaged beta estimate" 
      names(modavg.table)[2] <- "Unconditional SE"
      names(modavg.table)[3] <- paste(100*x$Conf.level, "%", " lower limit", sep = "")
      names(modavg.table)[4] <- paste(100*x$Conf.level, "%", " upper limit", sep = "")
    }
  
    ##format to data.frame
    class(modavg.table) <- c("xtable","data.frame")
    
    align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
    digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,2,2,2,2))
    display(modavg.table) <- switch(1+is.null(display), display, c("s","f","f","f","f"))
  }

  caption(modavg.table) <- caption
  label(modavg.table) <- label
  return(modavg.table)
}



##modavgPred
xtable.modavgPred <- function(x, caption = NULL, label = NULL, align = NULL,
                              digits = NULL, display = NULL, auto = FALSE, 
                              nice.names = TRUE, ...) {
  modavg.pred <- data.frame(x$matrix.output, check.names = FALSE)
  
  ##change to nicer names
  if(nice.names) {
    names(modavg.pred)[1] <- "Model-averaged predictions" 
    names(modavg.pred)[2] <- "Unconditional SE"
    names(modavg.pred)[3] <- paste(100*x$conf.level, "%", " lower limit", sep = "")
    names(modavg.pred)[4] <- paste(100*x$conf.level, "%", " upper limit", sep = "")
  }
  
  ##format to data.frame
  class(modavg.pred) <- c("xtable","data.frame")

  align(modavg.pred) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
  digits(modavg.pred) <- switch(1+is.null(digits), digits, c(0,2,2,2,2))
  display(modavg.pred) <- switch(1+is.null(display), display, c("s","f","f","f","f"))

  caption(modavg.pred) <- caption
  label(modavg.pred) <- label
  return(modavg.pred)
}



##dictab
xtable.dictab <- function(x, caption = NULL, label = NULL, align = NULL,
                          digits = NULL, display = NULL, auto = FALSE,
                          nice.names = TRUE, include.DIC = TRUE,
                          include.Cum.Wt = FALSE, ...) {

  ##change to nicer names
  if(nice.names) {
    names(x)[1] <- "Model"
    names(x)[2] <- "pD"
    names(x)[3] <- "DIC"
    names(x)[4] <- "Delta DIC"
    names(x)[6] <- "DIC weight"
    names(x)[7] <- "Cumulative weight"
  }

  #format to data.frame
  x <- data.frame(x, check.names = FALSE)
  class(x) <- c("xtable","data.frame")
  
  ##with DIC and Cum.Wt
  if(include.DIC && include.Cum.Wt) {
    x <- x[, c(1:4, 6:7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","f","f","f","f","f"))
  }

  ##with DIC but not Cum.Wt
  if(include.DIC && !include.Cum.Wt) {
    x <- x[, c(1:4, 6)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","f","f","f","f"))
  }

  ##without DIC but with Cum.Wt
  if(!include.DIC && include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6:7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","f","f","f","f"))
  }

  ##without DIC and Cum.Wt
  if(!include.DIC && !include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","f","f","f"))
  }

  caption(x) <- caption
  label(x) <- label
  return(x)
}



##modavgEffect
xtable.modavgEffect <- function(x, caption = NULL, label = NULL, align = NULL,
                                digits = NULL, display = NULL, auto = FALSE,
                                nice.names = TRUE, print.table = FALSE, ...) {

    if(print.table) {

        ##check if output from occuMulti or occuMS
        if(length(x$Mod.avg.eff) > 1) {
            warning("\nToo many effect sizes to print in table\n")
            ##extract model selection table
            modavg.table <- data.frame(x$Mod.avg.table[, c(1:4, 6)], check.names = FALSE)

            if(nice.names) {
                new.delta <- names(modavg.table)[4]
                new.weight <- names(modavg.table)[5]
                names(modavg.table)[1] <- "Model"
                names(modavg.table)[2] <- "K"
                ##names(x)[4] <- paste("$\\delta$", unlist(strsplit(new.delta, "_"))[2], collapse = " ") #requires sanitize.text.function( )
                names(modavg.table)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
                names(modavg.table)[5] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
            }

            ##format to data.frame
            class(modavg.table) <- c("xtable","data.frame")

            align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
            digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
            display(modavg.table) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))

        } else {
        
        ##extract model selection table
        modavg.table <- data.frame(x$Mod.avg.table[, c(1:4, 6, 8:9)], check.names = FALSE)
      
        ##change to nicer names
        if(nice.names) {
            new.delta <- names(modavg.table)[4]
            new.weight <- names(modavg.table)[5]
            names(modavg.table)[1] <- "Model"
            names(modavg.table)[2] <- "K"
            ##names(x)[4] <- paste("$\\delta$", unlist(strsplit(new.delta, "_"))[2], collapse = " ") #requires sanitize.text.function( )
            names(modavg.table)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
            names(modavg.table)[5] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
            names(modavg.table)[6] <- paste("Effect(", x$Group1, " - ", x$Group2, ")", sep = "")
            names(modavg.table)[7] <- paste("SE(", x$Group1, " - ", x$Group2, ")", sep = "")
        }

            ##format to data.frame
            class(modavg.table) <- c("xtable","data.frame")

            align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r","r"))
            digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2,2))
            display(modavg.table) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f","f"))
        }
    }


