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topicindex [2012/06/14 02:32]
gremau
topicindex [2014/02/01 13:22] (current)
gremau
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 ===== Active research projects ===== ===== Active research projects =====
 +
 Each research project has its own [[http://​www.dokuwiki.org/​namespaces|namespace]]. Within these project namespaces there are overview pages, methods pages (usually site-specific methods), project logs, and results pages. Overview pages describe the project objectives, hypotheses, and research approach, and should link to all other pages in the project namespace. Each research project has its own [[http://​www.dokuwiki.org/​namespaces|namespace]]. Within these project namespaces there are overview pages, methods pages (usually site-specific methods), project logs, and results pages. Overview pages describe the project objectives, hypotheses, and research approach, and should link to all other pages in the project namespace.
  
 ==Hidden Canyon ecohydrology (hc_ecohydrology)== ==Hidden Canyon ecohydrology (hc_ecohydrology)==
 +
   * [[hc_ecohydrology:​overview|Overview]]   * [[hc_ecohydrology:​overview|Overview]]
   * Experimental design: [[hiddencanyon:​snowmeltdesign]],​ [[hiddencanyon:​soilprofiles]]   * Experimental design: [[hiddencanyon:​snowmeltdesign]],​ [[hiddencanyon:​soilprofiles]]
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 ==Western U.S. soil climate analysis (west_stationdata)== ==Western U.S. soil climate analysis (west_stationdata)==
 +
   * [[west_stationdata:​overview|Overview]]   * [[west_stationdata:​overview|Overview]]
-  * Methods: [[west_stationdata:​data|Data collection and prep]], [[west_stationdata:​programdocs|Data programming documentation]] +  * Methods: [[west_stationdata:​data|Data collection and prep]], [[west_stationdata:​programdocs|Data programming documentation]][[west_stationdata:​data_qc|Data QC (cleaning)]], [[west_stationdata:​statistics|Statistical approach & methods]] 
-  * Logs: [[west_stationdata:​analysislog_1|Ts analysis log]], [[west_stationdata:​analysislog_2|SM analysis log]] +  * Logs: [[west_stationdata:​analysislog_1|Data ​analysis log]] 
-  * [[west_stationdata:​publicationoutline]]+  * [[west_stationdata:​publicationoutline|Publication outline]]
  
 ==Western U.S. soil carbon cycling (west_carboncycle)== ==Western U.S. soil carbon cycling (west_carboncycle)==
 +
   * [[west_carboncycle:​overview|Overview]]   * [[west_carboncycle:​overview|Overview]]
   * Methods: [[west_carboncycle:​snotelfieldprotocol|Protocol for SNOTEL visits]], [[west_carboncycle:​snotelsampleprocessing|Initial sample processing]]   * Methods: [[west_carboncycle:​snotelfieldprotocol|Protocol for SNOTEL visits]], [[west_carboncycle:​snotelsampleprocessing|Initial sample processing]]
   * Logs: [[west_carboncycle:​snotellog_1|SNOTEL visits]], [[west_carboncycle:​sampleprocessinglog_1|Sample processing]],​ [[west_carboncycle:​analysislog_1|Data analysis]], [[west_carboncycle:​sampletables|Sample processing tables]].   * Logs: [[west_carboncycle:​snotellog_1|SNOTEL visits]], [[west_carboncycle:​sampleprocessinglog_1|Sample processing]],​ [[west_carboncycle:​analysislog_1|Data analysis]], [[west_carboncycle:​sampletables|Sample processing tables]].
 +
 +==Niwot girdling study (niwot_girdling)==
 +
 +  * Methods: [[niwot_girdling:​data_qc|Data QC]], [[niwot_girdling:​soilanalysis|Soil analysis]], [[procedures:​soilextract_13c|Soil extract 13C procedure]]
 +  * [[niwot_girdling:​activitylog_1|Activity log]]
  
 ==Ion deposition in snow (snowdep)== ==Ion deposition in snow (snowdep)==
 +
   * [[wasatchsnowdep:​overview|Overview]]   * [[wasatchsnowdep:​overview|Overview]]
   * Methods: [[wasatchsnowdep:​sampling|Snow sampling and cleanliness procedures]],​ [[wasatchsnowdep:​labprocessing|Processing snow samples for analysis]], [[wasatchsnowdep:​standards|Mixing ion standards]]   * Methods: [[wasatchsnowdep:​sampling|Snow sampling and cleanliness procedures]],​ [[wasatchsnowdep:​labprocessing|Processing snow samples for analysis]], [[wasatchsnowdep:​standards|Mixing ion standards]]
   * [[wasatchsnowdep:​analysislog_1|Data analysis log]]   * [[wasatchsnowdep:​analysislog_1|Data analysis log]]
   * [[wasatchsnowdep:​activitylog_1|Activity log (not used)]]   * [[wasatchsnowdep:​activitylog_1|Activity log (not used)]]
 +
  
