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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-241-available in the `ade4` package. A principal component analysis (PCA) is
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd:242:applied on the `olympic$tab` table that contains the results for 33
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-243-participating athletes at the 1988 summer olympic games:
##############################################
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-475-
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd:476:The vector `olympic$score` contains the total number of points computed
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-477-for each participant. This vector is used to generate a `factor`
##############################################
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-642-
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd:643:Let us consider the `jv73` data set. The table `jv73$morpho` contains
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-644-the measures of 6 variables describing the geomorphology of 92 sites. A
##############################################
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-651-
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd:652:The sites are located on 12 rivers (`jv73$fac.riv`) and it is possible
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-653-to represent the PCA scores for each river using the `facets` argument:
##############################################
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-661-to focus on a given river (e.g., the Doubs river) by considering only a
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd:662:subplot (e.g., type `g8$Doubs`). The `facets` functionality is very
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-663-general and available for the majority of `adegraphics` functions. For
##############################################
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-695-between the global performance (`fac.score`) and the PCA scores on the
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd:696:first four axes (`pca1$li`):
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-697-```{r label=plot21, fig.width=6, fig.height=6}
##############################################
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-711-distribution of the 6 environmental variables on the PCA factorial map
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd:712:of the `jv73$tab` data set:
r-cran-adegraphics-1.0-15/inst/doc/adegraphics.Rmd-713-```{r label=plot22, fig.width=6, fig.height=4}
##############################################
r-cran-adegraphics-1.0-15/R/S2.image.R-36- } else {
r-cran-adegraphics-1.0-15/R/S2.image.R:37: dfxy <- eval(object@data$dfxy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.image.R:38: z <- eval(object@data$z, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.image.R-39- }
##############################################
r-cran-adegraphics-1.0-15/R/S2.image.R-125- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S2.image.R:126: df <- try(as.data.frame(eval(thecall$dfxy, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.image.R:127: z <- eval(thecall$z, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S2.image.R-128- if((class(df) == "try-error") | is.null(thecall$dfxy)) ## non convenient dfxy argument
##############################################
r-cran-adegraphics-1.0-15/R/Tr.class.R-34- } else {
r-cran-adegraphics-1.0-15/R/Tr.class.R:35: fac <- as.factor(eval(object@data$fac, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/Tr.class.R:36: df <- eval(object@data$dfxyz, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.class.R:37: wt <- eval(object@data$wt, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.class.R-38- }
##############################################
r-cran-adegraphics-1.0-15/R/Tr.class.R-109- } else {
r-cran-adegraphics-1.0-15/R/Tr.class.R:110: fac <- eval(object@data$fac, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.class.R:111: df <- eval(object@data$dfxyz, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.class.R:112: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.class.R-113- }
##############################################
r-cran-adegraphics-1.0-15/R/S2.distri.R-33- if(!object@data$storeData) {
r-cran-adegraphics-1.0-15/R/S2.distri.R:34: dfxy <- eval(object@data$dfxy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.distri.R:35: dfdistri <- eval(object@data$dfdistri, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.distri.R-36- } else {
##############################################
r-cran-adegraphics-1.0-15/R/S2.distri.R-88- else
r-cran-adegraphics-1.0-15/R/S2.distri.R:89: dfdistri <- eval(object@data$dfdistri, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.distri.R-90-
##############################################
r-cran-adegraphics-1.0-15/R/S2.distri.R-160- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S2.distri.R:161: df <- try(as.data.frame(eval(thecall$dfxy, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.distri.R-162- if((class(df) == "try-error") | is.null(dfxy))
##############################################
r-cran-adegraphics-1.0-15/R/S1.boxplot.R-28- else
r-cran-adegraphics-1.0-15/R/S1.boxplot.R:29: fac <- as.factor(eval(object@data$fac, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/S1.boxplot.R-30-
