Order raster images in a levelplot

Dear Both,
Thank you for your responses.
Oscar- I am still trying to get the indexing going. Hope it will be sorted out soon.
Just to provide some more background on my code- here is an example.

library(raster)
library(rasterVis)
library(raster)
library(rgdal)
library(zoo)

setwd("/Users/nasi/Google Drive/5KMNDVI_Monthly")

modis = stack(list.files(pattern='NDVI.tif'))
modis
names(modis)
d<-seq(as.Date("2010-01-01"),as.Date("2014-08-01"),by="month")
names(modis)<-d
NDVImod<-setZ(modis,d)
e<-extent(-17.96, 43.135, -30.055, 67.08)
NDVImodis<-crop(NDVImod,e)
NDVImodis[NDVImodis<0]<-0
NDVImodis<-setZ(NDVImodis,d)
names(NDVImodis)<-d

# The first problem occurs below. I am trying to get monthly means and other quantities. Although the function does give me an output, but the results are completely wrong. As it seems to be averaging the wrong months together. Can?t really paste the image here i suppose.

year.mon.max<-zApply(NDVImodis, by=months, fun=max, name="months")
year.mon.min<-zApply(NDVImodis, by=months, fun=min, name="months")
year.mon.diff<-year.mon.max-year.mon.min
year.mon.sd<-zApply(NDVImodis, by=months, fun=sd, name="months")
year.mon.cv<-zApply(NDVImodis, by=months, fun=cv, name="months?)

# I only manage to rearrange this one using the code after these lines. But since the images are wrong, its not of much use. Perhaps my use of ?by? argument above is not correct. Or my naming of the rasters isn?t either.

print(levelplot(year.mon.mean[[c(6,2,12,11,10,3,5,4,8,1,9,7)]], main="Mean Monthly NDVI (2010-2014)", par.settings=myTheme))

# perhaps here is where i need to use the par.cond
# I tried using ?index.cond? here like below:

levelplot(year.mon.mean, index.cond=list(c("January","February","March", "April", "May", "June","July", "August", "Septmeber", "Ocotber","November", "December")), par.settings=myTheme)

#But this doesn?t plot anything. Even the maps disappear. Perhaps this again has to do with the naming in the rasters.

#Anyhow, i would like to match these monthly images with data on spatial observations of animals where i have an x,y and a date matching the date of the raster.

#I tried doing this below -
df$layer<-lapply(df$month, function(x) which(grepl(tolower(x), tolower(names(year.mon.mean)))))
df$meanNDVI<-sapply(seq_len(nrow(df)), function(x) extract(mean.year.mon[[df$layer[x]]], df[x,1:2])) # 1,2 are columns with x and y.

#This also doesn?t work, perhaps also has to do with the names in the raster.

Your help is much appreciated.
Ill keep trying the par.cond argument in the meanwhile.

Best wishes,

Navinder

Navinder J Singh
Associate Professor
Department of Wildlife, Fish, and Environmental Studies
Faculty of Forest Sciences
Swedish University of Agricultural Sciences
SE-901 83 Umea, Sweden
O: +46 (0)90 786 8538;
M: +46 (0)70 676 0103
email: navinder.singh at slu.se<mailto:navinder.singh at slu.se>
Web: navinderjsingh.weebly.com<http://navinderjsingh.weebly.com/>

www.slu.se/viltfiskmiljo/navinder_singh<http://www.slu.se/viltfiskmiljo/navinder_singh>
http://slu-se.academia.edu/NSingh