Re: [R] MODISTools help - with reproducible examples

2017-06-23 Thread Caroline 
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
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  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  
> 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 
>> wrote:
>>> 
 
 On Jun 22, 2017, at 4:44 PM, Caroline
>>  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]]
>> 
>> __
>> R-help@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]]

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Re: [R] MODISTools help - with reproducible examples

2017-06-23 Thread Jeff Newmiller 
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  
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 
>wrote:
>> 
>>> 
>>> On Jun 22, 2017, at 4:44 PM, Caroline
> 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]]
>
>__
>R-help@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.

__
R-help@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.

Re: [R] MODISTools help - with reproducible examples

2017-06-23 Thread Caroline 
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  wrote:
> 
>> 
>> On Jun 22, 2017, at 4:44 PM, Caroline  
>> 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]]

__
R-help@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.

Re: [R] MODISTools help - with reproducible examples

2017-06-22 Thread David Winsemius 

> On Jun 22, 2017, at 4:44 PM, Caroline  
> 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

__
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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.

[R] MODISTools help - with reproducible examples

2017-06-22 Thread Caroline 
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?


__
R-help@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.