##############################################
r-cran-adegraphics-1.0-15/R/S1.boxplot.R-67- } else {
r-cran-adegraphics-1.0-15/R/S1.boxplot.R:68: fac <- eval(object@data$fac, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.boxplot.R:69: at <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.boxplot.R-70- }
##############################################
r-cran-adegraphics-1.0-15/R/S1.boxplot.R-195- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S1.boxplot.R:196: fac <- eval(thecall$fac, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S1.boxplot.R:197: score <- eval(thecall$score, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S1.boxplot.R-198- if(NROW(fac) != NROW(score))
##############################################
r-cran-adegraphics-1.0-15/R/T.cont.R-17- } else {
r-cran-adegraphics-1.0-15/R/T.cont.R:18: dftab <- eval(object@data$dftab, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/T.cont.R:19: coordsx <- eval(object@data$coordsx, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/T.cont.R:20: coordsy <- eval(object@data$coordsy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/T.cont.R-21- }
##############################################
r-cran-adegraphics-1.0-15/R/C1.interval.R-32- } else {
r-cran-adegraphics-1.0-15/R/C1.interval.R:33: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.interval.R:34: at <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.interval.R-35- }
##############################################
r-cran-adegraphics-1.0-15/R/C1.interval.R-114- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/C1.interval.R:115: score1 <- eval(thecall$score1, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/C1.interval.R:116: score2 <- eval(thecall$score2, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/C1.interval.R-117- if(NROW(score1) != NROW(score2))
##############################################
r-cran-adegraphics-1.0-15/R/S2.corcircle.R-74- else
r-cran-adegraphics-1.0-15/R/S2.corcircle.R:75: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.corcircle.R-76-
##############################################
r-cran-adegraphics-1.0-15/R/S2.corcircle.R-89- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S2.corcircle.R:90: df <- try(as.data.frame(eval(thecall$dfxy, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.corcircle.R-91- if((class(df) == "try-error") | is.null(thecall$dfxy)) ## non convenient dfxy argument
##############################################
r-cran-adegraphics-1.0-15/R/S2.density.R-25- else
r-cran-adegraphics-1.0-15/R/S2.density.R:26: dfxy <- eval(object@data$dfxy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.density.R-27-
##############################################
r-cran-adegraphics-1.0-15/R/S2.density.R-108- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S2.density.R:109: df <- try(as.data.frame(eval(thecall$dfxy, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.density.R-110- if((class(df) == "try-error") | is.null(thecall$dfxy)) ## non convenient dfxy argument
##############################################
r-cran-adegraphics-1.0-15/R/S2.match.R-74- else
r-cran-adegraphics-1.0-15/R/S2.match.R:75: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.match.R-76-
##############################################
r-cran-adegraphics-1.0-15/R/S2.match.R-87- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S2.match.R:88: data1 <- try(as.data.frame(eval(thecall$dfxy1, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.match.R:89: data2 <- try(as.data.frame(eval(thecall$dfxy2, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.match.R-90-
##############################################
r-cran-adegraphics-1.0-15/R/Tr.traject.R-31- } else {
r-cran-adegraphics-1.0-15/R/Tr.traject.R:32: df <- eval(object@data$dfxyz, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.traject.R:33: fac <- as.factor(eval(object@data$fac, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/Tr.traject.R-34- }
##############################################
r-cran-adegraphics-1.0-15/R/Tr.traject.R-72- } else {
r-cran-adegraphics-1.0-15/R/Tr.traject.R:73: fact <- eval(object@data$fac, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.traject.R:74: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.traject.R-75- }
##############################################
r-cran-adegraphics-1.0-15/R/utilskey.R-149- else
r-cran-adegraphics-1.0-15/R/utilskey.R:150: fac <- as.factor(eval(object@data$fac, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/utilskey.R-151-
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.T.R-30- } else {
r-cran-adegraphics-1.0-15/R/ADEg.T.R:31: coordsx <- eval(object@data$coordsx, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.T.R:32: coordsy <- eval(object@data$coordsy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.T.R-33- }
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.T.R-74- } else {
r-cran-adegraphics-1.0-15/R/ADEg.T.R:75: xpos <- eval(object@data$coordsx, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.T.R:76: ypos <- eval(object@data$coordsy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.T.R:77: labelsx <- eval(object@data$labelsx, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.T.R:78: labelsy <- eval(object@data$labelsy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.T.R-79- }
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.T.R-233- } else {
