Adam Thomas Clark, Hao Ye, Forest Isbell, Ethan R. Deyle, Jane Cowles, G. David Tilman, and George Sugihara. 2015. Spatial convergent cross mapping to detect causal relationships from short time series. Ecology 96:11741181. http://dx.doi.org/10.1890/14-1479.1


Supplement

Data for real-world examples, and source code for the multispatialCCM R package.
Ecological Archives E096-105-S1.

Copyright


Authors
File list (downloads)
Description


Author(s)

Adam Thomas Clark
University of Minnesota, Dept. of Ecology, Evolution, and Behavior
1987 Upper Buford Circle, Saint Paul, MN 55108, USA
E-mail: adam.tclark@gmail.com

Hao Ye
Scripps Institution of Oceanography, University of California, San Diego
9500 Gilman Drive, La Jolla, CA 92093, USA

Forest Isbell
University of Minnesota, Dept. of Ecology, Evolution, and Behavior
1987 Upper Buford Circle, Saint Paul, MN 55108, USA
and
Department of Plant Biology, University of Georgia
2502 Miller Plant Sciences, Athens, GA 30602

Ethan R. Deyle
Scripps Institution of Oceanography, University of California, San Diego
9500 Gilman Drive, La Jolla, CA 92093, USA

Jane Cowles
University of Minnesota, Dept. of Ecology, Evolution, and Behavior
1987 Upper Buford Circle, Saint Paul, MN 55108, USA

David Tilman
University of Minnesota, Dept. of Ecology, Evolution, and Behavior
1987 Upper Buford Circle, Saint Paul, MN 55108, USA
and
Bren School of Environmental Science and Management, University of California
2400 Bren Hall, Santa Barbara, CA 93106, USA

George Sugihara
Scripps Institution of Oceanography, University of California, San Diego
9500 Gilman Drive, La Jolla, CA 92093, USA


File list

e001_arssnlvl0.csv (MD5: 75f21b9949b87c018f3499b5d2a093e7)

e001_arssnlvl3.csv (MD5: 02cefd1cdb16fc25968f4e7d96a43378)

e026_aslit.csv (MD5: eea09f91f81dc7e5801d8f67ccded5c1)

e054_arssprecip.csv (MD5: 1d62c9ab92a6a1fc4caa53787d2c0cf1)

e120_bmins.csv (MD5: e8699cfd2d2c9a11d43abd572b6f3cd8)

e120_invnit1_2.csv (MD5: 6c023c438eb4c6e2625f526fafd9c17d)

e120_invnit4_8.csv (MD5: a304786a833b5c6e53063472b97ef93d)

e120_invnit16.csv (MD5: bda824cec8f8fdc2992c8732e03aa109)

e120_nitbm.csv (MD5: 212637b7ab08d0cc2146f26602061b64)

find_number_of_observations.R (MD5: a6a097d6633ee66b9c3531676320b929)

multispatialCCM.zip (MD5: 64647cc7d14d2df5398a76af9ec73e2a)

Description

e001_arssnlvl0.csv is a comma-separated text file containing the data for Agroypron (Elymus) repens and Schizachyrium scoparium dynamics in unfertilized plots for experiment 001 at Cedar Creek. Column definitions are:

1."index": concatenated text including the plot, field, and year sampled

2. "Exp": Cedar Creek experiment number

3. "Year": year data was sampled

4. "Field": ID for field that was sampled

5. "Plot": plot number for sample

6. "Ntrt": categorical fertilization treatment

7. "Nadd": g nitrogen added per square meter per year for each treatment

8. "NitrAdd": g nitrate added per square meter per year for each treatment

9. "Natm.Nadd": g nitrogen added per square meter per year for each treatment, including 1 g/m2/year atmospheric deposition

10. "fg": plant functional group: C3/C4 for grasses with C3/C4 photosynthetic pathway, F for non-legume forb, L for legume.