 ===== Procedures ===== ===== Procedures =====
 +
 Protocols for making measurements in the field or the lab, processing samples for analysis, or analyzing data. Intended as a general reference, but site or experiment-specific info can be appended as necessary. Protocols for making measurements in the field or the lab, processing samples for analysis, or analyzing data. Intended as a general reference, but site or experiment-specific info can be appended as necessary.
 +
  
 == Laboratory protocols == == Laboratory protocols ==
 +
   * [[procedures:​exetainer_co2|Measuring exetainer gas samples]] for CO<​sub>​2</​sub>​ and C isotopes   * [[procedures:​exetainer_co2|Measuring exetainer gas samples]] for CO<​sub>​2</​sub>​ and C isotopes
   * [[procedures:​soilacidtreatment|Acid treatment of soils]] to remove carbonates.   * [[procedures:​soilacidtreatment|Acid treatment of soils]] to remove carbonates.
   * [[procedures:​ea-irms_soilprep|Soil sample prep for EA-IRMS analysis]] at SIRFER.   * [[procedures:​ea-irms_soilprep|Soil sample prep for EA-IRMS analysis]] at SIRFER.
   * [[procedures:​14c_graphitization|Graphitization of soils]] for AMS <​sup>​14</​sup>​C analysis   * [[procedures:​14c_graphitization|Graphitization of soils]] for AMS <​sup>​14</​sup>​C analysis
-  * [[procedures:​soildensityfractionation:​ Soil density fractionation]] 
   * [[procedures:​treecores|Preparing and taking data from tree cores]]   * [[procedures:​treecores|Preparing and taking data from tree cores]]
 +  * [[procedures:​snowpackdustloading|Snowpack dust loading]]
 +  * [[procedures:​soilextract_13c|δ13C analysis of soil extracts]]
 +
  
 == Field protocols == == Field protocols ==
 +
   * [[procedures:​manual_soilresp|Manual soil respiration measurements]] (Hidden Canyon)   * [[procedures:​manual_soilresp|Manual soil respiration measurements]] (Hidden Canyon)
   * [[procedures:​belowsnow_soilresp|Below-snow respiration measurements]](Hidden Canyon)   * [[procedures:​belowsnow_soilresp|Below-snow respiration measurements]](Hidden Canyon)
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   * [[procedures:​measuringswe]]   * [[procedures:​measuringswe]]
   * [[procedures:​xylempressure]]   * [[procedures:​xylempressure]]
-  * [[procedures:​snowpackalbedo]] 
-  * [[procedures:​snowpackdustloading]] 
   * [[procedures:​snowpacksublimation]]   * [[procedures:​snowpacksublimation]]
   * [[procedures:​canopyphotos|Canopy photography]]   * [[procedures:​canopyphotos|Canopy photography]]
   * [[procedures:​gps|Georeferencing with GPS]]   * [[procedures:​gps|Georeferencing with GPS]]
 +
  
 == Data analysis and instrumentation programming == == Data analysis and instrumentation programming ==
 +
   * [[procedures:​programming|Data analysis programming]]:​ General info for using Python/​MATLAB/​Octave/​R for data analysis   * [[procedures:​programming|Data analysis programming]]:​ General info for using Python/​MATLAB/​Octave/​R for data analysis
   * [[procedures:​pythontips|Python tips]], [[procedures:​numpytips|Numpy tips]], [[procedures:​ipython|Using IPython]]   * [[procedures:​pythontips|Python tips]], [[procedures:​numpytips|Numpy tips]], [[procedures:​ipython|Using IPython]]
   * [[procedures:​matlabtips|Matlab tips]]   * [[procedures:​matlabtips|Matlab tips]]
-  * [[procedures:​bash|Bash scripting]] +  * [[procedures:​shellscripts|Shell scripts]][[procedures:​awk|AWK]], [[procedures:​vimtips|Vim]],​ and [[procedures:​textfiles|assorted textfile tips]]
-  * [[procedures:​awk|Awk scripts]]+
   * [[procedures:​mercurial|mercurial]],​ and [[procedures:​git|git]]:​ 2 version control systems.   * [[procedures:​mercurial|mercurial]],​ and [[procedures:​git|git]]:​ 2 version control systems.
   * [[procedures:​sensordata_tips|Tips for analyzing sensor timeseries]]   * [[procedures:​sensordata_tips|Tips for analyzing sensor timeseries]]
   * [[procedures:​data_analysis_workflow|Workflow for data analysis]]   * [[procedures:​data_analysis_workflow|Workflow for data analysis]]
   * [[procedures:​geospatial|Geospatial data analysis]]   * [[procedures:​geospatial|Geospatial data analysis]]
 +
 +
 +== Research writing ==
 +
 +  * [[procedures:​textfiles|Text file tips]]
 +  * [[procedures:​pandoc|Pandoc]] document converter and markup syntax.
 +  * [[procedures:​latextips|LaTeX tips]]
 +
  