r-cran-adegraphics-1.0-15/R/ADEg.T.R:234: xdata <- eval(object@data$coordsx, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.T.R:235: ydata <- eval(object@data$coordsy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.T.R-236- }
##############################################
r-cran-adegraphics-1.0-15/R/Tr.label.R-30- } else {
r-cran-adegraphics-1.0-15/R/Tr.label.R:31: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.label.R:32: df <- eval(object@data$dfxyz, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.label.R-33- }
##############################################
r-cran-adegraphics-1.0-15/R/Tr.label.R-100- } else {
r-cran-adegraphics-1.0-15/R/Tr.label.R:101: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.label.R:102: df <- eval(object@data$dfxyz, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.label.R-103- }
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.S1.R-32- } else {
r-cran-adegraphics-1.0-15/R/ADEg.S1.R:33: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.S1.R:34: at <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.S1.R-35- }
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.S1.R-40- } else {
r-cran-adegraphics-1.0-15/R/ADEg.S1.R:41: fac <- eval(object@data$fac, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.S1.R-42- }
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.S1.R-191- else
r-cran-adegraphics-1.0-15/R/ADEg.S1.R:192: fac <- as.factor(eval(object@data$fac, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/ADEg.S1.R-193- plines <- lapply(plines, FUN = function(x) return(rep(x, length.out = nlevels(fac))[fac]))
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.S1.R-306- else
r-cran-adegraphics-1.0-15/R/ADEg.S1.R:307: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.S1.R-308-
##############################################
r-cran-adegraphics-1.0-15/R/C1.curve.R-32- } else {
r-cran-adegraphics-1.0-15/R/C1.curve.R:33: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.curve.R:34: at <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.curve.R-35- }
##############################################
r-cran-adegraphics-1.0-15/R/T.image.R-25- } else {
r-cran-adegraphics-1.0-15/R/T.image.R:26: coordsx <- eval(object@data$coordsx, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/T.image.R:27: coordsy <- eval(object@data$coordsy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/T.image.R:28: z <- as.vector(as.matrix(eval(object@data$dftab, envir = sys.frame(object@data$frame))))
r-cran-adegraphics-1.0-15/R/T.image.R:29: dftab <- eval(object@data$dftab, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/T.image.R:30: labelsx <- eval(object@data$labelsx, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/T.image.R:31: labelsy <- eval(object@data$labelsy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/T.image.R-32- }
##############################################
r-cran-adegraphics-1.0-15/R/T.image.R-90- else
r-cran-adegraphics-1.0-15/R/T.image.R:91: dftab <- as.matrix(eval(object@data$dftab, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/T.image.R-92-
##############################################
r-cran-adegraphics-1.0-15/R/T.image.R-123- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/T.image.R:124: dftab <- eval(thecall$dftab, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/T.image.R-125-
##############################################
r-cran-adegraphics-1.0-15/R/S1.label.R-60- } else {
r-cran-adegraphics-1.0-15/R/S1.label.R:61: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.label.R:62: at <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.label.R-63- }
##############################################
r-cran-adegraphics-1.0-15/R/S1.label.R-124- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S1.label.R:125: score <- eval(thecall$score, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S1.label.R-126-
##############################################
r-cran-adegraphics-1.0-15/R/S1.match.R-61- } else {
r-cran-adegraphics-1.0-15/R/S1.match.R:62: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.match.R:63: at <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.match.R-64- }
##############################################
r-cran-adegraphics-1.0-15/R/S1.match.R-141- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S1.match.R:142: score1 <- eval(thecall$score1, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S1.match.R:143: score2 <- eval(thecall$score2, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S1.match.R-144- if(NROW(score1) != NROW(score2))
##############################################
r-cran-adegraphics-1.0-15/R/C1.barchart.R-33- } else {
r-cran-adegraphics-1.0-15/R/C1.barchart.R:34: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.barchart.R:35: at <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.barchart.R-36- }
##############################################
r-cran-adegraphics-1.0-15/R/C1.barchart.R-76- else
r-cran-adegraphics-1.0-15/R/C1.barchart.R:77: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.barchart.R-78-
##############################################
r-cran-adegraphics-1.0-15/R/C1.barchart.R-140- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/C1.barchart.R:141: score <- eval(thecall$score, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/C1.barchart.R-142-
##############################################
r-cran-adegraphics-1.0-15/R/C1.dotplot.R-32- } else {
