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## Label data
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2
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3
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4
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#' @title Export label and level: one variable
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5
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#' @description Export label and level: one variable
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6
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#' @param data data
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7
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#' @param vname variable to export label and level
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8
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#' @return if continuous variable - (label, NA), categorical variable - (label, level)
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9
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#' @details DETAILS
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10
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#' @examples
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11
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#' lapply(names(iris), function(x){jstable::mk.lev.var(iris, x)})
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#' @rdname mk.lev.var
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13
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#' @export
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15
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mk.lev.var = function(data , vname){
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v.vec = data[[vname]]
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out = ""
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if (is.numeric(v.vec)){
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out = c(vname, class(v.vec), NA)
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} else{
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v.level = levels(v.vec)
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nr = length(v.level)
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out = cbind(rep(vname, nr), rep(class(v.vec), nr), v.level)
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}
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return(out)
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}
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#' @title Export label and level: multiple variable
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#' @description Export label and level: multiple variable
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32
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#' @param data data
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33
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#' @return default label and level data
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#' @details DETAILS
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35
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#' @examples
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36
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#' mk.lev(iris)
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37
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#' @rdname mk.lev
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#' @export
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#' @importFrom data.table data.table :=
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41
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mk.lev = function(data){
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variable <- level <- val_label <- NULL
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44
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out.list = lapply(names(data), function(x){mk.lev.var(data, x)})
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out.dt = data.table::data.table(Reduce(rbind, out.list))
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names(out.dt) = c("variable", "class","level")
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48
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out.dt[, var_label := variable]
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out.dt[, val_label := level]
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return(out.dt[])
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}
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#' @title LabelepiDisplay: Apply label information to epiDisplay object using label data
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#' @description Apply label information to epiDisplay.object using label data
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#' @param epiDisplay.obj epiDisplay.object or glmshow.object
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#' @param label Apply label information, Default: F
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#' @param ref Label data made by mk.lev function
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#' @return epiDisplay.object with label information
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#' @details DETAILS
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#' @examples
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66
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#' fit <- glm(Sepal.Length ~ Sepal.Width + Species, data = iris)
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67
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#' fit.table <- glmshow.display(fit)
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68
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#' iris.label <- mk.lev(iris)
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#' LabelepiDisplay(fit.table, label = TRUE, ref = iris.label)
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#' @rdname LabelepiDisplay
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#' @export
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#' @importFrom data.table data.table :=
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73
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74
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75
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LabelepiDisplay = function(epiDisplay.obj, label = F, ref){
