function (content, measure, year, pmid, sortby, lefthand, righthand,
type, cofactorlabel, topic, theme)
{
temp <- content
temp <- gsub("\n", "", fixed = TRUE, temp, perl = TRUE)
temp <- gsub("\t", " ", fixed = TRUE, temp)
temp <- gsub(",", "\",\"", fixed = TRUE, temp)
temp <- paste("\"", temp, "\"", sep = "")
temp <- paste("Mymatrix <- matrix(c(", temp, "), ncol=8, byrow=TRUE, dimnames = list(NULL, c(\"Study\",\"year\", \"pmid\", \"TP\", \"FP\",\"FN\",\"TN\",\"cofactor\")))")
x <- eval(parse(file = "", n = NULL, text = temp))
myframe <- data.frame(x)
myframe$Study <- gsub("'", "", fixed = TRUE, myframe$Study)
myframe$Study <- as.character(str_trim(myframe$Study))
myframe$year <- as.numeric(as.character(str_trim(myframe$year)))
myframe$pmid <- as.numeric(as.character(str_trim(myframe$pmid)))
myframe$TP <- as.numeric(as.character(str_trim(myframe$TP)))
myframe$FP <- as.numeric(as.character(str_trim(myframe$FP)))
myframe$FN <- as.numeric(as.character(str_trim(myframe$FN)))
myframe$TN <- as.numeric(as.character(str_trim(myframe$TN)))
myframe$studysize <- (myframe$TP + myframe$FP + myframe$FN +
myframe$TN)
myframe$prevalence <- (myframe$TP + myframe$FN)/myframe$studysize
myframe$withoutcome <- (myframe$TP + myframe$FN)
myframe$sensitivity <- myframe$TP/(myframe$TP + myframe$FN)
myframe$specificity <- myframe$TN/(myframe$FP + myframe$TN)
myframe$dor <- (myframe$TP/myframe$FP)/(myframe$FN/myframe$TN)
msg = ""
if (sortby == "study") {
sortvalue <- myframe$Study
}
if (sortby == "year") {
sortvalue <- myframe$year
}
if (sortby == "prevalence") {
sortvalue <- myframe$prevalence
}
if (sortby == "sensitivity") {
sortvalue <- myframe$sensitivity
}
if (sortby == "specificity") {
sortvalue <- myframe$specificity
}
if (sortby == "cofactor") {
sortvalue <- myframe$cofactor
}
if (sortby == "studysize") {
sortvalue <- myframe$studysize
}
if (sortby == "weight") {
sortvalue <- myframe$weight
}
myframe <- myframe[order(sortvalue), ]
attach(myframe)
KUBlue = "#0022B4"
SkyBlue = "#6DC6E7"
pubbiastext = "Test for funnel plot asymmetry"
analyticmethod = "Hierarchical model (bivariate)"
msg = ""
meta1 <- madad(TP = TP, FN = FN, TN = TN, FP = FP, names = Study,
data = myframe, correction = 0.5, correction.control = "all")
height = 295 + length(myframe$Study) * 20
svgtext = paste("<?xml version=\"1.0\" encoding=\"UTF-8\"?><svg x=\"0\" y=\"0\" width=\"800px\" height=\"",
height, "px\" viewBox=\"0 0 800 ", height, "\" style=\"font-family:Arial, Helvetica, sans-serif\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">",
sep = "")
svgtext = paste(svgtext, "<text x=\"10\" y=\"20\" style=\"font-weight:bold;font-size: 1.17em\">",
topic, "</text>", sep = "")
svgtext = paste(svgtext, "<!-- Header of plot--><text x=\"10\" y=\"45\" fill=\"black\" style=\"font-weight:bold\">Study</text><text x=\"200\" y=\"45\" fill=\"black\" style=\"font-weight:bold\">Prev. (%)</text><text x=\"325\" y=\"45\" fill=\"black\" style=\"font-weight:bold\">Sensitivity (%)</text><text x=\"550\" y=\"45\" fill=\"black\" style=\"font-weight:bold\">Specificity (%)</text><text x=\"700\" y=\"45\" fill=\"black\" style=\"font-weight:bold\"><!--DOR--></text><!-- Start of studies-->",
