[R] Multi-line forestplots, how to in R

[mcknight e. (em8g14)]

Hello,


I am working on ecological data covering a meta-analysis on invasive species traits.


I am not very skilled in R and would love if someone could assist me in my production of multi-line forest plots.

The data I have is: random effects mixed model and is further divided into subsets, I have used metafor package and here is a breakdown of my code =

#this is my main data calculation into effect sizes

MA <- escalc (measure="SMD", m1i=Invasive..mean, sd1i=sd.invasive, n1i=N.invasive, m2i=Control.mean, sd2i=sd.control, n2i=N.control, data=dataset)

res.MA <- rma(yi,vi,data=MA,method="REML");res.MA  #random-effects models ; "HS" Viechtbauer (2005)


#separating data
lab <- subset (x=MA, Type.of.ex=="Lab")
field <- subset (x=MA, Type.of.ex=="Field")

res.MAlab <- rma(yi,vi,data=lab,method="REML");res.MAlab  #random-effects models ; "HS" Viechtbauer (2005)
res.MAfield <- rma(yi,vi,data=field,method="REML");res.MAfield  #random-effects models ; "HS" Viechtbauer (2005)

res.traitlab <- rma(yi,vi,mods= ~ factor(Trait)-1,data=lab);res.traitlab #model for traits

res.traitfield <- rma(yi,vi,mods= ~ factor(Trait)-1,data=field);res.traitfield

#model for each lab traits

res.labct <- rma(yi,vi,subset=Trait=="Consumption",data=lab);res.labct
res.labec <- rma(yi,vi,subset=Trait=="Exploitative competition",data=lab);res.labec
res.labgr <- rma(yi,vi,subset=Trait=="Growth",data=lab);res.labgr
res.labic <- rma(yi,vi,subset=Trait=="Interference competition",data=lab);res.labic
res.labpa <- rma(yi,vi,subset=Trait=="Predator avoidance",data=lab);res.labpa
res.labpe <- rma(yi,vi,subset=Trait=="Predator escape",data=lab);res.labpe

#model for each field traits

res.fieldct <- rma(yi,vi,subset=Trait=="Consumption",data=field);res.labct
res.fieldec <- rma(yi,vi,subset=Trait=="Exploitative competition",data=field);res.labec
res.fieldgr <- rma(yi,vi,subset=Trait=="Growth",data=field);res.labgr
res.fieldic <- rma(yi,vi,subset=Trait=="Interference competition",data=field);res.labic
res.fieldpa <- rma(yi,vi,subset=Trait=="Predator avoidance",data=field);res.labpa
res.fieldpe <- rma(yi,vi,subset=Trait=="Predator escape",data=field);res.labpe

#producing a graph for lab data

estimateslab <- c(coef(res.labct), coef(res.labec), coef(res.labgr), coef(res.labic), coef(res.labpa),coef(res.labpe))
varianceslab <- c(vcov(res.labct), vcov(res.labec), vcov(res.labgr), vcov(res.labic), vcov(res.labpa),vcov(res.labpe))
labelslab <- c("Consumption (109)","Exploitative competition (21)","Growth (33)","Interference competition (31)","Predator avoidance (4)","Predator escape (61)")
forest(estimateslab, varianceslab, slab=labelslab, digit=0, annotate=F, xlab="Mean effect size",ylim=c(0,11))

#producing a graph for field data

estimatesfield <- c(coef(res.fieldct),coef(res.fieldec), coef(res.fieldgr), coef(res.fieldic),coef(res.fieldpa),coef(res.fieldpe))
variancesfield <- c(vcov(res.fieldct),vcov(res.fieldec), vcov(res.fieldgr), vcov(res.fieldic), vcov(res.fieldpa),   vcov(res.fieldpe))
labelsfield <- c("Consumption (7)","Exploitative competition (19)","Growth (2)","Interference competition (34)","Predator avoidance (2)","Predator escape (15)")
forest(estimatesfield, variancesfield, slab=labelsfield,digit=0,annotate=F,xlab="Mean effect size",ylim=c(0,11)) # "psize=1" size of mean box on forest plot
addpoly(res.MAfield, row=0.2, cex=1, atransf=F, mlab="RE Model Field Studies (79)",annotate=F)


OK, so sorry for code overload... I hope you can understand what i have done.

What i need it to produce one graph with both data sets Lab and field showing effect sizes for each of the mentioned traits. Im not super up to scratch on R and some of the current code was shared through a colleague, however this person isnt great at plots.


Please please can someone help me. Im currently wasting heaps of my time and getting no where.

Sincerely grateful

Ella

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