ITEX Community Data - File Format ------------------------------------------------------------ Below are the required species and data file formats for the February 15-19th 2001 ITEX Community Synthesis Workshop. These formats are close to final, but as there may be small modifications required, please check www.lter.uaf.edu/~becru/ITEX_community_data_format.html regularly for updates. Updates and additions will be marked with a "new" symbol. Questions, suggestions, or concerns can be sent to Henrik Wahren(fnhaw@uaf.edu). There will be two files required: a data file and a species file. Deadline for sending these files is January 15. Those who recorded every species at every point (i.e. there is a quantity associated with each species at each point) should, in addition to the species and cover data files, submit a fully quantitative or quantity file. The required format for this file is similar to the cover data file format and is shown in a short sample file. Produce site climate data as a leith diagram (temperature x precipitation) and also bring this to the meeting. Some basic analysis should be completed before the meeting. This is a good way to explore the data and pick up errors or problems. For each plot, calculate the min, max, mean and standard deviation of cover for graminoids, forbs, shrubs, mosses, lichens, liverworts, and total live vegetation. In addition, we highly recommend that everyone determines diversity by plot and does a straight one-way (factor=warming) ANOVA on the broad growth form categories. The analyses and recommended order to do them: 1. Diversity by plot: species richness (no. of different species) and Pielou's evenness index. If desired, other indices, such as the Simpson dominance index, can also be determined. 2. ANOVA (warming treatment) 3. MANOVA 4. Ordination: CCA, with time and treatment (warming) as the constrained variables. Species file format Dave Murray is assisting with vascular species nomenclature. For non-vascular species we ask that you refer to the USDA plants database http://plants.usda.gov. This service is easy to use and should cover most species. The species file format should contain all species found in the community data file and be a tab delimited ASCII or Excel file with four columns: 6 or 8 character species code without spaces (CODE) Full species name (SPECIES) Narrow growth form category (GFNARROW) Broad growth form category (GFBROAD) The growth form categories are listed below. Before using a http://www.lter.uaf.edu/~becru/Lookup.html (lookup table) to insert the growth form categories in the data file, remember to sort on CODE (Ascending order). Data file format File type: ASCII (tab delimited) or Excel, consisting of up to 15 columns. All files should have columns 1-4, 6-15. Produce as complete a data file as possible. If a column variable has no data, leave it out. If data is missing, leave the cell blank. Do not include species with a cover i.e. species that occurred in the plot, but were not intercepted by a point. Thoroughly examine all data files before sending them; e.g. use http://www.lter.uaf.edu/~becru/Pivot.html (pivot table) in Excel to check that all species codes are correct and a lookup table to insert growth forms in the data file. Make sure that each point has a maximum of two hits; i.e. top and bottom. Additional treatment columns can be entered after column 4. Summary of column identifiers see (sample data file format) SITE: country/site code DATE: yyyymmdd PLOT: up to 8 digit plot code WARMING: main ITEX treatment TREATMENT: maximum 8 character code for additional treatment CODE: maximum 8 character species or ground condition code, no spaces. GFNARROW: narrow growth form category GFBROAD: broad growth form category CANOPYHT: height of hit by point (cm). MICROTOP: height of hit with respect to lowest point in frame (cm) XCOORD: X co-ordinate in cm. YCOORD: Y co-ordinate in cm. CONDITION: L (live) or O (other, for all non-living ground conditions; e.g. ROCK) WOODY: Y, N, or O (other, for all ground condition entries) REPEAT: Y or N Description of column identifiers 1. SITE Site codes: Alexandra Fjord, Canada: CALEXAND North-east Tibet: TIBET Audkuluheidi, Iceland: IAUDKULU Thingvellir, Iceland: ITHINGVE Thjorsarver, Iceland: THJORSA Kilpisjarvi, Finland: SFKILPIS Latnjajaure, Sweden: SLATNJAJ Svalbard, Norway: SVALBARD Finse, Norway: NFINSE Toolik Lake, U.S.A: USTOOL1, USTOOL2, USTOOL3 Niwot Ridge, U.S.A. : USNIWOT Barrow, U.S.A. : USBARROW Atqasuk, U.S.A. : USATQASU 4. WARMING The main ITEX design using open-topped chambers or 'corners'. Open-topped chamber: OTC ITEX 'corner': CORNER Control plot: CONTROL 5. TREATMENT Use this column if there is a treatment in addition to the standard ITEX design, such as fertilizer, varied snow depth regime, etc. Identify within-treatment levels using a maximum 8 character code; e.g. 'zone1', 'zone2', etc. 6. CODE Species codes Use a 6 or 8 character species code (genus/species); e.g. a 6 character code for Dryas octopetala would be DRYOCT. Ground condition codes Bare soil: SOIL Litter: LITTER Rock: ROCK Scat/Type: SCATB (bear), SCATC (caribou), SCATV (vole), SCATP (ptarmigan), SCATU (unknown) Additional optional codes Point frame tag: X Plant marker: MARKER Equipment (C02, thermistor, etc.): EQUIP 7. GF NARROW (Narrow growth form categories): Shrub: SEVER (evergreen), SDECID (deciduous), SHRUBU (unknown shrub) Grass: GRASS Sedge: SEDGE Rush: RUSH Unknown Graminoid: GRAMINU Forb: FORB Seedless Vascular: SLVASC (Lycophyta, Sphenophyta, Pteropyta) Lichen: LFOLI (foliose), LFRUT (fruticose), or LCRUS (crustose), LICHENU (unknown lichen) Moss: SPHAG (Sphagnum), MACRO (acrocarp), MPLEU (pleurocarp), MSEMI (semi-prostrate), MPOLY (Polytrichale), MOSSU (unknown moss). Liverwort: LIVERTH (thalloid), LIVERLE (leafy), LIVERU (unknown liverwort) Unknown Bryophyte: BRYOU Fungus: FUNGUS Algae: ALGAE 8. GF BROAD (Broad growth form categories): Shrub: SHRUB Graminoid: GRAMIN Forb or Seedless Vascular: FORBSV Lichen: LICHEN Moss: SPHAG (Sphagnum), MOSS Liverwort: LIVER Unknown Bryophyte: BRYOU Fungus: FUNGUS Algae: ALGAE 9. CANOPYHT Canopy height is calculated for each point in the frame. As measurements are taken from the bottom of the frame this figure is calculated by subtracting each hit from the bottom hit or largest number at the point. For example, if point touched an evergreen shrub at 20 cm below the frame and ground surface (or bottom hit) was 35.5 cm below frame, then height of shrub would be 35.5 - 20 = 15.5 cm. If this column has not been produced yet, a macro (www.lter.uaf.edu/~becru/Macros.html) is now available that will insert both the canopy height (CANOPYHT) and micro-topography (MICROTOP) columns. 10. MICROTOP The micro-topography of the plot is determined in relation to the lowest point in the plot; i.e. the highest number. If this was 45.5, for example, this would be set to zero and all other MICROTOP entries in the plot then determined by subtracting them from 45.5 cm. If this column has not been produced yet, a macro (www.lter.uaf.edu/~becru/Macros.html) is now available that will insert the micro-topography (MICROTOP) column. 13. CONDITION Use only L (live) or O (other, for all non-living ground conditions; e.g. ROCK), removing any rows with dead or standing dead (e.g. dead leaf on live shrub) vegetation. 15. REPEAT Subjective assessment on whether or not the species, growth form, or ground condition is likely to be encountered next sampling time; e.g. leaf-tip of a grass: N; rock: Y.