Data Set Citation:
When using this data, please cite the data package:
NCEAS 10645: Zhuang: Toward an adequate quantification of CH4 emissions from land ecosystems: Integrating field and in-situ observations, satellite data, and modeling , National Center for Ecological Analysis and Synthesis , and Walter K. 2008.
Siberian lake ebullition
nceas.891.3 (https://knb.ecoinformatics.org:443/knb/metacat/nceas.891.3/nceas)
General Information:
Title:Siberian lake ebullition
Identifier:nceas.891
Abstract:
Methane bubbling rates were measured in underwater/under-ice bubble traps (1-m diamter) in Siberian thermokarst lakes continuously for one year. Data are reported hourly as mg CH4 m-2 d-1 for background ebullition, and as mg CH4 spot-1 d-1 for point-source and hotspot bubbling.
Keywords:None:
  • methane
  • ebullition
  • Siberia
  • lake
  • thermokarst
  • permafrost
  • Arctic
Publication Date:2008-03-14
Data Table, Image, and Other Data Details:
Metadata download: Ecological Metadata Language (EML) File
Data Table:Walter_Lake_ebullition_fluxMat.csv ( View Metadata | Download File download)

Involved Parties

Data Set Creators:
Organization:NCEAS 10645: Zhuang: Toward an adequate quantification of CH4 emissions from land ecosystems: Integrating field and in-situ observations, satellite data, and modeling
Organization:National Center for Ecological Analysis and Synthesis
Individual: Katey Walter
Organization:University of Alaska, Fairbanks
Address:
525 Duckering Building WERC University of Alaska, Fairbanks Fairbanks, Alaska 99775,
Fairbanks, Alaska 99775 USA
Phone:
907-474-6095 (voice)
Phone:
907-474-7979 (Fax)
Email Address:
ftkmw1@uaf.edu
Data Set Contacts:
Individual: Katey Walter
Organization:University of Alaska, Fairbanks
Address:
525 Duckering Building WERC University of Alaska, Fairbanks Fairbanks, Alaska 99775,
Fairbanks, Alaska 99775 USA
Phone:
907-474-6095 (voice)
Phone:
907-474-7979 (Fax)
Email Address:
ftkmw1@uaf.edu
Associated Parties:
Individual: Katey Walter
Metadata Providers:
Individual: Katey Walter

Data Set Characteristics

Geographic Region:
Geographic Description:thermokarst lakes near Cherskii, Siberia- Northeast Russia along Kolyma River Lowlands
Bounding Coordinates:
West:  161.0  degrees
East:  161.0  degrees
North:  69.0  degrees
South:  69.0  degrees
Time Period:
Begin:
2003-04-23
End:
2004-06-01

Sampling, Processing and Quality Control Methods

Step by Step Procedures
Step 1:  
Description:

Methods used to transform the MS Excel spreadsheet into a comma delineated file

The program called "R" was used to combine the data from the individual bubble trap sections of the spreadsheet.

#

# R script for restructuring a Walter Lake methane dataset associated

# with the CH4 Emissions working group (NCEAS 10645: Zhuang). The

# restructuring is performed in accordance with a set of rules developed

# by Callie Bowdish.

#

# Note that this script standardizes column names, but does *not* fully

# clean up the data. For example, there are some character strings (e.g,

# "START", "#VALUE!") in columns that should probably only have numeric

# values. These are simply saved back out exactly as they were read in.

#

# Also note that values of "." (along with blank fields in numeric

# columns) in the original data are treated as NA, and subsequently

# written back out as blank fields. This behavior could be changed by

# removing the na.strings argument from the read.csv function.

#

# Author: Jim Regetz

# Date created: 18-Mar-2008

# NCEAS

#

# Read in the first 10319 rows of data (not including header). Don't

# change column names, and treat "." as NA

walter <- read.csv("Walter_Lake_ebullition_fluxMat.csv", nrow=10319,

na.strings = ".", check.names = FALSE, stringsAsFactors=FALSE)

# Clean up several column names for consistency

names(walter)[names(walter)=="Lake"] <- "lake"

names(walter)[grep("(mg CH4 m-2 d-1)", names(walter))] <-

"(mg_CH4_m-2_d-1)"

names(walter)[grep("(mgCH4_spot-1_d-1)", names(walter))] <-

"(mg_CH4_spot-1_d-1)"

names(walter)[grep("(mgCH4 spot-1 d-1)", names(walter))] <-

"(mg_CH4_spot-1_d-1)"

# Drop two empty columns (they're the ones without header names)

walter <- walter[, names(walter)!=""]

# Specify the desired order of the repeated columns

SORTORDER <- c("Bubble_Trap_No", "lake", "Bubble_Type",

"water_depth_(m)", "lake_section", "(mg_CH4_spot-1_d-1)",

"(mg_CH4_m-2_d-1)")

# Determine starting and ending col# for each batch of data

colIDs_start <- grep("Bubble_Trap", names(walter))

colIDs_end <- c(colIDs_start[-1] - 1, ncol(walter))

# Define a function for extracting a batch of columns from dframe,

# standardizing column names, and adding empty columns if any are

# missing.

extractBatch <- function(dframe, start, end, ord) {

batch <- dframe[start:end]

names(batch) <- gsub("^[[:digit:]]*_", "", names(batch))

names(batch) <- gsub("\\.[[:digit:]]*$", "", names(batch))

# If missing, create 'lake_section' and 'water_depth(m)' columns

if (!"lake_section" %in% names(batch)) {

batch$`lake_section` <- rep(NA, nrow(batch))

}

if (!"water_depth_(m)" %in% names(batch)) {

batch$`water_depth_(m)` <- rep(NA, nrow(batch))

}

# Add the missing CH4 column (or give error if both are missing)

if (!"(mg_CH4_m-2_d-1)" %in% names(batch)) {

batch$`(mg_CH4_m-2_d-1)` <- rep(NA, nrow(batch))

} else if (!"(mg_CH4_spot-1_d-1)" %in% names(batch)) {

batch$`(mg_CH4_spot-1_d-1)` <- rep(NA, nrow(batch))

} else {

stop("No CH4 column found")

}

# Re-sort columns and combine with first 5 columns of dataset

cbind(dframe[1:5], batch[ord])

}

# Break all the data into batches, using the function defined above

batches <- mapply(extractBatch, start=colIDs_start, end=colIDs_end,

MoreArgs=list(dframe=walter, ord=SORTORDER), SIMPLIFY=FALSE)

# Combine all the batches (by rows) into a big dataframe

final <- do.call("rbind", batches)

# Save as CSV, replacing NAs with blanks

write.csv(final, file="Walter_Lake_ebullition_fluxMat_FIXED.csv",

row.names=FALSE, na="", quote=FALSE)

Data Set Usage Rights

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Access Control:
Auth System:knb
Order:denyFirst
Metadata download: Ecological Metadata Language (EML) File