r-cran-adegraphics-1.0-15/R/C1.dotplot.R:33: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.dotplot.R:34: at <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.dotplot.R-35- }
##############################################
r-cran-adegraphics-1.0-15/R/C1.dotplot.R-91- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/C1.dotplot.R:92: score <- eval(thecall$score, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/C1.dotplot.R-93-
##############################################
r-cran-adegraphics-1.0-15/R/utilstriangle.R-108-## if(!is.null(data$frame))
r-cran-adegraphics-1.0-15/R/utilstriangle.R:109:## ta <- t(apply(eval(data$ta, envir = sys.frame(data$frame)), 1, function(x) x/sum(x)))
r-cran-adegraphics-1.0-15/R/utilstriangle.R-110-## else
##############################################
r-cran-adegraphics-1.0-15/R/C1.hist.R-33- else
r-cran-adegraphics-1.0-15/R/C1.hist.R:34: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.hist.R-35-
##############################################
r-cran-adegraphics-1.0-15/R/C1.hist.R-105- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/C1.hist.R:106: score <- eval(thecall$score, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/C1.hist.R-107-
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.C1.R-31- else
r-cran-adegraphics-1.0-15/R/ADEg.C1.R:32: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.C1.R-33-
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.C1.R-37- else
r-cran-adegraphics-1.0-15/R/ADEg.C1.R:38: at <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.C1.R-39- }
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.C1.R-150- else
r-cran-adegraphics-1.0-15/R/ADEg.C1.R:151: fac <- as.factor(eval(object@data$fac, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/ADEg.C1.R-152- plines <- lapply(plines, FUN = function(x) {return(rep(x, length.out = nlevels(fac))[fac])})
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.C1.R-267- else
r-cran-adegraphics-1.0-15/R/ADEg.C1.R:268: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.C1.R-269-
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.C1.R-279- else
r-cran-adegraphics-1.0-15/R/ADEg.C1.R:280: xdata <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.C1.R-281- }
##############################################
r-cran-adegraphics-1.0-15/R/C1.density.R-38- } else {
r-cran-adegraphics-1.0-15/R/C1.density.R:39: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.density.R:40: fac <- eval(object@data$fac, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.density.R-41- }
##############################################
r-cran-adegraphics-1.0-15/R/C1.density.R-161- else
r-cran-adegraphics-1.0-15/R/C1.density.R:162: fac <- eval(object@data$fac, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.density.R-163- nlev <- nlevels(as.factor(fac))
##############################################
r-cran-adegraphics-1.0-15/R/S2.value.R-36- else
r-cran-adegraphics-1.0-15/R/S2.value.R:37: z <- eval(object@data$z, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.value.R-38-
##############################################
r-cran-adegraphics-1.0-15/R/S2.value.R-104- else
r-cran-adegraphics-1.0-15/R/S2.value.R:105: zorig <- eval(object@data$z, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.value.R-106-
##############################################
r-cran-adegraphics-1.0-15/R/S2.value.R-127- thecall$symbol <- match.arg(symbol)
r-cran-adegraphics-1.0-15/R/S2.value.R:128: df <- try(as.data.frame(eval(thecall$dfxy, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.value.R:129: z <- eval(thecall$z, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S2.value.R-130- if((class(df) == "try-error") | is.null(thecall$dfxy)) ## non convenient dfxy argument
##############################################
r-cran-adegraphics-1.0-15/R/ade4-score.R-271- sortparameters$trellis, sortparameters$g.args, sortparameters$rest))
r-cran-adegraphics-1.0-15/R/ade4-score.R:272: g2 <- xyplot(eval(dfxy)[, 2] ~ eval(dfxy)[, 1], aspect = g1@adeg.par$paxes$aspectratio, panel = function(x, y) {panel.abline(lm(y ~ x))})
r-cran-adegraphics-1.0-15/R/ade4-score.R-273- g2$call <- call("xyplot", substitute(dfxy[, 2] ~ dfxy[, 1]), aspect = g1@adeg.par$paxes$aspectratio, panel = function(x, y) {panel.abline(lm(y ~ x))})
##############################################
r-cran-adegraphics-1.0-15/R/C1.gauss.R-37- } else {
r-cran-adegraphics-1.0-15/R/C1.gauss.R:38: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.gauss.R:39: fac <- eval(object@data$fac, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.gauss.R:40: wt <- eval(object@data$wt, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.gauss.R-41- }
##############################################
r-cran-adegraphics-1.0-15/R/C1.gauss.R-168- else
r-cran-adegraphics-1.0-15/R/C1.gauss.R:169: fac <- eval(object@data$fac, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/C1.gauss.R-170- nlev <- nlevels(as.factor(fac))
##############################################
r-cran-adegraphics-1.0-15/R/S1.class.R-30- else
r-cran-adegraphics-1.0-15/R/S1.class.R:31: fac <- as.factor(eval(object@data$fac, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/S1.class.R-32-
##############################################
r-cran-adegraphics-1.0-15/R/S1.class.R-81- } else {
r-cran-adegraphics-1.0-15/R/S1.class.R:82: fac <- eval(object@data$fac, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.class.R:83: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.class.R:84: wt <- eval(object@data$wt, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.class.R:85: at <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.class.R:86: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.class.R-87- }
