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]]
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. > [[alternative HTML version deleted]] > > ______________________________________________ > 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.
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. >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> 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. >
##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.
>>>> [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> 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.
>>
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