Spatial patterns in Pinus pinea regeneration transects

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Recovering transects data

stored in GoogleSheet ‘gsn’, worksheet name ‘wsn’ archived 2/1/2017 https://www.zenodo.org/deposit/228327

library(googlesheets)
suppressMessages(library(dplyr))
gsn <-"TransectPinusPinea"      # GoogleSheetName
gs_ls(gsn)
tpp <- gs_title(gsn)
wsn <- "PointPatternWithMarks"  # WorkSheetName
cat("Sheet '", wsn, "'", ifelse(wsn %in% gs_ws_ls(tpp),"", "NOT "), "found.")
ppwm <- tpp %>% gs_read(ws=wsn)
ppwm$nPf <- as.factor(ppwm$`N palchi`)
str(ppwm)

Preparing Marks

Some attributes have a single value for each registerede position, other ones can have more than on value. These these have been aggregated in the worksheet.

Initializing PPP

Spatia patterns windows are, partially, undefined (width=10m, length: open) and has to be estimated!!

library(spatstat)
Areas <- unique(ppwm$Area)
t_windows <- list()
for(tid in Areas) t_windows[[tid]] <- ripras(ppwm$X[ppwm$Area==tid],ppwm$Y[ppwm$Area==tid], shape = "rectangle")
# ripras():  Estimate window from points alone

Test anaysis on one of the transects

tid <- Areas[1]
trs <- ppp(ppwm$X[ppwm$Area==tid],ppwm$Y[ppwm$Area==tid]
           , xrange = t_windows[[tid]]$xrange, yrange = c(-10, 10)
           , marks = ppwm[ppwm$Area==tid, c(5:7, 9, 11:15)])
# , unlist(t_windows[t_windows$Area==tid,c('X0', 'X1')]), c(-10-marg, 10+marg)
unitname(trs) <- "m"
plot(trs, arrange=FALSE, par(mar=rep(3,4)))

Interpretation of arguments maxsize and markscale has changed (in spatstat version 1.37-0 and later). Size of a circle is now measured by its diameter.

summary(trs)$intensity

[1] 0.01971024

side <- 10 # m - tessellation step
nx <- floor((trs$window$xrange[2] - trs$window$xrange[1])/side)
ny <- floor((trs$window$yrange[2] - trs$window$yrange[1])/side)
Q <- quadratcount(trs, nx, ny)
plot(trs, arrange=FALSE,cex=.5, pch="+")

plot(Q, add=TRUE, cex=.5)

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