##############################################
r-cran-adegraphics-1.0-15/R/S1.class.R-169- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S1.class.R:170: labels <- eval(thecall$labels, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S1.class.R:171: fac <- eval(thecall$fac, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S1.class.R:172: score <- eval(thecall$score, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S1.class.R-173- if(NCOL(fac) == 1) {
##############################################
r-cran-adegraphics-1.0-15/R/Tr.match.R-25- } else {
r-cran-adegraphics-1.0-15/R/Tr.match.R:26: df <- eval(object@data$dfxyz, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.match.R-27- }
##############################################
r-cran-adegraphics-1.0-15/R/Tr.match.R-60- } else {
r-cran-adegraphics-1.0-15/R/Tr.match.R:61: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.match.R:62: df <- eval(object@data$dfxyz, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/Tr.match.R-63- }
##############################################
r-cran-adegraphics-1.0-15/R/Tr.match.R-91- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/Tr.match.R:92: data1 <- try(as.data.frame(eval(thecall$dfxyz1, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/Tr.match.R:93: data2 <- try(as.data.frame(eval(thecall$dfxyz2, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/Tr.match.R-94-
##############################################
r-cran-adegraphics-1.0-15/R/S2.arrow.R-72- else
r-cran-adegraphics-1.0-15/R/S2.arrow.R:73: arrownames <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.arrow.R-74-
##############################################
r-cran-adegraphics-1.0-15/R/S2.arrow.R-90- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S2.arrow.R:91: df <- try(as.data.frame(eval(thecall$dfxy, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.arrow.R-92- if((class(df) == "try-error") | is.null(thecall$dfxy)) ## non convenient dfxy argument
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-11- ## update some arguments
r-cran-adegraphics-1.0-15/R/multiplot.R:12: thenewcall$pos <- eval(thenewcall$pos) - 3
r-cran-adegraphics-1.0-15/R/multiplot.R-13- thenewcall$plot <- FALSE
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-20- ## evaluate some arguments in the correct frame
r-cran-adegraphics-1.0-15/R/multiplot.R:21: xax <- eval(thecall$xax, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R:22: yax <- eval(thecall$yax, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-23- ## create ADEg plots
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-55- thenewcall$plot <- FALSE
r-cran-adegraphics-1.0-15/R/multiplot.R:56: thenewcall$pos <- eval(thenewcall$pos) - 3
r-cran-adegraphics-1.0-15/R/multiplot.R-57- thenewcall$facets <- NULL
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-60- if(thecall[[1]] != "s.match")
r-cran-adegraphics-1.0-15/R/multiplot.R:61: dfxy <- eval(thecall$dfxy, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-62- else
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-64-
r-cran-adegraphics-1.0-15/R/multiplot.R:65: facets <- factor(eval(thecall$facets, envir = sys.frame(sys.nframe() + thenewcall$pos + 2)))
r-cran-adegraphics-1.0-15/R/multiplot.R-66-
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-68- if((isTRUE(samelimits) | is.null(samelimits)) & (thecall[[1]] != "s.corcircle")) {
r-cran-adegraphics-1.0-15/R/multiplot.R:69: xax <- eval(thecall$xax, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R:70: yax <- eval(thecall$yax, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-71- if(is.null(thenewcall$Sp))
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-74- else { ## Sp: ex map, alors par defaut on prend la bbox
r-cran-adegraphics-1.0-15/R/multiplot.R:75: limsSp <- bbox(eval(thenewcall$Sp))
r-cran-adegraphics-1.0-15/R/multiplot.R-76- lim.global <- setlimits2D(minX = limsSp[1, 1], maxX = limsSp[1, 2], minY = limsSp[2, 1], maxY = limsSp[2, 2], origin = rep(adegtot$porigin$origin, le = 2), aspect.ratio = adegtot$paxes$aspectratio, includeOr = adegtot$porigin$include)
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-123- ## same breaks for all groups
r-cran-adegraphics-1.0-15/R/multiplot.R:124: z <- eval(thecall$z, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-125- breaks <- pretty(z, thenewcall$n)
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-153- ## update some arguments
r-cran-adegraphics-1.0-15/R/multiplot.R:154: thenewcall$pos <- eval(thecall$pos) - 3
r-cran-adegraphics-1.0-15/R/multiplot.R-155- thenewcall$plot <- FALSE
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-158- name.vary <- thenewcall[[arg.vary]]
r-cran-adegraphics-1.0-15/R/multiplot.R:159: dfvary <- eval(name.vary, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-160-
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-194- ## update some arguments
r-cran-adegraphics-1.0-15/R/multiplot.R:195: thenewcall$pos <- eval(thenewcall$pos) - 3
r-cran-adegraphics-1.0-15/R/multiplot.R-196- thenewcall$plot <- FALSE
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-199- if(thenewcall[[1]] != "s1d.interval") {
r-cran-adegraphics-1.0-15/R/multiplot.R:200: score <- eval(thecall$score, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-201- name.score <- thecall$score
