##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 <[email protected]> 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
> <[email protected]> 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 <[email protected]> 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
>>> <[email protected]> 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]]
>>>>
>>>> ______________________________________________
>>>> [email protected] 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]]
______________________________________________
[email protected] 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.