  ##print model-averaged estimate, unconditional SE, CI
  if(!print.table) {

    modavg.table <- as.data.frame(x$Matrix.output)
    ##modavg.table <- data.frame(Mod.avg.beta = x$Mod.avg.eff, Uncond.SE = x$Uncond.se,
    ##                           Lower.CL = x$Lower.CL, Upper.CL = x$Upper.CL, check.names = FALSE)
    ##rownames(modavg.table) <- x$Group.variable ##TO CHANGE LABEL TO "Effect Size"

    ##change to nicer names
    if(nice.names) {
      names(modavg.table)[1] <- "Model-averaged effect size" 
      names(modavg.table)[2] <- "Unconditional SE"
      names(modavg.table)[3] <- paste(100*x$Conf.level, "%", " lower limit", sep = "")
      names(modavg.table)[4] <- paste(100*x$Conf.level, "%", " upper limit", sep = "")
      if(length(x$Mod.avg.eff) == 1) {rownames(modavg.table) <- paste("Effect size (", x$Group.variable, ")", sep = "")}
    }
  
      ##format to data.frame
      class(modavg.table) <- c("xtable","data.frame")

      align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
      digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,2,2,2,2))
      display(modavg.table) <- switch(1+is.null(display), display, c("s","f","f","f","f"))
  }

  caption(modavg.table) <- caption
  label(modavg.table) <- label
  return(modavg.table)
}



##multComp
xtable.multComp <- function(x, caption = NULL, label = NULL, align = NULL,
                            digits = NULL, display = NULL, auto = FALSE,
                            nice.names = TRUE, print.table = FALSE, ...) {

  if(print.table) {
    ##extract model selection table
    modavg.table <- data.frame(x$model.table[, c(1:4, 6)], check.names = FALSE)

    ##change to nicer names
    if(nice.names) {
      new.delta <- names(modavg.table)[4]
      new.weight <- names(modavg.table)[5]
      names(modavg.table)[1] <- "Group structure"
      names(modavg.table)[2] <- "K"
      ##names(x)[4] <- paste("$\\delta$", unlist(strsplit(new.delta, "_"))[2], collapse = " ") #requires sanitize.text.function( )
      names(modavg.table)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
      names(modavg.table)[5] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
    }

    ##format to data.frame
    class(modavg.table) <- c("xtable","data.frame")

    align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(modavg.table) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
  }  

  
  ##print model-averaged estimate, unconditional SE, CI
  if(!print.table) {
    modavg.table <- data.frame(Group = x$ordered.levels,
                               Model.avg.est = x$model.avg.est[, "Mod.avg.est"],
                               Uncond.SE = x$model.avg.est[, "Uncond.SE"],
                               Lower.CL = x$model.avg.est[, "Lower.CL"],
                               Upper.CL = x$model.avg.est[, "Upper.CL"], check.names = FALSE)
  
    ##change to nicer names
    if(nice.names) {
      names(modavg.table)[2] <- paste("Model-averaged estimates (", x$factor.id, ")", sep = "") 
      names(modavg.table)[3] <- "Unconditional SE"
      names(modavg.table)[4] <- paste(100*x$conf.level, "%", " lower limit", sep = "")
      names(modavg.table)[5] <- paste(100*x$conf.level, "%", " upper limit", sep = "")
    }
  
    ##format to data.frame
    class(modavg.table) <- c("xtable","data.frame")

    align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,2,2,2,2,2))
    display(modavg.table) <- switch(1+is.null(display), display, c("s","f","f","f","f","f"))

  }

  caption(modavg.table) <- caption
  label(modavg.table) <- label
  return(modavg.table)
}



##boot.wt - class aictab - potentially create new class for boot.wt
xtable.boot.wt <- function(x, caption = NULL, label = NULL, align = NULL,
                           digits = NULL, display = NULL, auto = FALSE,
                           nice.names = TRUE, include.AICc = TRUE,
                           include.AICcWt = FALSE, ...) {

  ##change to nicer names
  if(nice.names) {
    new.delta <- names(x)[4]
    new.weight <- names(x)[6]
    names(x)[1] <- "Model"
    names(x)[2] <- "K"
    names(x)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
    names(x)[6] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
    names(x)[7] <- "Pi weight"
  }

  #format to data.frame
  x <- data.frame(x, check.names = FALSE)
  class(x) <- c("xtable","data.frame")
  
  ##with AICc but not AICc.Wt
  if(include.AICc && !include.AICcWt) {
    x <- x[, c(1:4, 7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
  }

  ##with AICc and AICc.Wt
  if(include.AICc && include.AICcWt) {
    x <- x[, c(1:4, 6:7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f"))
  }

  ##without AICc, but with AICc.Wt
  if(!include.AICc && include.AICcWt) {
    x <- x[, c(1:2, 4, 6:7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
  }

  ##without AICc and AICc.Wt
  if(!include.AICc && !include.AICcWt) {
    x <- x[, c(1:2, 4, 7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f"))
  }

  caption(x) <- caption
  label(x) <- label
  return(x)
}



##mb.chisq - for single-season model
xtable.mb.chisq <- function(x, caption = NULL, label = NULL, align = NULL,
                            digits = NULL, display = NULL, auto = FALSE,
                            nice.names = TRUE,
                            include.detection.histories = TRUE, ...) {