 ===== Math ===== ===== Math =====
-Mathematic or statistical ​concepts ​and methods used in data analysis.+ 
 +Pages covering ​statistical and mathematical concepts, or numerical ​methods used in data analysis. Some of these pages are composed primarily of links to further information on the subject.
   * [[math:​toolboxes|Computation toolboxes]] - tools for computing math and statistics.   * [[math:​toolboxes|Computation toolboxes]] - tools for computing math and statistics.
   * [[math:​timeseries|Time series analysis]] - assorted methods for analyzing time series data to extract meaningful statistics.   * [[math:​timeseries|Time series analysis]] - assorted methods for analyzing time series data to extract meaningful statistics.
 +  * [[math:​anova|ANOVA]] - analysis of variance for various experimental designs.
   * [[math:​quadratic_eq_calib|Reversing calibration equations]] - using the quadratic equation to back out sensor output from calibrated data (if calibration is known).   * [[math:​quadratic_eq_calib|Reversing calibration equations]] - using the quadratic equation to back out sensor output from calibrated data (if calibration is known).
-  * [[math:​pca|Principal components analysis]]+  * [[math:​pca|Principal components analysis]] ​and [[math:​pcr|Principal components regression]] 
 +  * [[math:​correlation|Correlation]] 
 +  * [[math:​normalitytests|Testing for normality]] 
 +  * [[math:​linear_regression|Linear regression]] - Bivariate (one independent variable) and multiple regression (>1 ind. variable). 
 +  * [[math:​multilevel_models| Multilevel/​Mixed/​Heirarchical statistical models]] 
 +  * [[math:​integration|Integration]] - of functions, or sampled data such as a timeseries 
 +  * [[math:​decay_turnover|Decay and turnover]] functions. 
  
 ===== Instruments ===== ===== Instruments =====
-Contain documentation for operating, calibrating,​ and maintaining field and lab instruments,​ sensors, etc. There are  + 
-also notes on programs, calibration constants, and conversion coefficients for instruments currently in use.+Contain documentation for operating, calibrating,​ and maintaining field and lab instruments,​ sensors, etc. There are also notes on programs, calibration constants, and conversion coefficients for instruments currently in use.
  
   * [[instruments:​li-190|Li-Cor Quantum sensor (LI-190)]]   * [[instruments:​li-190|Li-Cor Quantum sensor (LI-190)]]
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   * [[instruments:​cr10dataloggers|Campbell cr10 dataloggers]] (several old ones in Red Butte Canyon)   * [[instruments:​cr10dataloggers|Campbell cr10 dataloggers]] (several old ones in Red Butte Canyon)
   * [[instruments:​sentek_enviroscan|Sentek EnviroSCAN soil moisture profiles]] (there are a couple at Hidden Canyon).   * [[instruments:​sentek_enviroscan|Sentek EnviroSCAN soil moisture profiles]] (there are a couple at Hidden Canyon).
 +  * [[instruments:​ea-irms_sirfer|EA-IRMS protocol]] at the SIRFER lab.
 +
  
 ===== Research Sites ===== ===== Research Sites =====
 +
 Research sites (or networks) have their own namespace. Pages in a site namespace should have descriptive information about the sites themselves, research instrumentation,​ or researcher activities there. For example: ​ site maps, research plot layouts, technical info and schematics for research installations (weather stations, etc.), activity/​maintenance logs,  etc. Research sites (or networks) have their own namespace. Pages in a site namespace should have descriptive information about the sites themselves, research instrumentation,​ or researcher activities there. For example: ​ site maps, research plot layouts, technical info and schematics for research installations (weather stations, etc.), activity/​maintenance logs,  etc.
  
