[R] MODISTools help - with reproducible examples

Caroline gliddeca at science.oregonstate.edu
Fri Jun 23 16:50:57 CEST 2017

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


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
2 B1-1108  28-Nov-08 28-Nov-08 -25.07324 31.936

firstobs after transformation

 id start.date   end.date       lat   long
2 B1-1108 2008-10-27 2008-11-28 -25.07324 31.936

The key point is that the time frame used for analysis should be greater than or equal to 32 days. 

> On Jun 23, 2017, at 7:37 AM, Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote:
> Please read up [1][2][3] on what constitutes reproducibility.  A sample of data that triggers the problem is essential. 
> [1] http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
> [2] http://adv-r.had.co.nz/Reproducibility.html
> [3] https://cran.r-project.org/web/packages/reprex/index.html
> -- 
> Sent from my phone. Please excuse my brevity.
> On June 23, 2017 6:54:48 AM PDT, Caroline <gliddeca at science.oregonstate.edu> wrote:
>> I have and they have not yet replied - however that was only two or
>> three days ago. 
>> I have included a code example. 
>>> On Jun 22, 2017, at 8:25 PM, David Winsemius <dwinsemius at comcast.net>
>> wrote:
>>>> On Jun 22, 2017, at 4:44 PM, Caroline
>> <gliddeca at science.oregonstate.edu> wrote:
>>>> I am using the R-package MODISTools (different than MODIS) and am
>> having a lot of difficulty troubleshooting my code. I have spent awhile
>> going through MODISTools tutorials, searching for my error code,
>> looking at the source code. However, I have not been able to find any
>> relevant information related to my error message. 
>>>> 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. 
>>>> I have attached the data file I have been using as well as my code
>> (subsetted to just one animal so the run time is faster) 
>>>> Has anyone seen this error message before/have any suggestions for
>> why I may be getting these errors?
>>> I don't and you have not provided the accepted means to investigate
>> which would be code and data . Have you contacted the package
>> maintainer?
>>> -- 
>>> David Winsemius
>>> Alameda, CA, USA
>> 	[[alternative HTML version deleted]]
>> ______________________________________________
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>> and provide commented, minimal, self-contained, reproducible code.

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