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lv2 <- variable <- level <- val_label <- NULL
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79
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tb.main <- epiDisplay.obj$table
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tb.compact <- tb.main[!rownames(tb.main)=="", ]
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if (nrow(tb.main) <= 2){
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tb.compact <- tb.main
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}
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85
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86
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## Var label
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87
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tb.rn = gsub(" \\(cont. var.\\)", "", rownames(tb.compact))
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rownames(tb.compact) <- tb.rn
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if (nrow(tb.main) < 2 & label == T){
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vname <- strsplit(rownames(tb.compact)[1], ":")[[1]][1]
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cond.lv2 <- grepl(":", rownames(tb.compact)[1]) & grepl("vs", rownames(tb.compact)[1])
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rownames(tb.compact) <- gsub(vname, ref[variable == vname, var_label][1], rownames(tb.compact))
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if (cond.lv2){
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vll <- ref[variable == vname & level %in% lv2, c("level", "val_label")]
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rownames(tb.compact) <- gsub(paste(vll[level == lv2[1], level], " vs ", vll[level == lv2[2], level], sep=""), paste(vll[level == lv2[1], val_label], " vs ", vll[level == lv2[2], val_label], sep=""), rownames(tb.compact))
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}
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}
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if (nrow(tb.main) > 2 & label == T){
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vn <- which(substr(tb.rn, 1, 1) != " ")
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102
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vns <- c(vn, length(tb.rn)+1 )
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103
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vl <- lapply(1:length(vn), function(x){tb.rn[vns[x]:(vns[x+1]-1)]})
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vl_label <- lapply(vl, function(x){
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105
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vname <- strsplit(x[1], ":")[[1]][1]
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106
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1
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cond.lv2 <- grepl(":", x[1]) & grepl("vs", x[1])
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107
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#x[1] <- gsub(vname, ref[variable == vname, var_label][1], x[1])
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108
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1
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if (cond.lv2){
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109
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0
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lv2 <- strsplit(strsplit(x[1], ": ")[[1]][[2]], " vs ")[[1]]
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110
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0
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vll <- ref[variable == vname & level %in% lv2, c("level", "val_label")]
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111
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0
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x <- paste(ref[variable == vname, var_label][1], ": ", vll[level == lv2[1], val_label], " vs ", vll[level == lv2[2], val_label], sep = "")
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112
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#x = gsub(paste(vll[2, 1], " vs ", vll[1,1], sep=""), paste(vll[2, 2], " vs ", vll[1,2], sep=""), x)
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113
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1
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} else if (ref[variable == vname, class][1] %in% c("factor", "character")){
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114
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x[1] <- paste(ref[variable == vname, var_label][1], ": ref.=", ref[variable == vname & level == strsplit(x[1], "\\.\\=")[[1]][2], val_label], sep = "")
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115
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1
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for (k in 2:length(x)){
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116
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1
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x[k] <- paste(" ", ref[variable == vname & level == strsplit(x[k], " ")[[1]][2], val_label], sep = "")
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117
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}
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118
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119
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#for (y in ref[variable == vname, level]) {x = gsub(y, ref[variable == vname & level == y, val_label], x)}
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120
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}
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121
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1
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return(x)
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122
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})
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123
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1
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rownames(tb.compact) <- unlist(vl_label)
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124
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}
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125