  ##stop if dynamic occupancy model
  if(identical(x$model.type, "dynamic")) {
    stop("\n'xtable' does not yet support dynamic occupancy models\n")
  }

  ##extract names
  x.names <- names(x)

  ##stop if no chi-square table is present
  if(!any(x.names == "chisq.table")) {
    stop("\nchi-square table must be included in the object\n")
  }

  
  ##extract table
  chisq.table <- data.frame("Detection.history" = rownames(x$chisq.table),
                            x$chisq.table, check.names = FALSE)

    
  ##change to nicer names
  if(nice.names) {
    colnames(chisq.table)[1] <- "Detection history"
    ##extract rownames
    rows <- rownames(x$chisq.table)
    ##replace NA by ".", here "" to avoid creating endash in LaTeX
    ##also possible to use {} between consecutive dashes - this requires sanitization in print( )
    new.rows <- gsub(pattern = "NA", replacement = ".", rows)
    chisq.table[, "Detection history"] <- new.rows
    rownames(chisq.table) <- new.rows
  }

  ##format to data.frame
  class(chisq.table) <- c("xtable", "data.frame")

  ##do not include detection history as a column (only rownames)
  if(!include.detection.histories) {

    ##exclude column with detection histories
    chisq.table <- chisq.table[, 2:5]
    
    align(chisq.table) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
    digits(chisq.table) <- switch(1+is.null(digits), digits, c(0,0,2,2,2))
    display(chisq.table) <- switch(1+is.null(display), display, c("s","s","d","f","f")) #2 columns as integers
  }

  ##include detection history as a column
  if(include.detection.histories) {

    ##exclude column with detection histories
    chisq.table <- chisq.table[, 1:5]
    
    align(chisq.table) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(chisq.table) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(chisq.table) <- switch(1+is.null(display), display, c("s","s","d","f","f","f")) #2 columns as integers
  }

  caption(chisq.table) <- caption
  label(chisq.table) <- label
  return(chisq.table)
}



##add method for detHist class
xtable.detHist <- function(x, caption = NULL, label = NULL, align = NULL,
                           digits = NULL, display = NULL, auto = FALSE, 
                           nice.names = TRUE, table.detHist = "freq",
                           ...) {
  ##for single season single species, display frequencies in a single matrix
  if(x$n.seasons == 1 && x$n.species == 1) {

    ##display detection histories
    if(identical(table.detHist, "hist")){
      det.hist <- x$hist.table.full
      det.mat <- matrix(det.hist, nrow = 1)
      
      if(nice.names) {
        det.names <- names(det.hist)
        new.names <- gsub(pattern = "NA", replacement = ".", det.names)
        colnames(det.mat) <- new.names
        rownames(det.mat) <- "Season-1"
      }
      
      det.frame <- as.data.frame(det.mat)
      n.cols <- ncol(det.frame)
    }

    ##display frequencies
    if(identical(table.detHist, "freq")) {
        det.frame <- as.data.frame(x$out.freqs)
        n.cols <- ncol(det.frame)
      }

    ##display proportions
    if(identical(table.detHist, "prop")){
      det.frame <- as.data.frame(x$out.props)
      n.cols <- ncol(det.frame)
    }
       
  }

    ##for single season multiple species, display frequencies in a single matrix
    if(x$n.seasons == 1 && x$n.species > 1) {

        ##display detection histories
        if(identical(table.detHist, "hist")){
            det.hist <- x$hist.table.full
            det.mat <- matrix(det.hist, nrow = 1)
      
            if(nice.names) {
                det.names <- names(det.hist)
                new.names <- gsub(pattern = "NA", replacement = ".", det.names)
                colnames(det.mat) <- new.names
                rownames(det.mat) <- "Season-1"
            }
      
            det.frame <- as.data.frame(det.mat)
            n.cols <- ncol(det.frame)
        }

        ##display frequencies
        if(identical(table.detHist, "freq")) {
            det.frame <- as.data.frame(x$out.freqs)
            n.cols <- ncol(det.frame)
        }

        ##display proportions
        if(identical(table.detHist, "prop")){
            det.frame <- as.data.frame(x$out.props)
            n.cols <- ncol(det.frame)
        }
       
    }
    
    if(x$n.seasons > 1 && x$n.species == 1) {
          
        ##display entire detection histories
        if(identical(table.detHist, "hist")) {
            det.hist <- x$hist.table.full
            det.mat <- matrix(det.hist, nrow = 1)
      
            if(nice.names) {
                det.names <- names(det.hist)
                new.names <- gsub(pattern = "NA", replacement = ".", det.names)
                colnames(det.mat) <- new.names
                rownames(det.mat) <- "All seasons"
            }
        
            det.frame <- as.data.frame(det.mat)
            n.cols <- ncol(det.frame)
        }

        ##display frequencies
        if(identical(table.detHist, "freq")) {
            det.frame <- as.data.frame(x$out.freqs)
            n.cols <- ncol(det.frame)
        }

        ##display proportions
        if(identical(table.detHist, "prop")) {
            det.frame <- as.data.frame(x$out.props)
            n.cols <- ncol(det.frame)
        }
    }

