leap.zig: Plot changes in ecosystem function between communities as...

In ctkremer/priceTools: Tools for analyzing biodiversity-ecosystem function relationships

Description

This wrapper function takes the data generated by pairwise.price() and produces vector plots using either BEF, CAFE, or 5-part Price components.

Usage

leap.zig(data, type = "cafe", group.vars = NULL, standardize = TRUE, ...)

Arguments

data	Pairwise Price data
type	Specify the type of vector diagram to draw ("cafe","bef","both", or "price")
group.vars	A vector of grouping variables, if any
standardize	Should ecosystem function values be standardized against baseline
...	Additional graphical options passed to lower-level functions. See leap.zig.bef, leap.zig.cafe, leap.zig.both, leap.zig.price

Value

A ggplot object.

Examples

# Data setup
data(cedarcreek)
head(cedarcreek)

#Identify one grouping columns
cc2<-group_by(cedarcreek,NTrt,NAdd,Plot)

# Perform pairwise comparisons of all communities in cms identified by comm.id
# (takes ~30 sec)
pp<-pairwise.price(cc2,species='Species',func='Biomass')

# Organize/format the results, and pull out a subset using NAdd.x=0 as the control/baseline site
pp<-group.columns(pp,gps=c('NTrt','NAdd'))
pp<-pp[pp$NAdd.x=='0',]
dat1<-pp[pp$NAdd %in% c('0 27.2'),]
dat1.ctrl<-pp[pp$NAdd %in% c('0 0'),]

# Demonstrate vector plotting for comparisons between the control level of N addition (0) and the highest level of N addition (27.2):
leap.zig(dat1,type='cafe')

# Or sets of vectors grouped by N addition level:
leap.zig(pp,type='cafe',group.vars=c('NAdd.y'),raw.points=F,ylim=c(-100,700))

# The plots returned are ggplot objects, so additional design specifications can be added on:
leap.zig(dat1,type='cafe')+
  ggtitle('Enrichment \n(0 vs. 27.2)')

# Control plot window
leap.zig(dat1,type='cafe',xlim=c(3,18),ylim=c(-100,700))

# Turn on errorbars associated with vector endpoints
leap.zig(dat1,type='cafe',xlim=c(3,18),ylim=c(-100,700),error.bars=T)

# Turn on/off standardization of vector magnitude (taken as % change relative to baseline)
leap.zig(dat1,type='cafe',standardize=F)

# Make a plot without showing individual points:
leap.zig(dat1,type='cafe',standardize=F,raw.points=F)

# Use other styles of vector arrangements:
leap.zig(dat1,type='bef',standardize=F,raw.points=F)
leap.zig(dat1,type='price',standardize=F,raw.points=F)

# BUSTED!
# leap.zig(dat1,type='both')

# Turn legend off
leap.zig(dat1,type='price',standardize=F,raw.points=F,legend=F)

# Combine multiple plots in separate panels 
# (note: faceting currently doesn't work with leap.zig)
s1 <- leap.zig(dat1,type='cafe', xlim=c(3,18),ylim=c(-100,700),
               error.bars=T,vectors=T,raw.points = F,legend=F)
s2 <- leap.zig(dat1,type='bef', xlim=c(3,18),ylim=c(-100,700),
               error.bars=T,vectors=T,raw.points = F,legend=F)

library(gridExtra)
grid.arrange(s1,s2,nrow=1)

# Or on top of each other
s1 <- leap.zig(dat1,type='cafe', xlim=c(3,18),ylim=c(-100,700),
               error.bars=F,vectors=T,raw.points = F,legend=F)
leap.zig(dat1.ctrl,type='cafe', xlim=c(3,18),ylim=c(-100,700),
               error.bars=F,vectors=T,raw.points = F,legend=F,
               add=T,old.plot=s1)

# BUSTED - due to conflicting color scales
# s1 <- leap.zig(dat1,type='cafe', xlim=c(3,18),ylim=c(-100,700),
#                error.bars=T,vectors=T,raw.points = F,legend=F)
# leap.zig(dat1,type='bef', xlim=c(3,18),ylim=c(-100,700),
#                error.bars=T,vectors=T,raw.points = F,legend=F,
#                add=T,old.plot=s1)

ctkremer/priceTools documentation built on May 28, 2019, 7:49 p.m.