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126
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1
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ll <- strsplit(epiDisplay.obj$last.lines,"\n")[[1]]
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127
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1
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ll.vec <- matrix(unlist(lapply(ll,function(x){strsplit(x," = ")})), ncol =2, byrow=T)
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128
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1
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ll.mat <- matrix(rep("", nrow(ll.vec)* ncol(tb.compact)), nrow = nrow(ll.vec))
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129
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1
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ll.mat[,1] = ll.vec[,2]
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130
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1
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rownames(ll.mat) <- ll.vec[,1]
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131
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1
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out <- rbind(tb.compact, rep("", ncol(tb.compact)), ll.mat)
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132
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133
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1
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if (nrow(tb.main) == 2){
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134
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0
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out <- rbind(tb.compact, ll.mat)
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135
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}
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136
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137
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1
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p.colnum <- which(colnames(out) %in% c("P value", "adj. P value", "P(t-test)", "P(Wald's test)"))
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138
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1
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p.colnum <- p.colnum[length(p.colnum)]
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139
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140
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1
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pn <- gsub("< ","", out[, p.colnum])
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141
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142
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1
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colnames(out)[p.colnum] <- ifelse(colnames(out)[p.colnum] == "P value", "P value", "adj. P value")
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143
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1
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sig <- ifelse(as.numeric(pn) <= 0.05, "**", "")
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144
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1
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return(cbind(out,sig))
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145
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}
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146
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147
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148
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149
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150
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151
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#' @title LabeljsTable: Apply label information to jstable object using label data
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152
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#' @description Apply label information to table of geeglm.display, lmer.display, coxme.display using label data
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153
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#' @param obj.table table of geeglm.display, lmer.display, coxme.display
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154
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#' @param ref Label data made by mk.lev function
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155
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#' @return table of geeglm.display, lmer.display, coxme.display with label information
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156
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#' @details DETAILS
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157
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#' @examples
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|
158
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#' library(coxme)
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159
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#' fit <- coxme(Surv(time, status) ~ sex + ph.ecog + ph.karno + (1|inst) +(1|sex), lung)
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160
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#' fit.table <- coxme.display(fit)
|
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161
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#' lung.label <- mk.lev(lung)
|
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162
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#' LabeljsTable(fit.table$table, ref = lung.label)
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163
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#' @rdname LabeljsTable
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164
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#' @export
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|
165
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#' @importFrom data.table data.table :=
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166
|
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|
|
167
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LabeljsTable = function(obj.table, ref){
|
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168