r-cran-adegraphics-1.0-15/R/multiplot.R-202- } else {
r-cran-adegraphics-1.0-15/R/multiplot.R:203: score <- eval(thecall$score1, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-204- name.score <- thecall$score1
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-249- thenewcall$plot <- FALSE
r-cran-adegraphics-1.0-15/R/multiplot.R:250: thenewcall$pos <- eval(thenewcall$pos) - 3
r-cran-adegraphics-1.0-15/R/multiplot.R-251- thenewcall$facets <- NULL
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-254- if(thenewcall[[1]] != "s1d.interval") {
r-cran-adegraphics-1.0-15/R/multiplot.R:255: score <- eval(thecall$score, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-256- } else {
r-cran-adegraphics-1.0-15/R/multiplot.R:257: score1 <- eval(thecall$score1, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R:258: score2 <- eval(thecall$score2, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-259- score <- c(score1, score2)
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-261-
r-cran-adegraphics-1.0-15/R/multiplot.R:262: facets <- factor(eval(thecall$facets, envir = sys.frame(sys.nframe() + thenewcall$pos + 2)))
r-cran-adegraphics-1.0-15/R/multiplot.R-263-
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-339- ## update some arguments
r-cran-adegraphics-1.0-15/R/multiplot.R:340: thenewcall$pos <- eval(thecall$pos) - 3
r-cran-adegraphics-1.0-15/R/multiplot.R-341- thenewcall$plot <- FALSE
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-344- name.vary <- thenewcall[[arg.vary]]
r-cran-adegraphics-1.0-15/R/multiplot.R:345: dfvary <- eval(name.vary, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-346-
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-373- ## update some arguments
r-cran-adegraphics-1.0-15/R/multiplot.R:374: thenewcall$pos <- eval(thenewcall$pos) - 3
r-cran-adegraphics-1.0-15/R/multiplot.R-375- thenewcall$plot <- FALSE
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-378- if(thenewcall[[1]] != "s1d.match") {
r-cran-adegraphics-1.0-15/R/multiplot.R:379: score <- eval(thecall$score, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-380- name.score <- thecall$score
r-cran-adegraphics-1.0-15/R/multiplot.R-381- } else {
r-cran-adegraphics-1.0-15/R/multiplot.R:382: score <- eval(thecall$score1, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-383- name.score <- thecall$score1
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-423- thenewcall$plot <- FALSE
r-cran-adegraphics-1.0-15/R/multiplot.R:424: thenewcall$pos <- eval(thenewcall$pos) - 3
r-cran-adegraphics-1.0-15/R/multiplot.R-425- thenewcall$facets <- NULL
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-428- if(thenewcall[[1]] != "s1d.match") {
r-cran-adegraphics-1.0-15/R/multiplot.R:429: score <- eval(thecall$score, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-430- } else {
r-cran-adegraphics-1.0-15/R/multiplot.R:431: score1 <- eval(thecall$score1, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R:432: score2 <- eval(thecall$score2, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-433- score <- c(score1, score2)
r-cran-adegraphics-1.0-15/R/multiplot.R-434- }
r-cran-adegraphics-1.0-15/R/multiplot.R:435: facets <- factor(eval(thecall$facets, envir = sys.frame(sys.nframe() + thenewcall$pos + 2)))
r-cran-adegraphics-1.0-15/R/multiplot.R-436-
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-494- ## update some arguments
r-cran-adegraphics-1.0-15/R/multiplot.R:495: thenewcall$pos <- eval(thecall$pos) - 3
r-cran-adegraphics-1.0-15/R/multiplot.R-496- thenewcall$plot <- FALSE
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-499- name.vary <- thenewcall[[arg.vary]]
r-cran-adegraphics-1.0-15/R/multiplot.R:500: dfvary <- eval(name.vary, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-501-
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-534- thenewcall$plot <- FALSE
r-cran-adegraphics-1.0-15/R/multiplot.R:535: thenewcall$pos <- eval(thenewcall$pos) - 3
r-cran-adegraphics-1.0-15/R/multiplot.R-536- thenewcall$facets <- NULL
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-539- if(thecall[[1]] != "triangle.match")
r-cran-adegraphics-1.0-15/R/multiplot.R:540: dfxyz <- eval(thecall$dfxyz, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-541- else
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-543-
r-cran-adegraphics-1.0-15/R/multiplot.R:544: facets <- factor(eval(thecall$facets, envir = sys.frame(sys.nframe() + thenewcall$pos + 2)))
r-cran-adegraphics-1.0-15/R/multiplot.R-545-
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-598- ## update some arguments
r-cran-adegraphics-1.0-15/R/multiplot.R:599: thenewcall$pos <- eval(thecall$pos) - 3
r-cran-adegraphics-1.0-15/R/multiplot.R-600- thenewcall$plot <- FALSE
##############################################
r-cran-adegraphics-1.0-15/R/multiplot.R-603- name.vary <- thenewcall[[arg.vary]]
r-cran-adegraphics-1.0-15/R/multiplot.R:604: dfvary <- eval(name.vary, envir = sys.frame(sys.nframe() + thenewcall$pos + 2))
r-cran-adegraphics-1.0-15/R/multiplot.R-605-
##############################################
r-cran-adegraphics-1.0-15/R/S2.label.R-29- } else {
r-cran-adegraphics-1.0-15/R/S2.label.R:30: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.label.R-31- }
##############################################
r-cran-adegraphics-1.0-15/R/S2.label.R-61- else
r-cran-adegraphics-1.0-15/R/S2.label.R:62: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.label.R-63-
