MODISTools Help

##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.
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