<div dir="ltr"><div>Hi, All:</div><div><br></div><div>This is my code to use REddyProc for my two sites, n stands for north tower and s stands for south. This code is used for H and LE, but it similar to CO2. Hope it helps you to write your own code.</div><div><br></div><div><br></div><div>##############=============================Gap Filling========================####</div><div>######load data</div><div>###remember to add storage to flux for H and LE</div><div><br></div><div><br></div><div>######load data</div><div># data(tower_n_2016_all)</div><div>tower_n_2016_all$new_NEE=tower_n_2016_all$co2_flux + tower_n_2016_all$co2_strg</div><div>tower_n_2016_all$new_H=tower_n_2016_all$H + tower_n_2016_all$H_strg </div><div>tower_n_2016_all$new_LE=tower_n_2016_all$LE +tower_n_2016_all$LE_strg</div><div>tower_n_2016_all <- createTimestamp(tower_n_2016_all)</div><div>tower_n_2016_all <- fillTimestamp(tower_n_2016_all, "timestamp")</div><div>EddyData_north <- tower_n_2016_all[ ,c("year","DOY","hour","new_NEE","new_LE","new_H","Rg_1_1_1","air_temperature","Ts_1_1_1","RH","VPD","u.")]</div><div>EddyData_north <- plyr::rename(EddyData_north, c("year"="Year", "DOY"="DoY", "hour"="Hour", "new_NEE"="NEE","new_LE"="LE", "new_H"="H","Rg_1_1_1"="Rg", "air_temperature"= "Tair", "Ts_1_1_1"= "Tsoil","RH"="rH","VPD"= "VPD","u."="Ustar"))</div><div><br></div><div>##EddyData_north$NEE <-EddyData_north$co2_flux + EddyData_north$co2_strg</div><div><br></div><div>## EddyData_north <- EddyData_north[, -grep("co2_flux", names(EddyData_north))]</div><div>### EddyData_north <- EddyData_north[, -grep("co2_strg",names(EddyData_north))]</div><div>summary(EddyData_north)</div><div>#EddyData_north$Tair = EddyData_north$Tair -273.15</div><div>EddyData_north$Tsoil = EddyData_north$Tsoil -273.15</div><div>EddyData_north$DoY = floor(EddyData_north$DoY)</div><div>EddyData_north$VPD = EddyData_north$VPD/100</div><div><br></div><div>#summary(EddyData_north$NEE) =removeOutliers(EddyData_north$NEE, na.rm=TRUE)</div><div>#EddyData_north$LE =removeOutliers(EddyData_north$LE, na.rm=TRUE)</div><div>#EddyData_north$H =removeOutliers(EddyData_north$H, na.rm=TRUE)</div><div>#EddyData_north$Tsoil =removeOutliers(EddyData_north$Tsoil, na.rm=TRUE)</div><div>#EddyData_north$Rg =removeOutliers(EddyData_north$Rg, na.rm=TRUE)</div><div>EddyData_north = EddyData_north[-1,]</div><div><br></div><div>#######################################</div><div>library(REddyProc)</div><div><br></div><div>EddyData_north_WithPosix <- fConvertTimeToPosix(EddyData_north, 'YDH', Year.s='Year', Day.s='DoY', Hour.s='Hour')</div><div><br></div><div>EddyProc.C_north <- sEddyProc$new("north", EddyData_north_WithPosix, c('LE','Rg','Tair','VPD', 'Ustar'))</div><div><br></div><div>(uStarTh <- EddyProc.C_north$sEstUstarThreshold(NEEColName = "LE")$uStarTh)</div><div><br></div><div>EddyProc.C_north$sMDSGapFillAfterUstar('LE')</div><div># Note the collumns with suffix _WithUstar</div><div>colnames(EddyProc.C_north$sExportResults()) <span class="gmail-Apple-tab-span" style="white-space:pre"> </span></div><div><br></div><div>#+++ Export gap filled and partitioned data to standard data frame</div><div>FilledEddyData.F_north_LE <- EddyProc.C_north$sExportResults()</div><div>############################</div><div>EddyProc.C_north <- sEddyProc$new("north", EddyData_north_WithPosix, c('H','Rg','Tair','VPD', 'Ustar'))</div><div><br></div><div>(uStarTh <- EddyProc.C_north$sEstUstarThreshold(NEEColName = "H")$uStarTh)</div><div><br></div><div>EddyProc.C_north$sMDSGapFillAfterUstar('H',UstarSuffix.s = "WithUstar_H")</div><div><br></div><div>FilledEddyData.F_north_H <- EddyProc.C_north$sExportResults()</div><div><br></div><div>## colnames(EddyProc.C_north$sExportResults()) # Note the collumns with suffix _WithUstar<span class="gmail-Apple-tab-span" style="white-space:pre"> </span></div><div><br></div><div><br></div><div>#+++ Save results into (tab-delimited) text file in directory \out</div><div>CombinedData.F_north <- cbind(EddyData_north, FilledEddyData.F_north_LE, FilledEddyData.F_north_H)</div><div><br></div><div><br></div><div>CombinedData.F_north_1 <- fConvertTimeToPosix(CombinedData.F_north, TFormat.s='YDH', Year.s = "Year", </div><div> Month.s = "none", Day.s = "DoY", Hour.s = "Hour", </div><div> Min.s = "none", TName.s = "timestamp")</div><div>names(CombinedData.F_north)</div><div>head(CombinedData.F_north_1)</div><div><br></div><div>Gap_filled_north_final_result <- </div><div> CombinedData.F_north_1[, c("timestamp", "Year", "DoY","Hour", "LE_WithUstar_f","H_WithUstar_H_f","Rg")]</div><div>###==========================================gap Filling Done==============================#####</div><div><br></div></div><div hspace="streak-pt-mark" style="max-height:1px"><img alt="" style="width:0px;max-height:0px;overflow:hidden" src="https://mailfoogae.appspot.com/t?sender=ac3VueG0xOUBnbWFpbC5jb20%3D&type=zerocontent&guid=6589925b-1979-418f-836c-3f0d7f31e80f"><font color="#ffffff" size="1">ᐧ</font></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jun 9, 2017 at 2:11 AM, Thomas Wutzler <span dir="ltr"><<a href="mailto:twutz@bgc-jena.mpg.de" target="_blank">twutz@bgc-jena.mpg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Fulin Yang,<br>
<br>
thanks for your interest in our REddyProc package.<br>
<br>
Unfortunately, we cannot offer general help on R.<br>
The package is developed for people to make use of the power and<br>
flexibility of a general programming language such as R.<br>
<br>
For simple standard applications we provide the web-tool, which is<br>
completely based on REddyProc:<br>
<a href="https://www.bgc-jena.mpg.de/bgi/index.php/Services/REddyProcWeb" rel="noreferrer" target="_blank">https://www.bgc-jena.mpg.de/<wbr>bgi/index.php/Services/<wbr>REddyProcWeb</a><br>
<br>
If you are near Jena, you may apply for an R beginners course of the<br>
IMPRS at our institute: <a href="http://www.imprs-gbgc.de" rel="noreferrer" target="_blank">http://www.imprs-gbgc.de</a><br>
Probably, you will find something similar near to you.<br>
<br>
Otherwise there are good R tutorials on the web for different backgrounds.<br>
<br>
I strongly recommend you, finding a colleague with some R experience to<br>
help you getting started and help you with problems. Most of the<br>
R-related problems are difficult to describe in general but are quickly<br>
solved by case by people with some experience.<br>
<br>
<br>
Yours,<br>
Thomas<br>
<br>
On 09.06.2017 03:58, Fulin Yang wrote:<br>
> Dear Prof. Thomas Wutzler,<br>
><br>
><br>
><br>
> I am a new user of REddyPro in R, which is great contributions to the<br>
> eddy flux data processing.<br>
><br>
><br>
><br>
> Previously, I used online version to perform flux data gap-filling and<br>
> partioning. It worked very well.<br>
><br>
><br>
><br>
> Now, I try the R version, and have a big problem, due to not familiar to<br>
> R language. Maybe there are lots people like me, I think.<br>
><br>
><br>
><br>
> I have to ask you for help. Do you have something like simple training<br>
> PPT with pictures on using of REddyPro in R, or some training videos,<br>
> please share me. This is very helpful for beginners. Many thanks,<br>
><br>
><br>
><br>
> Best wishes,<br>
><br>
><br>
><br>
> Fulin Yang<br>
><br>
><br>
<br>
<br>______________________________<wbr>_________________<br>
Reddyproc-users mailing list<br>
<a href="mailto:Reddyproc-users@lists.r-forge.r-project.org">Reddyproc-users@lists.r-forge.<wbr>r-project.org</a><br>
<a href="http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/reddyproc-users" rel="noreferrer" target="_blank">http://lists.r-forge.r-<wbr>project.org/cgi-bin/mailman/<wbr>listinfo/reddyproc-users</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><font color="#999999" face="tahoma, sans-serif">Xiangmin (Sam) Sun</font><div><div><span style="color:rgb(153,153,153)"><font face="tahoma, sans-serif"><br></font></span></div><div><font color="#999999" face="tahoma, sans-serif">PhD student</font></div><div><font color="#999999" face="tahoma, sans-serif">Department of Ecosystem Science and Management (ESSM)</font></div><div><font face="tahoma, sans-serif"><br></font></div><div><font color="#999999" face="tahoma, sans-serif">Search, Search, Research!</font></div></div></div></div></div></div></div></div></div>
</div>