I've been working on an HTML document with Rmarkdown.
The document has several sp plots and ggplots, and all of them appear in the HTML.
But when I call plotK (which is a function from the stpp package to plot the spatio-temporal inhomogeneous k-function - STIKhat), the plot doesn't appear in the HTML.
Here's a reproducible example for Rmarkdown:
---
title: "Untitled"
output: html_document
---
```{r}
library(stpp)
data(fmd)
data(northcumbria)
FMD<-as.3dpoints(fmd[,1]/1000,fmd[,2]/1000,fmd[,3])
Northcumbria=northcumbria/1000
# estimation of the temporal intensity
Mt<-density(FMD[,3],n=1000)
mut<-Mt$y[findInterval(FMD[,3],Mt$x)]*dim(FMD)[1]
# estimation of the spatial intensity
h<-mse2d(as.points(FMD[,1:2]), Northcumbria, nsmse=50, range=4)
h<-h$h[which.min(h$mse)]
Ms<-kernel2d(as.points(FMD[,1:2]), Northcumbria, h, nx=5000, ny=5000)
atx<-findInterval(x=FMD[,1],vec=Ms$x)
aty<-findInterval(x=FMD[,2],vec=Ms$y)
mhat<-NULL
for(i in 1:length(atx)) mhat<-c(mhat,Ms$z[atx[i],aty[i]])
# estimation of the STIK function
u <- seq(0,10,by=1)
v <- seq(0,15,by=1)
stik1 <- STIKhat(xyt=FMD, s.region=northcumbria/1000,t.region=c(1,200),
lambda=mhat*mut/dim(FMD)[1], dist=u, times=v, infectious=TRUE)
```
```{r}
plotK(stik1)
```
After knitting, the plot doesn't appear in the HTML output. Does anyone have any idea what is going on?
Thank you so much!
Try this with some extra packages in your plotting chunk:
library(png)
library(grid)
library(gridExtra)
plotK(stik1)
dev.print(png, "plot.png", width=480, height=480)
img <- readPNG("plot.png")
img <- rasterGrob(img)
grid.draw(img)