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|
169
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1
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lv2 <- variable <- level <- val_label <- NULL
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|
170
|
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|
171
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1
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tb.main <- obj.table
|
|
172
|
1
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tb.compact <- tb.main
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|
173
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|
174
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## Var label
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|
175
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1
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tb.rn <- rownames(tb.compact)
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176
|
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177
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1
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if (nrow(tb.main) == 1){
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178
|
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|
179
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0
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vname <- strsplit(rownames(tb.compact)[1], ":")[[1]][1]
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180
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0
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cond.lv2 <- grepl(":", rownames(tb.compact)[1]) & grepl("vs", rownames(tb.compact)[1])
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181
|
0
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rownames(tb.compact) <- gsub(vname, ref[variable == vname, var_label][1], rownames(tb.compact))
|
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182
|
0
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if (cond.lv2){
|
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183
|
0
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vll <- ref[variable == vname & level %in% lv2, c("level", "val_label")]
|
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184
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0
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rownames(tb.compact) <- gsub(paste(vll[level == lv2[1], level], " vs ", vll[level == lv2[2], level], sep=""), paste(vll[level == lv2[1], val_label], " vs ", vll[level == lv2[2], val_label], sep=""), rownames(tb.compact))
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|
185
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|
}
|
|
186
|
|
|
|
187
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}
|
|
188
|
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|
|
189
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1
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if (nrow(tb.main) > 1){
|
|
190
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1
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vn <- which(substr(tb.rn, 1, 1) != " ")
|
|
191
|
1
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vns <- c(vn, length(tb.rn)+1 )
|
|
192
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1
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vl <- lapply(1:length(vn), function(x){tb.rn[vns[x]:(vns[x+1]-1)]})
|
|
193
|
1
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vl_label = lapply(vl, function(x){
|
|
194
|
1
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vname <- strsplit(x[1], ":")[[1]][1]
|
|
195
|
1
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x[1] <- gsub(vname, ref[variable == vname, var_label][1], x[1])
|
|
196
|
1
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cond.lv2 <- grepl(":", x[1]) & grepl("vs", x[1])
|
|
197
|
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#x[1] <- gsub(vname, ref[variable == vname, var_label][1], x[1])
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198
|
1
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if (cond.lv2){
|
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199
|
0
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lv2 <- strsplit(strsplit(x[1], ": ")[[1]][[2]], " vs ")[[1]]
|
|
200
|
0
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vll <- ref[variable == vname & level %in% lv2, c("level", "val_label")]
|
|
201
|
0
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x <- paste(ref[variable == vname, var_label][1], ": ", vll[level == lv2[1], val_label], " vs ", vll[level == lv2[2], val_label], sep = "")
|
|
202
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#x = gsub(paste(vll[2, 1], " vs ", vll[1,1], sep=""), paste(vll[2, 2], " vs ", vll[1,2], sep=""), x)
|
|
203
|
1
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} else if (ref[variable == vname, class][1] %in% c("factor", "character")){
|
|
204
|
1
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x[1] <- paste(ref[variable == vname, var_label][1], ": ref.=", ref[variable == vname & level == strsplit(x[1], "\\.\\=")[[1]][2], val_label], sep = "")
|
|
205
|
1
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for (k in 2:length(x)){
|
|
206
|
1
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x[k] <- paste(" ", ref[variable == vname & level == strsplit(x[k], " ")[[1]][2], val_label], sep = "")
|
|
207
|
|
}
|
|
208
|
|
|
|
209
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|
#for (y in ref[variable == vname, level]) {x = gsub(y, ref[variable == vname & level == y, val_label], x)}
|
|
210
|
|
}
|
|
211
|
1
|
return(x)
|
|
212
|
|
})
|
|
213
|
1
|
rownames(tb.compact) = unlist(vl_label)
|
|
214
|
|
}
|
|
215
|
|
|
|
216
|
1
|
out <- tb.compact
|
|
217
|
|
#sig.colnum = which(colnames(out) %in% c("P value", "adj. P value"))
|
|
218
|
|
#pn = gsub("< ","", out[, sig.colnum])
|
|
219
|
|
#sig = ifelse(as.numeric(pn) <= 0.05, "**", "")
|
|
220
|
|
|
|
221
|
|
#pv.colnum = which(colnames(out) %in% c("P value", "crude P value", "adj. P value"))
|
|
222
|
|
#for (i in pv.colnum){
|
|
223
|
|
# out[, i] = ifelse(as.numeric(out[, i]) < 0.001, "< 0.001", round(as.numeric(out[, i]), 3))
|
|
224
|
|
#}
|
|
225
|
1
|
return(out)
|
|
226
|
|
}
|
|
227
|
|
|
|
228
|
|
|
|
229
|
|
|
|
230
|
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|
|
231
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|
