In case anyone else experiences the same error:
The package creators responded and the issue was that I was using time frames between 14-30 days. EVI and NDVI are only calculated every 16 days so using that time span entailed that there was only one pixel per observation. I expanded my timeframe to 32 days and my analysis now works.
I.E. changed:
firstobs$start.date <- firstobs[,2] - as.difftime(14, unit='days') ###time frame now spands two weeks
To
firstobs$start.date <- firstobs[,2] - as.difftime(32, unit='days') ###time frame now stands 32 days
Where first obs is the data set that contains the date that the data was collected, latitude, and longitude of collection site from one observation. I used the date the data was collected as the end date and transformed the date the data was collected to 32 days prior as the start date.
firstobs before transformation:
id start.date end.date lat long
B1-1108 28-Nov-08 28-Nov-08 -25.07324 31.936
firstobs after transformation
id start.date end.date lat long
B1-1108 2008-10-27 2008-11-28 -25.07324 31.936
> On Jun 23, 2017, at 8:49 AM, Robert Baer <rbaer at atsu.edu> wrote:
>
>
>
> On 6/22/2017 7:05 PM, Caroline wrote:
>> ##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')
> Since this dataset is only on your desktop it cannot help us reproduce your error. Can you supply a small dataset that cause the
> error you are talking about?
>
> One way to do this is to use supply the results of
> dput(tbdata)
> if it is small enough. If not, maybe create a subset of the data and then use dput()
>
> Did you get the problem when you tried with the tutorial Bert suggested?
>> 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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>>>>>>
>>>>>> ______________________________________________
>>>>>> 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]]
>>
>> ______________________________________________
>> R-help at r-project.org <mailto:R-help at r-project.org> mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help <https://stat.ethz.ch/mailman/listinfo/r-help>
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html <http://www.r-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>
> --
>
>
> --
> Robert W. Baer, Ph.D.
> Professor of Physiology
> Kirksville College of Osteopathic Medicine
> A T Still University of Health Sciences
> 800 W. Jefferson St
> Kirksville, MO 63501
> 660-626-2321 Department
> 660-626-2965 FAX
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