[R] MODISTools Help

[Caroline]

##MODISTools example
library(MODISTools)
library(lubridate)
setwd('~/Documents/Modis data')

#####MODISTools with buffalo data

###Read in data rename for easier coding
tbdata <- read.csv('~/Desktop/All TB data for EVI, NDVI.csv')
firstobs <- subset(tbdata, capture.ID == 'B1-1108')
firstobs <- firstobs[,c(1,2,2,3,4)]
colnames(firstobs) <- c('id', 'start.date','end.date','lat','long')

###change date format and change start date to previous 14 days
firstobs$start.date <- dmy(firstobs$start.date)
firstobs$end.date <- dmy(firstobs$end.date)
firstobs$start.date <- firstobs[,2] - as.difftime(14, unit='days') ###time frame now spands two weeks

###define parameters 
product <- "MOD13Q1"
bands <- c('250m_16_days_EVI', '250m_16_days_NDVI', '250m_16_days_VI_Quality')
pixel <- c(0,0)

###define data
period <- data.frame(lat=firstobs$lat, long=firstobs$long, start.date =firstobs$start.date, end.date = firstobs$end.date, id=firstobs$id)


###MODISSubsets
MODISSubsets(LoadDat = period, Products = product, Bands=bands, Size=pixel, SaveDir='.', StartDate=T)


###MODISSummaries
MODISSummaries(LoadDat = period, FileSep=',',Product='MOD13Q1', Bands = '250m_16_days_EVI', ValidRange=c(-2000,10000), NoDataFill=-3000, ScaleFactor = 0.0001, StartDate = TRUE, Interpolate = T, QualityScreen = TRUE, QualityThreshold = 0, QualityBand = '250m_16_days_VI_Quality')


> On Jun 22, 2017, at 4:50 PM, Bert Gunter <bgunter.4567 at gmail.com> wrote:
> 
> 1. You should always cc the list unless there is a clear reason not to.
> 
> 2. You still have failed to follow the posting guide: You say you have
> difficulty troubleshooting your code, but you have shown us no code.
> You got an error message that seems explicit, but with neither code
> nor data, I do not know whether anyone can make sense of it. In any
> case, I certainly cannot.
> 
> 
> Cheers,
> Bert
> 
> 
> Bert Gunter
> 
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
> 
> 
> On Thu, Jun 22, 2017 at 4:41 PM, Caroline
> <gliddeca at science.oregonstate.edu> wrote:
>> Hi Bert,
>> 
>> I have spent a lot of time searching the web for my error message and have gone through multiple tutorials. I have not found anything relevant to my error message which is why I posted on R-help.
>> 
>> Caroline
>> 
>>> On Jun 22, 2017, at 4:38 PM, Bert Gunter <bgunter.4567 at gmail.com> wrote:
>>> 
>>> This is a specialized package that fairly few of us are likely to have
>>> familiarity with, especialy when you have not followed the posting
>>> guide (below) and posted code and a reproducible example.
>>> 
>>> That said, a web search on R MODIS appeared to bring up relevant hits,
>>> including a MODIS tutorial. Have you tried that?
>>> 
>>> Cheers,
>>> Bert
>>> 
>>> 
>>> Bert Gunter
>>> 
>>> "The trouble with having an open mind is that people keep coming along
>>> and sticking things into it."
>>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>>> 
>>> 
>>> On Thu, Jun 22, 2017 at 2:12 PM, Caroline
>>> <gliddeca at science.oregonstate.edu> wrote:
>>>> I am using MODIS Tools and am having a lot of difficulty troubleshooting my code.
>>>> 
>>>> I am a PhD student studying African buffalo in Kruger National Park, South Africa. The study I am currently working on involves a herd of 200 African buffalo caught every six months for 4 years. I am trying to use EVI and NDVI to assess seasonal variation thus I would like mean EVI and NDVI for each observation (each time each buffalo was captured). I have capture date, lat and long for each observation.
>>>> 
>>>> However, when using ‘250m_16_days_pixel_reliability’ as my quality control band I keep getting the warning message:
>>>> 
>>>> Warning in MODISSummaries(LoadDat = period, FileSep = ",", Product = "MOD13Q1",  :
>>>> Only single data point that passed the quality screen: cannot summarise
>>>> 
>>>> When using ‘250m_16_days_VI_Quality’ as my quality control band I keep getting the warning message:
>>>> 
>>>> Error in QualityCheck(Data = band.time.series, QualityScores = QA.time.series,  :
>>>> QualityScores not all in range of MOD13Q1's QC: 0-3
>>>> 
>>>> I seem to get this message with all subsets of my data (I have tried running all of my data at once and then just one data point at a time). I have also tried using wider date ranges as well as wider size ranges (in case the pixel reliability is poor within a certain area or time frame) but still get the same messages.
>>>>       [[alternative HTML version deleted]]
>>>> 
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>> 


	[[alternative HTML version deleted]]