## ----setup, include = FALSE------------------------------------------------ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## -------------------------------------------------------------------------- library(SMAD) data("TestDatInput") head(TestDatInput) ## ----echo=TRUE, message=FALSE, warning=FALSE------------------------------- scoreCompPASS <- CompPASS(TestDatInput) head(scoreCompPASS) ## ----CompPASS output figure, echo=FALSE, fig.height=7, fig.width=7, message=FALSE, warning=FALSE, paged.print=FALSE---- par(mfrow = c(2, 2)) plot(sort(scoreCompPASS$scoreZ, decreasing = TRUE), pch = 16, xlab = "Ranked bait-prey interactions", ylab = "Z-score") plot(sort(scoreCompPASS$scoreS, decreasing = TRUE), pch = 16, xlab = "Ranked bait-prey interactions", ylab = "S-score") plot(sort(scoreCompPASS$scoreD, decreasing = TRUE), pch = 16, xlab = "Ranked bait-prey interactions", ylab = "D-score") plot(sort(scoreCompPASS$scoreWD, decreasing = TRUE), pch = 16, xlab = "Ranked bait-prey interactions", ylab = "WD-score") ## -------------------------------------------------------------------------- scoreHG <- HG(TestDatInput) head(scoreHG) ## ----HG output figure, echo=FALSE, fig.height=7, fig.width=7, message=FALSE, warning=FALSE, paged.print=FALSE---- plot(sort(scoreHG$HG, decreasing = TRUE), pch = 16, xlab = "Ranked prey-prey interactions", ylab = "HGscore")