    
    ##format to data.frame
    class(det.frame) <- c("xtable","data.frame")
  
    align(det.frame) <- switch(1+is.null(align), align, c("l", rep("r", n.cols)))
    
    if(identical(table.detHist, "prop")) {
        digits(det.frame) <- switch(1+is.null(digits), digits, c(0, rep(2, n.cols)))
    } else {
        digits(det.frame) <- switch(1+is.null(digits), digits, c(0, rep(0, n.cols)))
    }
    display(det.frame) <- switch(1+is.null(display), display, c("s", rep("f", n.cols)))
  
    caption(det.frame) <- caption
    label(det.frame) <- label
    return(det.frame)
}



##add method for countHist class
xtable.countHist <- function(x, caption = NULL, label = NULL, align = NULL,
                             digits = NULL, display = NULL, auto = FALSE,
                             nice.names = TRUE, table.countHist = "count",
                             ...) {
  ##for single season, display frequencies in a single matrix
  if(x$n.seasons == 1) {

    ##display count histories
    if(identical(table.countHist, "hist")){
      det.hist <- x$hist.table.full
      det.mat <- matrix(det.hist, nrow = 1)
      
      if(nice.names) {
        det.names <- names(det.hist)
        new.names <- gsub(pattern = "NA", replacement = ".", det.names)
        colnames(det.mat) <- new.names
        rownames(det.mat) <- "Season-1"
      }
      
      det.frame <- as.data.frame(det.mat)
      n.cols <- ncol(det.frame)
    }

    ##display frequencies
    if(identical(table.countHist, "freq")) {
        det.frame <- as.data.frame(x$out.freqs)
        n.cols <- ncol(det.frame)
      }

    ##display counts
    if(identical(table.countHist, "count")) {
        det.mat <- matrix(x$count.table.full, nrow = 1)
        colnames(det.mat) <- names(x$count.table.full)

        if(nice.names) {
          rownames(det.mat) <- "Season-1"
        }
        
        n.cols <- ncol(det.mat)
        det.frame <- as.data.frame(det.mat)
      }

    ##display proportions
    if(identical(table.countHist, "prop")){
      det.frame <- as.data.frame(x$out.props)
      n.cols <- ncol(det.frame)
    }
       
  } else {

      ##display entire detection histories
      if(identical(table.countHist, "hist")) {
        det.hist <- x$hist.table.full
        det.mat <- matrix(det.hist, nrow = 1)
      
        if(nice.names) {
          det.names <- names(det.hist)
          new.names <- gsub(pattern = "NA", replacement = ".", det.names)
          colnames(det.mat) <- new.names
          rownames(det.mat) <- "All seasons"
        }
        
        det.frame <- as.data.frame(det.mat)
        n.cols <- ncol(det.frame)
      }

      ##display frequencies
      if(identical(table.countHist, "freq")) {
        det.frame <- as.data.frame(x$out.freqs)
        #det.frame[1, 3:6] <- "."
        n.cols <- ncol(det.frame)
      }

      ##display counts
      if(identical(table.countHist, "count")) {
        det.mat <- matrix(x$count.table.full, nrow = 1)
        colnames(det.mat) <- names(x$count.table.full)

        if(nice.names) {
          rownames(det.mat) <- "All seasons"
        }
        n.cols <- ncol(det.mat)
        det.frame <- as.data.frame(det.mat)
      }

      ##display proportions
      if(identical(table.countHist, "prop")) {
        det.frame <- as.data.frame(x$out.props)
#        det.frame[1, 2:4] <- "."
        n.cols <- ncol(det.frame)
      }

    }

    
  ##format to data.frame
  class(det.frame) <- c("xtable","data.frame")
  
  align(det.frame) <- switch(1+is.null(align), align, c("l", rep("r", n.cols)))

  if(identical(table.countHist, "prop")) {
    digits(det.frame) <- switch(1+is.null(digits), digits, c(0, rep(2, n.cols)))
  } else {
    digits(det.frame) <- switch(1+is.null(digits), digits, c(0, rep(0, n.cols)))
  }
  display(det.frame) <- switch(1+is.null(display), display, c("s", rep("f", n.cols)))
  
  caption(det.frame) <- caption
  label(det.frame) <- label
  return(det.frame)
}



##add method for countDist class
xtable.countDist <- function(x, caption = NULL, label = NULL, align = NULL,
                             digits = NULL, display = NULL, auto = FALSE,
                             nice.names = TRUE, table.countDist = "distance",
                             ...) {
  ##for single season, display frequencies in a single matrix
  if(x$n.seasons == 1) {

    ##display counts across distance classes
    if(identical(table.countDist, "distance")){
      det.dist <- matrix(x$dist.sums.full, nrow = 1)
      colnames(det.dist) <- names(x$dist.sums.full)

      if(nice.names) {
        rownames(det.dist) <- "Season-1"
      }
      
      n.cols <- ncol(det.dist)
      det.frame <- as.data.frame(det.dist)
    }

    ##display frequencies
    if(identical(table.countDist, "freq")) {
        det.frame <- as.data.frame(x$out.freqs)
        n.cols <- ncol(det.frame)
      }