sep = "")
for (i in 1:length(myframe$Study)) {
svgtext = paste(svgtext, "<a xlink:href=\"http://pubmed.gov/",
myframe$pmid[i], "\" xlink:title=\"Study size is ",
myframe$studysize[i], ". Prevalence of the outcome is ",
round(myframe$prevalence[i] * 100, 0), "%. Click citation to open abstract at PubMed in a new window.\" target=\"_blank\"><text x=\"10\" y=\"",
45 + i * 20, "\" fill=\"rgba(0,0,255,1)\">", myframe$Study[i],
", ", myframe$year[i], "</text></a>", sep = "")
svgtext = paste(svgtext, "<text x=\"230\" y=\"", 45 +
i * 20, "\" fill=\"black\" style=\"font-weight:normal\">",
round(myframe$prevalence[i] * 100, 0), "</text>",
sep = "")
x = 375 + 100 * meta1$sens[[1]][i]
svgtext = paste(svgtext, "<text x=\"275\" y=\"", 45 +
i * 20, "\" fill=\"black\" style=\"font-weight:normal\">",
round(meta1$sens[[1]][i] * 100, 0), " (", round(meta1$sens$sens.ci[i,
1] * 100, 0), " - ", round(meta1$sens$sens.ci[i,
2] * 100, 0), ")</text>", sep = "")
svgtext = paste(svgtext, "<circle cx=\"", x, "\" cy=\"",
40 + i * 20, "\" r=\"3\" stroke-width=\"0\" style=\"fill:black;\"/>",
sep = "")
cl.lower = 375 + 100 * meta1$sens$sens.ci[i, 1]
ci.upper = 375 + 100 * meta1$sens$sens.ci[i, 2]
svgtext = paste(svgtext, "<line x1=\"", cl.lower, "\" y1=\"",
40 + i * 20, "\" x2=\"", ci.upper, "\" y2=\"", 40 +
i * 20, "\" style=\"stroke:rgba(0,0,0,1);stroke-width:2\" />",
sep = "")
x = 600 + 100 * meta1$spec[[1]][i]
svgtext = paste(svgtext, "<text x=\"500\" y=\"", 45 +
i * 20, "\" fill=\"black\" style=\"font-weight:normal\">",
round(meta1$spec[[1]][i] * 100, 0), " (", round(meta1$spec$spec.ci[i,
1] * 100, 0), " - ", round(meta1$spec$spec.ci[i,
2] * 100, 0), ")</text>", sep = "")
svgtext = paste(svgtext, "<circle cx=\"", x, "\" cy=\"",
40 + i * 20, "\" r=\"3\" stroke-width=\"0\" style=\"fill:black;\"/>",
sep = "")
cl.lower = 600 + 100 * meta1$spec$spec.ci[i, 1]
ci.upper = 600 + 100 * meta1$spec$spec.ci[i, 2]
svgtext = paste(svgtext, "<line x1=\"", cl.lower, "\" y1=\"",
40 + i * 20, "\" x2=\"", ci.upper, "\" y2=\"", 40 +
i * 20, "\" style=\"stroke:rgba(0,0,0,1);stroke-width:2\" />",
sep = "")
}
svgtext = paste(svgtext, "<!-- Bottom of plot--><!-- Axes --><g style=\"stroke:rgba(0,0,0,0.2);stroke-width:2\">",
sep = "")
svgtext = paste(svgtext, "<line x1=\"375\" y1=\"", 55 + i *
20, "\" x2=\"475\" y2=\"", 55 + i * 20, "\" />", sep = "")
svgtext = paste(svgtext, "<line x1=\"600\" y1=\"", 55 + i *
20, "\" x2=\"700\" y2=\"", 55 + i * 20, "\" /></g>",
sep = "")
svgtext = paste(svgtext, "<!-- Ticks -->", sep = "")
svgtext = paste(svgtext, "<g stroke=\"rgba(0,0,0,0.2)\" stroke-width=\"1\" fill=\"rgba(0,0,0,0.2)\">",
sep = "")
svgtext = paste(svgtext, "<g transform=\"translate(475,",
55 + i * 20, ") rotate(180)\"><path d=\"M 0,0 L 0,5 M 50,0 L 50,5 M 100,0 L 100,5\" /></g>",
sep = "")
svgtext = paste(svgtext, "<g transform=\"translate(700,",
55 + i * 20, ") rotate(180)\"><path d=\"M 0,0 L 0,5 M 50,0 L 50,5 M 100,0 L 100,5\" /></g></g>",
sep = "")