#' @title LabeljsRanef: Apply label information to jstable random effect object using label data
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|
232
|
|
#' @description Apply label information to ranef object of jstable using label data
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|
233
|
|
#' @param obj.ranef ranef of lmer.display, coxme.display, cox2.display
|
|
234
|
|
#' @param ref Label data made by mk.lev function
|
|
235
|
|
#' @return ranef of lmer.display, coxme.display, cox2.display with label information
|
|
236
|
|
#' @details DETAILS
|
|
237
|
|
#' @examples
|
|
238
|
|
#' library(coxme)
|
|
239
|
|
#' fit <- coxme(Surv(time, status) ~ sex + ph.ecog + ph.karno + (1|inst) +(1|sex), lung)
|
|
240
|
|
#' fit.table <- coxme.display(fit)
|
|
241
|
|
#' lung.label <- mk.lev(lung)
|
|
242
|
|
#' LabeljsTable(fit.table$table, ref = lung.label)
|
|
243
|
|
#' LabeljsRanef(fit.table$ranef, ref = lung.label)
|
|
244
|
|
#' @rdname LabeljsRanef
|
|
245
|
|
#' @export
|
|
246
|
|
|
|
247
|
|
LabeljsRanef = function(obj.ranef, ref){
|
|
248
|
|
|
|
249
|
1
|
variable <- NULL
|
|
250
|
|
|
|
251
|
1
|
ranef <- obj.ranef
|
|
252
|
1
|
ranef.split <- strsplit(rownames(ranef)[-1], "\\(")
|
|
253
|
1
|
ranef.vname <- unlist(lapply(ranef.split, function(x){x[[1]]}))
|
|
254
|
1
|
ranef.vname.label <- sapply(ranef.vname, function(x){ref[variable == x, var_label][1]})
|
|
255
|
1
|
if (length(ranef.split) ==1){
|
|
256
|
1
|
rownames(ranef)[-1] <- ranef.vname.label
|
|
257
|
|
} else{
|
|
258
|
1
|
rownames(ranef)[-1] <- paste(ranef.vname.label, "(", unlist(lapply(ranef.split, function(x){x[[2]]})), sep="")
|
|
259
|
|
}
|
|
260
|
1
|
return(ranef)
|
|
261
|
|
}
|
|
262
|
|
|
|
263
|
|
|
|
264
|
|
|
|
265
|
|
|
|
266
|
|
#' @title LabeljsMetric: Apply label information to jstable metric object using label data
|
|
267
|
|
#' @description Apply label information to metric object of jstable using label data
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#' @param obj.metric metric of lmer.display, coxme.display
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#' @param ref Label data made by mk.lev function
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#' @return metric of lmer.display, coxme.display with label information
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#' @details DETAILS
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#' @examples
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#' library(coxme)
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#' fit <- coxme(Surv(time, status) ~ sex + ph.ecog + ph.karno + (1|inst) +(1|sex), lung)
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#' fit.table <- coxme.display(fit)
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#' lung.label <- mk.lev(lung)
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#' LabeljsTable(fit.table$table, ref = lung.label)
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#' LabeljsRanef(fit.table$ranef, ref = lung.label)
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#' LabeljsMetric(fit.table$metric, ref = lung.label)
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#' @rdname LabeljsMetric
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#' @export
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LabeljsMetric = function(obj.metric, ref){
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variable <- NULL
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metric <- obj.metric
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rname <- rownames(metric)
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group.rnum <- grep("No. of group", rname)
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group.vars <- unlist(lapply(strsplit(rname[group.rnum], "\\("), function(x){x[[2]]}))
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group.vname <- unlist(strsplit(group.vars, "\\)"))
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group.vname.label <- sapply(group.vname, function(x){ref[variable == x, var_label][1]})
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rownames(metric)[group.rnum] <- paste("No. of group(", group.vname.label, ")", sep="")
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return(metric)
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}
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#' @title LabeljsMixed: Apply label information to jstable object using label data
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#' @description Apply label information to object of jstable using label data
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#' @param obj lmer.display, coxme.display
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#' @param ref Label data made by mk.lev function
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#' @return lmer.display, coxme.display with label information
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#' @details DETAILS
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#' @examples
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#' library(coxme)
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#' fit <- coxme(Surv(time, status) ~ sex + ph.ecog + ph.karno + (1|inst) +(1|sex), lung)
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#' fit.table <- coxme.display(fit)
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#' lung.label <- mk.lev(lung)
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#' LabeljsMixed(fit.table, ref = lung.label)
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#' @rdname LabeljsMixed
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#' @export
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LabeljsMixed = function(obj, ref){
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variable <- NULL
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out <- list()
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out$table <- LabeljsTable(obj$table, ref = ref)
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out$ranef <- LabeljsRanef(obj$ranef, ref = ref)
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out$metric <- LabeljsMetric(obj$metric, ref = ref)
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out$caption <- obj$caption
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if (grep("Mixed effects Cox model", obj$caption) == 1){
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surv.vname <- strsplit(obj$caption, "'")[[1]][c(2,4)]
