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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