    ##display counts
    if(identical(table.countDist, "count")) {
        det.mat <- matrix(x$count.table.full, nrow = 1)
        colnames(det.mat) <- names(x$count.table.full)

        if(nice.names) {
          rownames(det.mat) <- "Season-1"
        }
        
        n.cols <- ncol(det.mat)
        det.frame <- as.data.frame(det.mat)
      }

    ##display proportions
    if(identical(table.countDist, "prop")){
      det.frame <- as.data.frame(x$out.props)
      n.cols <- ncol(det.frame)
    }
       
  } else {

      ##display counts across distance classes
      if(identical(table.countDist, "distance")) {
        ##assumes the same distance classes were used each year
        det.dist <- matrix(unlist(x$dist.table.seasons),
                           nrow = x$n.seasons)
        colnames(det.dist) <- names(x$dist.sums.full)

        if(nice.names) {
          rownames(det.dist) <- paste("Season-", 1:x$n.seasons, sep = "")
        }
      
        n.cols <- ncol(det.dist)
        det.frame <- as.data.frame(det.dist)
      }

      ##display frequencies
      if(identical(table.countDist, "freq")) {
        det.frame <- as.data.frame(x$out.freqs)
        #det.frame[1, 3:6] <- "."
        n.cols <- ncol(det.frame)
      }

      ##display counts
      if(identical(table.countDist, "count")) {
        det.mat <- matrix(x$count.table.full, nrow = 1)
        colnames(det.mat) <- names(x$count.table.full)

        if(nice.names) {
          rownames(det.mat) <- "All seasons"
        }
        
        n.cols <- ncol(det.mat)
        det.frame <- as.data.frame(det.mat)
      }

      ##display proportions
      if(identical(table.countDist, "prop")) {
        det.frame <- as.data.frame(x$out.props)
#        det.frame[1, 2:4] <- "."
        n.cols <- ncol(det.frame)
      }

    }

    
  ##format to data.frame
  class(det.frame) <- c("xtable","data.frame")
  
  align(det.frame) <- switch(1+is.null(align), align, c("l", rep("r", n.cols)))

  if(identical(table.countDist, "prop")) {
    digits(det.frame) <- switch(1+is.null(digits), digits, c(0, rep(2, n.cols)))
  } else {
    digits(det.frame) <- switch(1+is.null(digits), digits, c(0, rep(0, n.cols)))
  }
  display(det.frame) <- switch(1+is.null(display), display, c("s", rep("f", n.cols)))
  
  caption(det.frame) <- caption
  label(det.frame) <- label
  return(det.frame)
}



##add method for detTime class
xtable.detTime <- function(x, caption = NULL, label = NULL, align = NULL,
                           digits = NULL, display = NULL, auto = FALSE,
                           nice.names = TRUE, table.detTime = "freq",
                           ...) {
  ##for single season, display frequencies in a single matrix
  if(x$n.seasons == 1) {

    ##display detection histories
    if(identical(table.detTime, "dist")){
      det.time <- x$time.table.full
      det.mat <- matrix(det.time, nrow = 1)
      
      if(nice.names) {
        det.names <- names(det.time)
        colnames(det.mat) <- det.names
        rownames(det.mat) <- "Season-1"
      }
      
      det.frame <- as.data.frame(det.mat)
      n.cols <- ncol(det.frame)
    }

    ##display frequencies
    if(identical(table.detTime, "freq")) {
        det.frame <- as.data.frame(x$out.freqs)
        n.cols <- ncol(det.frame)
      }

    ##display proportions
    if(identical(table.detTime, "prop")){
      det.frame <- as.data.frame(x$out.props)
      n.cols <- ncol(det.frame)
    }
       
  }

    
    if(x$n.seasons > 1) {
          
        ##display distribution of detection times across seasons
        if(identical(table.detTime, "dist")) {
            det.time <- x$time.table.full
            det.mat <- matrix(det.time, nrow = 1)
      
            if(nice.names) {
                det.names <- names(det.time)
                colnames(det.mat) <- det.names
                rownames(det.mat) <- "All seasons"
            }
        
            det.frame <- as.data.frame(det.mat)
            n.cols <- ncol(det.frame)
        }

        ##display frequencies
        if(identical(table.detTime, "freq")) {
            det.frame <- as.data.frame(x$out.freqs)
            n.cols <- ncol(det.frame)
        }

        ##display proportions
        if(identical(table.detTime, "prop")) {
            det.frame <- as.data.frame(x$out.props)
            n.cols <- ncol(det.frame)
        }
    }

    
    ##format to data.frame
    class(det.frame) <- c("xtable","data.frame")
  
    align(det.frame) <- switch(1+is.null(align), align, c("l", rep("r", n.cols)))
    
    if(identical(table.detTime, "prop")) {
        digits(det.frame) <- switch(1+is.null(digits), digits, c(0, rep(2, n.cols)))
    } else {
        digits(det.frame) <- switch(1+is.null(digits), digits, c(0, rep(0, n.cols)))
    }
    display(det.frame) <- switch(1+is.null(display), display, c("s", rep("f", n.cols)))
  
    caption(det.frame) <- caption
    label(det.frame) <- label
    return(det.frame)
}



##bictab
xtable.bictab <- function(x, caption = NULL, label = NULL, align = NULL,
                          digits = NULL, display = NULL, auto = FALSE,
                          nice.names = TRUE, include.BIC = TRUE,
                          include.LL = TRUE, include.Cum.Wt = FALSE, ...) {

  ##change to nicer names
  if(nice.names) {
    new.delta <- names(x)[4]
    new.weight <- names(x)[6]
    names(x)[1] <- "Model"
    names(x)[2] <- "K"
    #names(x)[4] <- paste("$\\delta$", unlist(strsplit(new.delta, "_"))[2], collapse = " ") #requires sanitize.text.function( )
    names(x)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
    names(x)[6] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
    names(x)[7] <- "log-Likelihood"
    names(x)[8] <- "Cumulative weight"
  }

  #format to data.frame
  x <- data.frame(x, check.names = FALSE)
  class(x) <- c("xtable","data.frame")
  
  ##with BIC and LL but not Cum.Wt
  if(include.BIC && include.LL && !include.Cum.Wt) {
    x <- x[, c(1:4, 6:7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f"))
  }

  ##with BIC, but not LL and Cum.Wt
  if(include.BIC && !include.LL && !include.Cum.Wt) {
    x <- x[, c(1:4, 6)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
  }

  ##without BIC, but with LL but not Cum.Wt
  if(!include.BIC && include.LL && !include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6:7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
  }

  ##without BIC and LL and Cum.Wt
  if(!include.BIC && !include.LL && !include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f"))
  }

  ##with BIC and LL and Cum.Wt
  if(include.BIC && include.LL && include.Cum.Wt) {
    x <- x[, c(1:4, 6:8)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f","f"))
  }

  ##with BIC, but not LL but with Cum.Wt
  if(include.BIC && !include.LL && include.Cum.Wt) {
    x <- x[, c(1:4, 6, 8)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f"))
  }

  ##without BIC, but with LL and Cum.Wt
  if(!include.BIC && include.LL && include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6:8)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f"))
  }

  ##without BIC and LL but with Cum.Wt
  if(!include.BIC && !include.LL && include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6, 8)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
  }

  caption(x) <- caption
  label(x) <- label
  return(x)
}



##checkParms
xtable.checkParms <- function(x, caption = NULL, label = NULL, align = NULL,
                              digits = NULL, display = NULL, auto = FALSE,
                              nice.names = TRUE, include.variable = TRUE,
                              include.max.se = TRUE,
                              include.n.high.se = TRUE, ...) {

    ##change to nicer names
    if(nice.names) {
        se.max <- x$se.max
        names(x$result)[1] <- "Variable"
        names(x$result)[2] <- "Maximum SE"
        names(x$result)[3] <- paste("Num parms with SE >", se.max, sep = " ")
    }
          

    ##format to data.frame
    x <- data.frame(x$result, check.names = FALSE)
    class(x) <- c("xtable","data.frame")
  
    ##with variable, max.se, and n.high.se
    if(include.variable && include.max.se && include.n.high.se) {
        x <- x[, c(1:3)]
        align(x) <- switch(1+is.null(align), align, c("l","r","r","r"))
        digits(x) <- switch(1+is.null(digits), digits, c(0,2,2,0))
        display(x) <- switch(1+is.null(display), display, c("s","f","f","f"))
    }

    ##with variable and max.se, but not n.high.se
    if(include.variable && include.max.se && !include.n.high.se) {
        x <- x[, c(1:2)]
        align(x) <- switch(1+is.null(align), align, c("l","r","r"))
        digits(x) <- switch(1+is.null(digits), digits, c(0,2,2))
        display(x) <- switch(1+is.null(display), display, c("s","f","f"))
    }

    ##with variable and n.high.se, but not max.se
    if(include.variable && !include.max.se && include.n.high.se) {
        x <- x[, c(1, 3)]
        align(x) <- switch(1+is.null(align), align, c("l","r","r"))
        digits(x) <- switch(1+is.null(digits), digits, c(0,2,0))
        display(x) <- switch(1+is.null(display), display, c("s","f","f"))
    }
    
    ##with n.high.se and max.se, but without variable
    if(!include.variable && include.max.se && include.n.high.se) {
        x <- x[, c(2:3)]
        align(x) <- switch(1+is.null(align), align, c("l","r","r"))
        digits(x) <- switch(1+is.null(digits), digits, c(0,2,0))
        display(x) <- switch(1+is.null(display), display, c("s","f","f"))
    }

    ##with n.high.se
    if(!include.variable && !include.max.se && include.n.high.se) {
        x <- x[, 3, drop = FALSE]
        align(x) <- switch(1+is.null(align), align, c("l","r"))
        digits(x) <- switch(1+is.null(digits), digits, c(0,0))
        display(x) <- switch(1+is.null(display), display, c("s","f"))
    }

    ##with max.se
    if(!include.variable && include.max.se && !include.n.high.se) {
        x <- x[, 2, drop = FALSE]
        align(x) <- switch(1+is.null(align), align, c("l","r"))
        digits(x) <- switch(1+is.null(digits), digits, c(0,2))
        display(x) <- switch(1+is.null(display), display, c("s","f"))
    }

    ##with variable
    if(include.variable && !include.max.se && !include.n.high.se) {
        x <- x[, 1, drop = FALSE]
        align(x) <- switch(1+is.null(align), align, c("l","r"))
        digits(x) <- switch(1+is.null(digits), digits, c(0,2))
        display(x) <- switch(1+is.null(display), display, c("s","f"))
    }

    caption(x) <- caption
    label(x) <- label
    return(x)
}



##summaryOD
xtable.summaryOD <- function(x, caption = NULL, label = NULL, align = NULL,
                             digits = NULL, display = NULL, auto = FALSE,
                             nice.names = TRUE, ...) {