if (type == "ignore") {
meta2 <- fit.bivar(TP = TP, FN = FN, TN = TN, FP = FP,
study = Study, data = myframe)
meta2 <- summary(meta2$bi.simple)
sensitivity = c(meta2$coefficients[1, 1], meta2$coefficients[1,
1] - qnorm(0.975) * meta2$coefficients[1, 2], meta2$coefficients[1,
1] + qnorm(0.975) * meta2$coefficients[1, 2])
sensitivity = plogis(sensitivity)
sensitivity = round(100 * sensitivity, 1)
specificity = c(meta2$coefficients[2, 1], meta2$coefficients[2,
1] - qnorm(0.975) * meta2$coefficients[2, 2], meta2$coefficients[2,
1] + qnorm(0.975) * meta2$coefficients[2, 2])
specificity = plogis(specificity)
specificity = round(100 * specificity, 1)
meta2 <- perfect.trees(TP = TP, FN = FN, TN = TN, FP = FP,
study = Study, data = myframe)
svgtext = paste(svgtext, "<!-- Vertical summary lines -->",
sep = "")
svgtext = paste(svgtext, "<g style=\"stroke:rgba(0,0,0,0.2);stroke-width:2\" ><line x1=\"",
375 + sensitivity[1], "\" y1=\"55\" x2=\"", 375 +
sensitivity[1], "\" y2=\"", 55 + i * 20, "\" />",
sep = "")
svgtext = paste(svgtext, "<line x1=\"", 600 + specificity[1],
"\" y1=\"55\" x2=\"", 600 + specificity[1], "\" y2=\"",
55 + i * 20, "\"/></g>", sep = "")
svgtext = paste(svgtext, "<!-- Summary text --><g fill=\"black\" style=\"color:black;opacity:1\"><text x=\"10\" y=\"",
70 + i * 20, "\" style=\"font-weight:bold\">Summary</text>",
sep = "")
pooledprevalence = (sum(TP) + sum(FN))/sum(studysize)
svgtext = paste(svgtext, "<text x=\"230\" y=\"", 70 +
i * 20, "\" fill=\"black\" style=\"font-weight:bold\">",
round(pooledprevalence * 100, 0), "</text>", sep = "")
svgtext = paste(svgtext, "<text x=\"275\" y=\"", 70 +
i * 20, "\" fill=\"black\" style=\"font-weight:bold\">",
round(sensitivity[1], 0), " (", round(sensitivity[2],
0), " - ", round(sensitivity[3], 0), ")</text>",
sep = "")
svgtext = paste(svgtext, "<text x=\"", 375 + -10 + round(sensitivity[1],
0), "\" y=\"", 70 + i * 20, "\" fill=\"black\" style=\"font-weight:bold\">",
round(sensitivity[1], 0), "</text>", sep = "")
svgtext = paste(svgtext, "<text x=\"500\" y=\"", 70 +
i * 20, "\" fill=\"black\" style=\"font-weight:bold\">",
round(specificity[1], 0), " (", round(specificity[2],
0), " - ", round(specificity[3], 0), ")</text>",
sep = "")
svgtext = paste(svgtext, "<text x=\"", 600 + -10 + round(specificity[1],
0), "\" y=\"", 70 + i * 20, "\" fill=\"black\" style=\"font-weight:bold\">",
round(specificity[1], 0), "</text>", sep = "")
LRpos = meta2$coef[[2]][1]/(1 - meta2$coef[[3]][1])
LRneg = (1 - meta2$coef[[2]][1])/meta2$coef[[3]][1]
auc <- AUC(phm(myframe))
svgtext = paste(svgtext, "<text x=\"10\" y=\"", 125 +
i * 20, "\" style=\"font-weight:bold\">Area under the ROC curve: ",
round(auc$AUC[[1]][1], 3), "</text>", sep = "")
meta3 <- madauni(myframe, correction = 0.5, correction.control = "all")
I2 <- summary(meta3)$Isq
svgtext = paste(svgtext, "<text x=\"10\" y=\"", 145 +
i * 20, "\" style=\"font-weight:bold\">Heterogeneity: ",
round(I2, 1), "%</text>", sep = "")
svgtext = paste(svgtext, "<text x=\"10\" y=\"", 160 +
i * 20, "\" style=\"font-weight:normal\">(For diagnostic odds ratio: Q = ",
round(meta3$CQ["Q"], 1), ", DF = ", meta3$CQ["df"],
")</text>", sep = "")
svgtext = paste(svgtext, "<text x=\"10\" y=\"", 180 +
i * 20, "\" style=\"font-weight:bold\">Predictive values:</text>",
sep = "")
PreTestOdds = pooledprevalence/(1 - pooledprevalence)
PostTestOdds = PreTestOdds * LRpos
ppv = sprintf("%.1f", (PostTestOdds/(1 + PostTestOdds) *
100))
PostTestOdds = PreTestOdds * LRneg
npv = PostTestOdds/(1 + PostTestOdds)
npv = sprintf("%.1f", (npv * 100))
svgtext = paste(svgtext, "<text x=\"10\" y=\"", 200 +
i * 20, "\">At the prevalences studied (mean ", round(pooledprevalence *
100, 0), "%, median ", round(median(prevalence *
100, ), 0), "%, range ", round(min(prevalence * 100),
0), " - ", round(max(prevalence * 100), 0), ", odds ",
round(PreTestOdds, 2), "):</text>", sep = "")
svgtext = paste(svgtext, "<text x=\"20\" y=\"", 215 +
i * 20, "\">Positive ", ppv, "%; negative ", 100 -
as.numeric(npv), "%; 1- negative ", npv, "%</text>",
sep = "")
svgtext = paste(svgtext, "<a xlink:href=\"http://sumsearch.org/calc/calc.aspx?calc_dx_SnSp.aspx?prevalence=",
round(pooledprevalence * 100, 0), "&sensitivity=",
round(meta2$coefficients[[2]][1] * 100, 0), "&specificity=",
round(meta2$coefficients[[3]][1] * 100, 0), "\" xlink:title=\"Adjust prevalence and recalculate predictive values\" target=\"_blank\"><text x=\"20\" y=\"",
230 + i * 20, "\" fill=\"rgba(0,0,255,1)\" style=\"font-weight:normal;text-decoration:underline;\">Click here to recalculate predictive values at other prevalences</text></a>",
sep = "")
svgtext = paste(svgtext, "<!-- About the studies --><text x=\"10\" y=\"",
255 + i * 20, "\" style=\"font-weight:bold\">About the studies:</text>",
sep = "")
svgtext = paste(svgtext, "<text x=\"10\" y=\"", 275 +
i * 20, "\">", prettyNum(sum(studysize), big.mark = ","),
" persons (median ", prettyNum(median(studysize),
big.mark = ","), ", range ", min(studysize),
" - ", max(studysize), ") in ", length(myframe$Study),
" studies.</text>", sep = "")
svgtext = paste(svgtext, "<text x=\"10\" y=\"", 290 +
i * 20, "\">", prettyNum(sum(withoutcome), big.mark = ","),
" persons with the outcome (median ", prettyNum(round(median(withoutcome,
0)), big.mark = ","), ", range ", min(withoutcome),
" - ", max(withoutcome), ").</text>", sep = "")
}
svgtext = paste(svgtext, "</g>", sep = "")
if (type == "subgroup") {
msg = "Under construction (s)"
}
if (type == "metaregression (m)") {
msg = "Under construction"
}
svgtext = paste(svgtext, "Sorry, your browser does not support inline SVG for dynamic graphics.</svg>")
msg = svgtext
msg = paste(msg, "<table style=\"background-color:#CFCFCF\" border=\"0\"><tbody><tr><td><a class=\"selectall\" href=\"javascript:document.getElementById('svgfile').select()\">Select source code for graphics below</a> (then press control and C together to copy.)<br><textarea id=\"svgfile\" cols=\"80\" rows=\"10\" wrap=\"virtual\" onfocus=\"this.select()\">",
svgtext, "</textarea></td></tr></tbody></table>", sep = "")
list(message = msg)
}
<bytecode: 0x5572ee906850>
<environment: namespace:home>