11. "isspecies": Binary indicator describing whether or not a row had plant species found in it that year (should be 1 for all rows)

12. "richness": Species richness for all species found in the sample

13. "Agropyron repens": g dry aboveground biomass per meter square of A. repens

14. "Schizachyrium scoparium": g dry aboveground biomass per meter square of S. scoparium

15. "Miscellaneous litter": g dry aboveground biomass per meter square of leaf litter

16. "Ncat": Fertilization intensity category, with 1 being the lowest and 3 being the highest

17. "FieldPlot": concatenated text including the field and plot

e001_arssnlvl3.csv is a comma-separated text file containing the data for Agroypron (Elymus) repens and Schizachyrium scoparium dynamics in heavily plots for experiment 001 at Cedar Creek. Column definitions are as described for e001_arssnlvl0.csv.

e026_aslit.csv is a comma-separated text file containing the data for Agrostic scabra and leaf litter dynamics in plots with varying soil fertility in experiment 026 at Cedar Creek. Column definitions are:

1. "monoculture": plant species grown in subplot (should always be A. scabra)

2. "litbiomass": g dry aboveground biomass per meter square of leaf litter

3. "year": year of sampling

4. "plot": plot sampled (soil N treatments vary among plots)

5. "subplot": subplot sampled

6. "abvbiomass": g dry aboveground biomass per meter square of A. scabra

7. "totaln": total soil nitrogen (in percent of soil by mass)

8. "exp": Cedar Creek experiment number

9. "yearest": year in which the experiment was established

10. "nlevel": categorical level for total soil nitrogen treatment

11. "plotsubplot": concatenated text including the plot and subplot

12. "Field": ID for field that was sampled

13. "FieldPlot": concatenated text including the field and plot

e054_arssprecip.csv is a comma-separated text file containing the data for A. repens, S. scoparium, leaf litter, and precipitation dynamics for experiment 054 at Cedar Creek. Column definitions are:

1. "index": concatenated text including the year, field, plot, transect sampled

2. "Exp": experiment number

3. "Year": year of sample

4. "OldField": old field ID

5. "Plot": plot number for sample

6. "Transect": transect ID

7. "YearAb": Year that the field was abandoned from agricultural use

8. "Agropyron repens": g dry aboveground biomass per meter square of A. repens

9. "Schizachyrium scoparium": g dry aboveground biomass per meter square of S. scoparium

10: "Miscellaneous litter": g dry aboveground biomass per meter square of leaf litter

11: "precipmm": total summer annual precipitation (June-August) in mm

12: "FieldPlot": concatenated text including the field and plot

e120_bmins.csv is a comma-separated text file describing plant biomass and insect dynamics for Cedar Creek experiment 120. Column definitions are:

1. "Exp": Cedar Creek experiment number

2. "Year": sampling year

3. "Month": sampling month

4. "Plot": plot sampled

5. "NumSp": number of species in treatment

6. "SpNum": number of species maintained in plot

7. "AbvBioAnnProd": g plant aboveground biomass harvested per square meter per year

8. "noh020tot": mg soil nitrate per kg soil, sampled in top 20 cm of soil

9. "insectcount": number of insect individuals in sweep net sample

10. "insectsp": number of insect species in sweep net sample

11. "Field": field ID

12. "FieldPlot": concatenated text including the field and plot

e120_invnit1_2.csv is a comma-separated text file describing invading plant species dynamics and soil nitrate dynamics in monoculture plots for experiment 120 at Cedar Creek. Column definitions are as described for e120_bmins.csv, except for:

9. “invrichness”: number of non-planted “invading” plant species

e120_invnit4_8.csv is a comma-separated text file describing invading plant species dynamics and soil nitrate dynamics in 4 and 8 species mixture plots for experiment 120 at Cedar Creek. Column definitions are as described for e120_invnit1_2.csv.

e120_invnit16.csv is a comma-separated text file describing invading plant species dynamics and soil nitrate dynamics in 16 species mixture plots for experiment 120 at Cedar Creek. Column definitions are as described for e120_invnit1_2.csv.

e120_nitbm.csv is a comma-separated text file describing soil nitrate and aboveground plant biomass dynamics. Column definitions are as described for e120_bmins.csv.

find_number_of_observations.R is an R source code file that can be used to determine the number of sequential observations in subplots for all of the data sets listed above. The data should be in the working directory of R when the R code is run.

multispatialCCM.zip is an archive containing the source code for the multispatialCCM R package. For the most recent version of the package, please see cran.r-project.org/web/packages/multispatialCCM/index.html.