graph - calculate AUC (GAM) in R -

i used following script calculate auc in r:

library(mgcv) library(rocr) library(auc)  data1=read.table("d:\\2005.txt", header=t) gam<-gam(tuna ~ s(chla)+s(sst)+s(ssha)+s(eke), family=binomial, data=data1)  gampred<- predict(gam, type="response")  rp <- prediction(gampred, data1$tuna)   auc <- performance( rp, "auc")@y.values[[1]] auc  roc <- performance( rp, "tpr", "fpr") plot( roc ) 

but when running script, result is:

rp <- prediction(gampred, data1$tuna)  error in prediction(gampred, data1$tuna) :    format of predictions invalid.  auc <- performance( rp, "auc")@y.values[[1]] error in performance(rp, "auc") : object 'rp' not found  auc function (x, min = 0, max = 1)  {     if (any(class(x) == "roc")) {         if (min != 0 || max != 1) {             x$fpr <- x$fpr[x$cutoffs >= min & x$cutoffs <= max]             x$tpr <- x$tpr[x$cutoffs >= min & x$cutoffs <= max]         }         ans <- 0         (i in 2:length(x$fpr)) {             ans <- ans + 0.5 * abs(x$fpr[i] - x$fpr[i - 1]) *                  (x$tpr[i] + x$tpr[i - 1])         }     }     else if (any(class(x) %in% c("accuracy", "sensitivity", "specificity"))) {         if (min != 0 || max != 1) {             x$cutoffs <- x$cutoffs[x$cutoffs >= min & x$cutoffs <=                  max]             x$measure <- x$measure[x$cutoffs >= min & x$cutoffs <=                  max]         }         ans <- 0         (i in 2:(length(x$cutoffs))) {             ans <- ans + 0.5 * abs(x$cutoffs[i - 1] - x$cutoffs[i]) *                  (x$measure[i] + x$measure[i - 1])         }     }     return(as.numeric(ans)) } <bytecode: 0x03012f10> <environment: namespace:auc>  roc <- performance( rp, "tpr", "fpr") error in performance(rp, "tpr", "fpr") : object 'rp' not found  plot( roc ) error in levels(labels) : argument "labels" missing, no default** 

can me solve problem? thank in advance.

the data:

structure(list(x.y.chla.sst.ssha.eke.tuna = structure(c(3l,  2l, 1l, 6l, 5l, 4l, 9l, 8l, 7l, 12l, 11l, 10l, 17l, 16l, 15l,  14l, 13l, 23l, 22l, 21l, 20l, 19l, 18l, 29l, 28l, 27l, 26l, 25l,  24l, 34l, 33l, 32l, 31l, 30l, 39l, 38l, 37l, 36l, 35l, 44l, 43l,  42l, 41l, 40l, 49l, 48l, 47l, 46l, 45l, 54l, 53l, 52l, 51l, 50l,  57l, 56l, 55l, 60l, 59l, 58l, 63l, 62l, 61l, 66l, 65l, 64l, 69l,  68l, 67l, 72l, 71l, 70l, 75l, 74l, 73l, 76l, 79l, 78l, 77l, 82l,  81l, 80l, 85l, 84l, 83l, 88l, 87l, 86l, 91l, 90l, 89l, 94l, 93l,  92l, 97l, 96l, 95l, 98l, 101l, 100l), .label = c("140.01178,44.666668,0.21406905,19.939999,6.931947586,213.8725429,87",  "140.01178,44.675674,0.20695277,19.99,6.896174947,211.7077132,50",  "140.01178,44.684685,0.20695277,19.99,6.860499828,209.3726636,209",  "140.02354,44.666668,0.21406905,19.939999,7.035145153,207.8331119,330",  "140.02354,44.675674,0.20695277,19.99,6.999857682,205.7884775,260",  "140.02354,44.684685,0.20695277,19.99,6.964626474,203.5812475,122",  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you have mucked data1 dataframe. @ str() gives you:

> str(data1) 'data.frame':   100 obs. of  1 variable:  $ x.y.chla.sst.ssha.eke.tuna: factor w/ 311 levels "140.01178,44.666668,0.21406905,19.939999,6.931947586,213.8725429,87",..: 3 2 1 6 5 4 9 8 7 12 ... 

you thinking dataframe numericcolumns when in fact dataframe single column. appears used read.table without proper 'sep'-argument. column names got mushed , values got bundled single factor-strings. mess!

better go beginning , redo read.table effort. suppose 1 parse apart name of single column , use read.table on as.character() result of sending factor column, seems baroque.

editorial comment: think people reaching auc tool don't understand offering. seems used more deserves.