-  - Hidden Canyon +==Hidden Canyon== 
-    * [[hiddencanyon:​sitedescription|Site description]],​ [[hiddencanyon:​trees|Tree location data]] + 
-    * Instrumentation:​ [[hiddencanyon:​communicationsystem]],​ [[hiddencanyon:​dataloggers]],​ [[hiddencanyon:​mettowers]],​ [[hiddencanyon:​soilprofiles]],​ [[hiddencanyon:​georeferencing]] +  ​* [[hiddencanyon:​sitedescription|Site description]],​ [[hiddencanyon:​trees|Tree location data]] 
-    * [[hiddencanyon:​hc2010_log|2010 activity log]], [[hiddencanyon:​hc2011_log|2011 activity log]], [[hiddencanyon:​hc2012_log|2012 activity log]], [[hiddencanyon:​analysislog_1|data analysis log]] +  * Instrumentation:​ [[hiddencanyon:​communicationsystem]],​ [[hiddencanyon:​dataloggers]],​ [[hiddencanyon:​mettowers]],​ [[hiddencanyon:​soilprofiles]],​ [[hiddencanyon:​georeferencing]] 
-  ​- ​Red Butte Canyon +  * [[hiddencanyon:​hc2010_log|2010 activity log]], [[hiddencanyon:​hc2011_log|2011 activity log]], [[hiddencanyon:​hc2012_log|2012 activity log]], [[hiddencanyon:​analysislog_1|data analysis log]] 
-    * Above the University of Utah campus. There is a weather station network there. + 
-    * [[redbutte:​weatherstations|RBC Weather Station info]], [[redbutte:​rbweather_log|WS maintenance log]], [[instruments:​cr10dataloggers|Using cr10 dataloggers]] +==Red Butte Canyon== 
-  - [[sites:​snowsurvey|NRCS Snow Survey sites]] located ​in mountains around ​the western U.S. (http://​www.wcc.nrcs.usda.gov/​) +  * Above the University of Utah campus. There is a weather station network there. 
-    * This is a network of mountain sites where manual (snow courses) and automated (SNOTEL sites) measurements of snowpack (SWE) are taken for water supply forecasting. Manual measurements date back to the 1930'​s. +  * [[redbutte:​weatherstations|RBC Weather Station info]], [[redbutte:​rbweather_log|WS maintenance log]], [[instruments:​cr10dataloggers|Using cr10 dataloggers]] 
-  ​[[sites:niwotridge|Niwot Ridge]] - a high elevation [[http://​www.lternet.edu/​|LTER]] and [[http://​public.ornl.gov/​ameriflux/​|Ameriflux]] site in Colorado. + 
-    A high elevation supalpine forest and alpine tundra site. Extensive research on tundra and forest ecology has been in progress here for a long time. The Bowling lab has instrumentation that measures biosphere-atmosphere interactions (CO<​sub>​2</​sub>​ mainly).+==NRCS Snow Survey sites== 
 +  * A network of mountain sites in the western U.S. where manual (snow courses) and automated (SNOTEL sites) measurements of snowpack (SWE) are taken for water supply forecasting. Manual measurements date back to the 1930'​s. 
 +  ​[[http://​www.wcc.nrcs.usda.gov/​|Official site]] 
 + 
 +==Niwot Ridge LTER== 
 +  *A high elevation [[http://​www.lternet.edu/​|LTER]] and [[http://​public.ornl.gov/​ameriflux/​|Ameriflux]] site in Colorado. 
 +  * Extensive research on tundra and forest ecology has been in progress here for a long time. The Bowling lab has instrumentation that measures biosphere-atmosphere interactions (CO<​sub>​2</​sub>​ mainly). 
  
 ===== Inactive research projects ===== ===== Inactive research projects =====
 +
 These are either completed or on hold. These are either completed or on hold.
 +
   * [[niwot_labeldecomp_overview| Niwot Ridge label decomposition - overview]] ON HOLD --- //​[[primaryproductivity@gmail.com|Greg Maurer]] 2010/08/09 13:11//   * [[niwot_labeldecomp_overview| Niwot Ridge label decomposition - overview]] ON HOLD --- //​[[primaryproductivity@gmail.com|Greg Maurer]] 2010/08/09 13:11//
topicindex.1339655575.txt.gz · Last modified: 2012/06/14 02:32 by gremau