##############################################
r-cran-adegraphics-1.0-15/R/S2.label.R-72- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S2.label.R:73: df <- try(as.data.frame(eval(thecall$dfxy, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.label.R-74- if((class(df) == "try-error") | is.null(thecall$dfxy)) ## non convenient dfxy argument
##############################################
r-cran-adegraphics-1.0-15/R/S2.class.R-39- } else {
r-cran-adegraphics-1.0-15/R/S2.class.R:40: fac <- as.factor(eval(object@data$fac, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/S2.class.R:41: dfxy <- eval(object@data$dfxy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.class.R:42: wt <- eval(object@data$wt, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.class.R-43- }
##############################################
r-cran-adegraphics-1.0-15/R/S2.class.R-100- } else {
r-cran-adegraphics-1.0-15/R/S2.class.R:101: fac <- eval(object@data$fac, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.class.R:102: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.class.R-103- }
##############################################
r-cran-adegraphics-1.0-15/R/S2.class.R-197- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S2.class.R:198: labels <- eval(thecall$labels, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S2.class.R:199: fac <- eval(thecall$fac, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S2.class.R:200: df <- try(as.data.frame(eval(thecall$dfxy, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.class.R-201- if((class(df) == "try-error") | is.null(thecall$dfxy)) ## non convenient dfxy argument
##############################################
r-cran-adegraphics-1.0-15/R/S2.logo.R-49- else
r-cran-adegraphics-1.0-15/R/S2.logo.R:50: logos <- eval(object@data$logos, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.logo.R-51-
##############################################
r-cran-adegraphics-1.0-15/R/S2.logo.R-61- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S2.logo.R:62: df <- try(as.data.frame(eval(thecall$dfxy, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.logo.R-63- if((class(df) == "try-error") | is.null(thecall$dfxy)) ## non convenient dfxy argument
r-cran-adegraphics-1.0-15/R/S2.logo.R-64- stop("non convenient selection for dfxy (can not be converted to dataframe)")
r-cran-adegraphics-1.0-15/R/S2.logo.R:65: logos <- eval(thecall$logos, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S2.logo.R-66- if(!is.list(logos))
##############################################
r-cran-adegraphics-1.0-15/R/S2.traject.R-30- else
r-cran-adegraphics-1.0-15/R/S2.traject.R:31: fac <- as.factor(eval(object@data$fac, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/S2.traject.R-32-
##############################################
r-cran-adegraphics-1.0-15/R/S2.traject.R-68- } else {
r-cran-adegraphics-1.0-15/R/S2.traject.R:69: fact <- eval(object@data$fac, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.traject.R:70: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S2.traject.R-71- }
##############################################
r-cran-adegraphics-1.0-15/R/S2.traject.R-131- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S2.traject.R:132: labels <- eval(thecall$labels, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S2.traject.R:133: fac <- eval(thecall$fac, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S2.traject.R:134: df <- try(as.data.frame(eval(thecall$dfxy, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
r-cran-adegraphics-1.0-15/R/S2.traject.R-135- if((class(df) == "try-error") | is.null(thecall$dfxy)) ## non convenient dfxy argument
##############################################
r-cran-adegraphics-1.0-15/R/addhist.R-16- } else {
r-cran-adegraphics-1.0-15/R/addhist.R:17: dfxy <- eval(object@data$dfxy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/addhist.R:18: xax <- eval(object@data$xax, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/addhist.R:19: yax <- eval(object@data$yax, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/addhist.R-20- }
##############################################
r-cran-adegraphics-1.0-15/R/T.value.R-23- } else {
r-cran-adegraphics-1.0-15/R/T.value.R:24: z <- as.vector(as.matrix(eval(object@data$dftab, envir = sys.frame(object@data$frame))))
r-cran-adegraphics-1.0-15/R/T.value.R:25: dftab <- eval(object@data$dftab, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/T.value.R:26: labelsx <- eval(object@data$labelsx, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/T.value.R:27: labelsy <- eval(object@data$labelsy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/T.value.R-28- }
##############################################
r-cran-adegraphics-1.0-15/R/T.value.R-95- else
r-cran-adegraphics-1.0-15/R/T.value.R:96: dftab <- as.matrix(eval(object@data$dftab, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/T.value.R-97- adeg.panel.values(x = x[col(dftab)], y = y[row(dftab)], z = as.vector(dftab), center = object@g.args$center, method = object@g.args$method,
##############################################
r-cran-adegraphics-1.0-15/R/T.value.R-112- thecall$symbol <- match.arg(symbol)
r-cran-adegraphics-1.0-15/R/T.value.R:113: dftab <- eval(thecall$dftab, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/T.value.R-114- if(any(is.na(dftab)))
##############################################
r-cran-adegraphics-1.0-15/R/S1.distri.R-37- } else {