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for (vn in surv.vname){
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out$caption <- gsub(paste("'", vn, "'", sep = ""), paste("'", ref[variable == vn, var_label][1], "'", sep = ""), out$caption)
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}
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group.vname.comma <- strsplit(obj$caption, "- Group ")[[1]][2]
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group.vname <- strsplit(group.vname.comma, ", ")[[1]]
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group.vname.label <- sapply(group.vname, function(x){ref[variable == x, var_label][1]})
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out$caption <- gsub(group.vname.comma, paste(group.vname.label, collapse = ", "), out$caption)
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}
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return(out)
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}
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#' @title LabeljsCox: Apply label information to cox2.display object using label data
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#' @description Apply label information to cox2.display object using label data
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#' @param obj cox2.display object
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#' @param ref Label data made by mk.lev function
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#' @return cox2.display object with label information
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#' @details DETAILS
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#' @examples
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#' library(survival)
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348
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#' fit <- coxph(Surv(time, status) ~ sex + ph.ecog + ph.karno + cluster(inst),
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349
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#' data = lung, model = TRUE)
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350
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#' fit.table <- cox2.display(fit)
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351
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#' lung.label <- mk.lev(lung)
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#' LabeljsCox(fit.table, ref = lung.label)
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353
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#' @rdname LabeljsCox
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354
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#' @export
|
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355
|
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356
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LabeljsCox = function(obj, ref){
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357
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358
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1
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variable <- NULL
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359
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360
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1
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out <- list()
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361
|
1
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out$table <- LabeljsTable(obj$table, ref = ref)
|
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362
|
1
|
if (!is.null(obj$ranef)){
|
|
363
|
1
|
out$ranef <- LabeljsRanef(obj$ranef, ref = ref)
|
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364
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|
}
|
|
365
|
1
|
out$metric <- obj$metric
|
|
366
|
1
|
out$caption <- obj$caption
|
|
367
|
1
|
surv.vname <- strsplit(obj$caption, "'")[[1]][c(2,4)]
|
|
368
|
1
|
for (vn in surv.vname){
|
|
369
|
1
|
out$caption <- gsub(paste("'", vn, "'", sep = ""), paste("'", ref[variable == vn, var_label][1], "'", sep = ""), out$caption)
|
|
370
|
|
}
|
|
371
|
1
|
if (length(grep("- Group", obj$caption)) >= 1){
|
|
372
|
1
|
group.vname.comma <- strsplit(obj$caption, "- Group ")[[1]][2]
|
|
373
|
1
|
group.vname <- strsplit(group.vname.comma, ", ")[[1]]
|
|
374
|
1
|
group.vname.label <- sapply(group.vname, function(x){ref[variable == x, var_label][1]})
|
|
375
|
1
|
out$caption <- gsub(group.vname.comma, paste(group.vname.label, collapse = ", "), out$caption)
|
|
376
|
|
}
|
|
377
|
|
|
|
378
|
1
|
return(out)
|
|
379
|
|
}
|
|
380
|
|
|
|
381
|
|
|
|
382
|
|
|
|
383
|
|
|
|
384
|
|
#' @title LabeljsGeeglm: Apply label information to geeglm.display object using label data
|
|
385
|
|
#' @description Apply label information to geeglm.display object using label data
|
|
386
|
|
#' @param obj geeglm.display object
|
|
387
|
|
#' @param ref Label data made by mk.lev function
|
|
388
|
|
#' @return geeglm.display object with label information
|
|
389
|
|
#' @details DETAILS
|
|
390
|
|
#' @examples
|
|
391
|
|
#' library(geepack);library(jstable)
|
|
392
|
|
#' data(dietox)
|
|
393
|
|
#' dietox$Cu <- as.factor(dietox$Cu)
|
|
394
|
|
#' gee01 <- geeglm (Weight ~ Time + Cu , id =Pig, data = dietox,
|
|
395
|
|
#' family=gaussian,corstr="ex")
|
|
396
|
|
#' g1 <- geeglm.display(gee01)
|
|
397
|
|
#' LabeljsGeeglm(g1, ref = mk.lev(dietox))
|
|
398
|
|
#' @rdname LabeljsGeeglm
|
|
399
|
|
#' @export
|
|
400
|
|
|
|
401
|
|
LabeljsGeeglm = function(obj, ref){
|
|
402
|
|
|
|
403
|
1
|
variable <- NULL
|
|
404
|
|
|
|
405
|
1
|
out <- list()
|
|
406
|
1
|
out$table <- LabeljsTable(obj$table, ref = ref)
|
|
407
|
1
|
out$metric <- obj$metric
|
|
408
|
1
|
out$caption <- obj$caption
|
|
409
|
1
|
cap.split <- strsplit(obj$caption, "predicting ")[[1]]
|
|
410
|
1
|
yxc <- cap.split[2]
|
|
411
|
1
|
yxc1 <- strsplit(yxc, " by ")[[1]]
|
|
412
|
1
|
y <- yxc1[1]
|
|
413
|
1
|
x <- strsplit(yxc1[2], " - Group ")[[1]]
|
|
414
|
1
|
xx <- strsplit(x[1], ", ")[[1]]
|
|
415
|
1
|
xc <- x[2]
|
|
416
|
1
|
out$caption <- paste(cap.split[1], "predicting ", ref[variable == y, var_label][1], " by ", paste(sapply(xx, function(vn){ref[variable == vn, var_label][1]}), collapse = ", "), " - Group ", ref[variable == xc, var_label][1], sep="")
|
|
417
|
|
|
|
418
|
1
|
return(out)
|
|
419
|
|
}
|
|
420
|
|
|
|
421
|
|
|
jinseob2kim