    ##extract model table
    summaryOD.table <- data.frame(x$outMat, check.names = FALSE)

    ##change to nicer names
    if(nice.names) {
        if(identical(x$out.type, "interval")) {
            names(summaryOD.table)[1] <- "Estimate"
            names(summaryOD.table)[2] <- "Standard error"
            lowLab <- paste("Lower ", x$conf.level * 100, "%", " CL", sep = "")
            uppLab <- paste("Upper ", x$conf.level * 100, "%", " CL", sep = "")
            names(summaryOD.table)[3] <- lowLab
            names(summaryOD.table)[4] <- uppLab
        }
        if(identical(x$out.type, "nhst")) {
            names(summaryOD.table)[1] <- "Estimate"
            names(summaryOD.table)[2] <- "Standard error"
            names(summaryOD.table)[3] <- "Wald Z"
            names(summaryOD.table)[4] <- "P value"
        }
    }

    ##format to data.frame
    class(summaryOD.table) <- c("xtable","data.frame")

    align(summaryOD.table) <- switch(1+is.null(align), align, c("l","r","r","r", "r"))
    digits(summaryOD.table) <- switch(1+is.null(digits), digits, c(0,2,2,2,2))
    display(summaryOD.table) <- switch(1+is.null(display), display, c("s","f","f","f","f"))

    caption(summaryOD.table) <- caption
    label(summaryOD.table) <- label
    return(summaryOD.table)
}



##anovaOD
xtable.anovaOD <- function(x, caption = NULL, label = NULL, align = NULL,
                           digits = NULL, display = NULL, auto = FALSE,
                           nice.names = TRUE, ...) {

    ##extract model selection table
    anovaOD.table <- data.frame(x$devMat, check.names = FALSE)

    ##change to nicer names
    if(nice.names) {

        rownames(anovaOD.table) <- c("Model 1", "Model 2")
        names(anovaOD.table)[2] <- "log-likelihood"
        names(anovaOD.table)[3] <- "Delta K"
        names(anovaOD.table)[4] <- "-2(Delta log-likelihoods)"
        names(anovaOD.table)[6] <- "P value"
        
        if(x$c.hat == 1) {
            names(anovaOD.table)[5] <- "Chi-square"
        } else {
            names(anovaOD.table)[5] <- "F"
        }
    }

    ##format to data.frame
    class(anovaOD.table) <- c("xtable","data.frame")

    align(anovaOD.table) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r"))
    digits(anovaOD.table) <- switch(1+is.null(digits), digits, c(0,2,2,2,2,2,2))
    display(anovaOD.table) <- switch(1+is.null(display), display, c("s","d","f","d","f","f","f"))

    caption(anovaOD.table) <- caption
    label(anovaOD.table) <- label
    return(anovaOD.table)
}


##ictab
xtable.ictab <- function(x, caption = NULL, label = NULL, align = NULL,
                         digits = NULL, display = NULL, auto = FALSE,
                         nice.names = TRUE, include.IC = TRUE,
                         include.Cum.Wt = FALSE, ...) {
 
  ##change to nicer names
  if(nice.names) {
    new.delta <- names(x)[4]
    new.weight <- names(x)[6]
    names(x)[1] <- "Model"
    names(x)[2] <- "K"
    #names(x)[4] <- paste("$\\delta$", unlist(strsplit(new.delta, "_"))[2], collapse = " ") #requires sanitize.text.function( )
    names(x)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
    names(x)[6] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
    names(x)[7] <- "Cumulative weight"
  }

  #format to data.frame
  x <- data.frame(x, check.names = FALSE)
  class(x) <- c("xtable","data.frame")
  
  ##with IC but not Cum.Wt
  if(include.IC && !include.Cum.Wt) {
    x <- x[, c(1:4, 6)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    if(all(x[, 2] %% 1 == 0)) {
        display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
    } else {
        display(x) <- switch(1+is.null(display), display, c("s","s","f","f","f","f"))
    }
  }

  ##without IC and Cum.Wt
  if(!include.IC && !include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2))
    if(all(x[, 2] %% 1 == 0)) {
        display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f"))
    } else {
        display(x) <- switch(1+is.null(display), display, c("s","s","f","f","f"))
    }
  }

  ##with IC and Cum.Wt
  if(include.IC && include.Cum.Wt) {
    x <- x[, c(1:4, 6:7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2))
    if(all(x[, 2] %% 1 == 0)) {
        display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f"))
    } else {
        display(x) <- switch(1+is.null(display), display, c("s","s","f","f","f","f","f"))
    }
  }

  ##without IC, but with Cum.Wt
  if(!include.IC && include.Cum.Wt) {
    x <- x[, c(1:2, 4, 6:7)]
    align(x) <- switch(1+is.null(align), align, c("l","r","r","r","r","r"))
    digits(x) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2))
    if(all(x[, 2] %% 1 == 0)) {
        display(x) <- switch(1+is.null(display), display, c("s","s","d","f","f","f"))
    } else {
        display(x) <- switch(1+is.null(display), display, c("s","s","f","f","f","f"))
    }
  }

  caption(x) <- caption
  label(x) <- label
  return(x)
}



##modavgIC
xtable.modavgIC <- function(x, caption = NULL, label = NULL, align = NULL,
                            digits = NULL, display = NULL, auto = FALSE,
                            nice.names = TRUE, print.table = FALSE, ...) {

  if(print.table) {
    ##extract model selection table
    modavg.table <- data.frame(x$Mod.avg.table[, c(1:4, 6:8)], check.names = FALSE)

    ##change to nicer names
    if(nice.names) {
      new.delta <- names(modavg.table)[4]
      new.weight <- names(modavg.table)[5]
      names(modavg.table)[1] <- "Model"
      names(modavg.table)[2] <- "K"
      ##names(x)[4] <- paste("$\\delta$", unlist(strsplit(new.delta, "_"))[2], collapse = " ") #requires sanitize.text.function( )
      names(modavg.table)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
      names(modavg.table)[5] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
      names(modavg.table)[6] <- "Estimate"
      names(modavg.table)[7] <- "SE"
    }

    ##format to data.frame
    class(modavg.table) <- c("xtable","data.frame")

    align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r","r"))
    digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2,2))
      if(all(modavg.table$K %% 1 == 0)) {
          display(modavg.table) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f","f"))
      } else {
          display(modavg.table) <- switch(1+is.null(display), display, c("s","s","f","f","f","f","f","f"))
      }
  }  
    

    ##print model-averaged estimate, unconditional SE, CI
    if(!print.table) {
      
      ##model-averaged estimate                          
      modavg.table <- data.frame(Mod.avg.est = x$Mod.avg.est, Uncond.SE = x$Uncond.SE,
                                 Lower.CL = x$Lower.CL, Upper.CL = x$Upper.CL, check.names = FALSE)
      rownames(modavg.table) <- "Parameter"
    
      ##change to nicer names
      if(nice.names) {
        names(modavg.table)[1] <- "Model-averaged estimate" 
        names(modavg.table)[2] <- "Unconditional SE"
        names(modavg.table)[3] <- paste(100*x$Conf.level, "%", " lower limit", sep = "")
        names(modavg.table)[4] <- paste(100*x$Conf.level, "%", " upper limit", sep = "")
      }
  
      ##format to data.frame
      class(modavg.table) <- c("xtable","data.frame")

      align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
      digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,2,2,2,2))
      display(modavg.table) <- switch(1+is.null(display), display, c("s","f","f","f","f"))
    }

  caption(modavg.table) <- caption
  label(modavg.table) <- label
  return(modavg.table)
}



##modavgCustom
xtable.modavgCustom <- function(x, caption = NULL, label = NULL, align = NULL,
                                digits = NULL, display = NULL, auto = FALSE,
                                nice.names = TRUE, print.table = FALSE, ...) {

    if(print.table) {
        ##extract model selection table
        modavg.table <- data.frame(x$Mod.avg.table[, c(1:4, 6, 8:9)], check.names = FALSE)

        ##change to nicer names
        if(nice.names) {
            new.delta <- names(modavg.table)[4]
            new.weight <- names(modavg.table)[5]
            names(modavg.table)[1] <- "Model"
            names(modavg.table)[2] <- "K"
            ##names(x)[4] <- paste("$\\delta$", unlist(strsplit(new.delta, "_"))[2], collapse = " ") #requires sanitize.text.function( )
            names(modavg.table)[4] <- paste(unlist(strsplit(new.delta, "_")), collapse = " ")
            names(modavg.table)[5] <- paste(unlist(strsplit(new.weight, "Wt")), "weight", collapse = " ")
            names(modavg.table)[6] <- "Estimate"
            names(modavg.table)[7] <- "SE"
        }

        ##format to data.frame
        class(modavg.table) <- c("xtable","data.frame")
        
        align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r","r","r","r"))
        digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,0,2,2,2,2,2,2))
        display(modavg.table) <- switch(1+is.null(display), display, c("s","s","d","f","f","f","f","f"))
    }  
    

    ##print model-averaged estimate, unconditional SE, CI
    if(!print.table) {
      
        ##model-averaged estimate                          
        modavg.table <- data.frame(Mod.avg.beta = x$Mod.avg.est, Uncond.SE = x$Uncond.SE,
                                   Lower.CL = x$Lower.CL, Upper.CL = x$Upper.CL, check.names = FALSE)
        rownames(modavg.table) <- "Parameter"
    
        ##change to nicer names
        if(nice.names) {
            names(modavg.table)[1] <- "Model-averaged estimate" 
            names(modavg.table)[2] <- "Unconditional SE"
            names(modavg.table)[3] <- paste(100*x$Conf.level, "%", " lower limit", sep = "")
            names(modavg.table)[4] <- paste(100*x$Conf.level, "%", " upper limit", sep = "")
        }
  
        ##format to data.frame
        class(modavg.table) <- c("xtable","data.frame")

        align(modavg.table) <- switch(1+is.null(align), align, c("l","r","r","r","r"))
        digits(modavg.table) <- switch(1+is.null(digits), digits, c(0,2,2,2,2))
        display(modavg.table) <- switch(1+is.null(display), display, c("s","f","f","f","f"))
    }

    caption(modavg.table) <- caption
    label(modavg.table) <- label
    return(modavg.table)
}