r-cran-adegraphics-1.0-15/R/S1.distri.R:38: dfdistri <- eval(object@data$dfdistri, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.distri.R:39: score <- eval(object@data$score, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.distri.R:40: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.distri.R-41- }
##############################################
r-cran-adegraphics-1.0-15/R/S1.distri.R-71- } else {
r-cran-adegraphics-1.0-15/R/S1.distri.R:72: labels <- eval(object@data$labels, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.distri.R:73: at <- eval(object@data$at, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/S1.distri.R-74- }
##############################################
r-cran-adegraphics-1.0-15/R/S1.distri.R-153- thecall <- .expand.call(match.call())
r-cran-adegraphics-1.0-15/R/S1.distri.R:154: dfdistri <- eval(thecall$dfdistri, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S1.distri.R:155: score <- eval(thecall$score, envir = sys.frame(sys.nframe() + pos))
r-cran-adegraphics-1.0-15/R/S1.distri.R-156- if(NROW(dfdistri) != NROW(score))
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.S2.R-26- else
r-cran-adegraphics-1.0-15/R/ADEg.S2.R:27: dfxy <- eval(object@data$dfxy, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.S2.R-28-
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.S2.R-297- } else {
r-cran-adegraphics-1.0-15/R/ADEg.S2.R:298: dfxy <- as.matrix(eval(object@data$dfxy, envir = sys.frame(object@data$frame)))
r-cran-adegraphics-1.0-15/R/ADEg.S2.R:299: yax <- eval(object@data$yax, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.S2.R:300: xax <- eval(object@data$xax, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.S2.R-301- }
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.Tr.R-26- else
r-cran-adegraphics-1.0-15/R/ADEg.Tr.R:27: df <- eval(object@data$dfxyz, envir = sys.frame(object@data$frame))
r-cran-adegraphics-1.0-15/R/ADEg.Tr.R-28-
##############################################
r-cran-adegraphics-1.0-15/R/ADEg.Tr.R-105- else
r-cran-adegraphics-1.0-15/R/ADEg.Tr.R:106: axisN <- colnames(eval(object@data$dfxyz, envir = sys.frame(object@data$frame)))[c(2, 1, 3)]
r-cran-adegraphics-1.0-15/R/ADEg.Tr.R-107-
##############################################
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-241-available in the `ade4` package. A principal component analysis (PCA) is
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd:242:applied on the `olympic$tab` table that contains the results for 33
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-243-participating athletes at the 1988 summer olympic games:
##############################################
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-475-
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd:476:The vector `olympic$score` contains the total number of points computed
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-477-for each participant. This vector is used to generate a `factor`
##############################################
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-642-
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd:643:Let us consider the `jv73` data set. The table `jv73$morpho` contains
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-644-the measures of 6 variables describing the geomorphology of 92 sites. A
##############################################
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-651-
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd:652:The sites are located on 12 rivers (`jv73$fac.riv`) and it is possible
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-653-to represent the PCA scores for each river using the `facets` argument:
##############################################
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-661-to focus on a given river (e.g., the Doubs river) by considering only a
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd:662:subplot (e.g., type `g8$Doubs`). The `facets` functionality is very
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-663-general and available for the majority of `adegraphics` functions. For
##############################################
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-695-between the global performance (`fac.score`) and the PCA scores on the
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd:696:first four axes (`pca1$li`):
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-697-```{r label=plot21, fig.width=6, fig.height=6}
##############################################
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-711-distribution of the 6 environmental variables on the PCA factorial map
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd:712:of the `jv73$tab` data set:
r-cran-adegraphics-1.0-15/vignettes/adegraphics.Rmd-713-```{r label=plot22, fig.width=6, fig.height=4}
##############################################
r-cran-adegraphics-1.0-15/debian/tests/run-unit-test-3-oname=adegraphics
r-cran-adegraphics-1.0-15/debian/tests/run-unit-test:4:pkg=r-cran-`echo $oname | tr '[A-Z]' '[a-z]'`
r-cran-adegraphics-1.0-15/debian/tests/run-unit-test-5-
r-cran-adegraphics-1.0-15/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
r-cran-adegraphics-1.0-15/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
r-cran-adegraphics-1.0-15/debian/tests/run-unit-test-8-# trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM