dpeatdecomposition is an R interface to the Peatland Decomposition
Database. The Peatland Decomposition
Database (Teickner and Knorr
2024) stores data from published litterbag experiments related to
peatlands.
dpeatdecomposition uses functions from the
dm and
RMariaDB package.
You can install the development version of dpeatdecomposition like so:
remotes::install_github("henningte/dpeatdecomposition")You will also need to download the Peatland Decomposition Database and open it in a running MariaDB instance.
library(dpeatdecomposition)
# connect to database
con <-
RMariaDB::dbConnect(
drv = RMariaDB::MariaDB(),
dbname = "dpeatdecomposition",
default.file = "~/my.cnf"
)
# get database as dm object
dm_dpeatdecomposition <-
dpeatdecomposition::dp_get_dm(con, learn_keys = TRUE)
# get information on samples
d <-
dm_dpeatdecomposition |>
dm::pull_tbl(samples) |>
as.data.frame()
# disconnect
RMariaDB::dbDisconnect(con)
Fig. 1: Database schema for the Sphagnum Decomposition Database. Each table is represented as a box. Tables contain unique identifiers for data entities (e.g. datasets, samples, or measurements) — primary keys (underlined) and foreign keys — which are listed in each box. Keys are used to link data entities between tables. These links are shown as curves pointing to the respective links which connect tables.
Datasets currently included in the Peatland Decomposition Database are: Farrish and Grigal (1985), Bartsch and Moore (1985), Farrish and Grigal (1988), Vitt (1990), Hogg, Lieffers, and Wein (1992), Sanger, Billett, and Cresser (1994), Hiroki and Watanabe (1996), Szumigalski and Bayley (1996), Prevost, Belleau, and Plamondon (1997), Arp, Cooper, and Stednick (1999), Robbert A. Scheffer and Aerts (2000), R. A. Scheffer, Van Logtestijn, and Verhoeven (2001), Limpens and Berendse (2003), Waddington, Rochefort, and Campeau (2003), Asada, Warner, and Banner (2004), Thormann, Bayley, and Currah (2001), Asada and Warner (2005), Trinder, Johnson, and Artz (2008), Breeuwer et al. (2008), Trinder, Johnson, and Artz (2009), Bragazza and Iacumin (2009), Hoorens, Stroetenga, and Aerts (2010), Straková et al. (2010), Straková et al. (2012), Orwin and Ostle (2012), Lieffers (1988), Manninen et al. (2016), Johnson and Damman (1991), Bengtsson, Rydin, and Hájek (2018a), Bengtsson, Rydin, and Hájek (2018b), Bengtsson, Granath, and Rydin (2017), Bengtsson, Granath, and Rydin (2016), Hagemann and Moroni (2015), Hagemann and Moroni (2016), B. Piatkowski et al. (2021), B. T. Piatkowski et al. (2021), Mäkilä et al. (2018), Golovatskaya and Nikonova (2017)
Cite this package as:
Henning Teickner and Klaus-Holger Knorr (2024): dpeatdecomposition: R Interface to the Peatland Decomposition Database. https://github.com/henningte/dpeatdecomposition. accessed: 2024-05-24.
If you use data from the Peatland Decomposition Database, cite the database and the sources linked to each entry you use. For details, see (Teickner and Knorr 2024)
We welcome contributions from everyone. Please note that the dpeatdecomposition project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Development of this database was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) grant no. KN 929/23-1 to Klaus-Holger Knorr and grant no. PE 1632/18-1 to Edzer Pebesma.
Arp, Christopher D., David J. Cooper, and John D. Stednick. 1999. “The Effects of Acid Rock Drainage on Carex Aquatilis Leaf Litter Decomposition in Rocky Mountain Fens.” Wetlands 19 (3): 665–74. https://doi.org/10.1007/BF03161703.
Asada, Taro, and Barry G. Warner. 2005. “Surface Peat Mass and Carbon Balance in a Hypermaritime Peatland.” Soil Science Society of America Journal 69 (2): 549–62. https://doi.org/10.2136/sssaj2005.0549.
Asada, Taro, Barry G Warner, and Allen Banner. 2004. “Sphagnum Invasion After Clear-Cutting and Excavator Mounding in a Hypermaritime Forest of British Columbia.” Canadian Journal of Forest Research 34 (8): 1730–46. https://doi.org/10.1139/x04-042.
Bartsch, I., and T. R. Moore. 1985. “A Preliminary Investigation of Primary Production and Decomposition in Four Peatlands Near Schefferville, Québec.” Canadian Journal of Botany 63 (7): 1241–48. https://doi.org/10.1139/b85-171.
Bengtsson, Fia, Gustaf Granath, and Håkan Rydin. 2016. “Photosynthesis, Growth, and Decay Traits in Sphagnum – a Multispecies Comparison.” Ecology and Evolution 6 (10): 3325–41. https://doi.org/10.1002/ece3.2119.
———. 2017. “Data from: Photosynthesis, Growth, and Decay Traits in Sphagnum – a Multispecies Comparison.” Dryad. https://doi.org/10.5061/DRYAD.62054.
Bengtsson, Fia, Håkan Rydin, and Tomáš Hájek. 2018a. “Data from: Biochemical Determinants of Litter Quality in 15 Species of Sphagnum.” Dryad. https://doi.org/10.5061/DRYAD.4F8D2.
———. 2018b. “Biochemical Determinants of Litter Quality in 15 Species of Sphagnum.” Plant and Soil 425 (1-2): 161–76. https://doi.org/10.1007/s11104-018-3579-8.
Bragazza, Luca, and Paola Iacumin. 2009. “Seasonal Variation in Carbon Isotopic Composition of Bog Plant Litter During 3 Years of Field Decomposition.” Biology and Fertility of Soils 46 (1): 73–77. https://doi.org/10.1007/s00374-009-0406-7.
Breeuwer, Angela, Monique Heijmans, Bjorn J. M. Robroek, Juul Limpens, and Frank Berendse. 2008. “The Effect of Increased Temperature and Nitrogen Deposition on Decomposition in Bogs.” Oikos 117 (8): 1258–68. https://doi.org/10.1111/j.0030-1299.2008.16518.x.
Farrish, K. W., and D. F. Grigal. 1985. “Mass Loss in a Forested Bog: Relation to Hummock and Hollow Microrelief.” Canadian Journal of Soil Science 65 (2): 375–78. https://doi.org/10.4141/cjss85-042.
———. 1988. “Decomposition in an Omrotrophic Bog and a Minerotrophic Fen in Minnesota.” Soil Science 145 (5): 353–58. https://doi.org/10.1097/00010694-198805000-00005.
Golovatskaya, E. A., and L. G. Nikonova. 2017. “The Influence of the Bog Water Level on the Transformation of Sphagnum Mosses in Peat Soils of Oligotrophic Bogs.” Eurasian Soil Science 50 (5): 580–88. https://doi.org/10.1134/S1064229317030036.
Hagemann, Ulrike, and Martin T. Moroni. 2015. “Moss and Lichen Decomposition in Old-Growth and Harvested High-Boreal Forests Estimated Using the Litterbag and Minicontainer Methods.” Soil Biology and Biochemistry 87 (August): 10–24. https://doi.org/10.1016/j.soilbio.2015.04.002.
———. 2016. “Data on Moss and Lichen Decomposition Rates and Nutrient Loss from Old-Growth and Harvested High-Boreal Forests Estimated Using the Litterbag and Minicontainer Methods.” Leibniz-Zentrum für Agrarlandschaftsforschung (ZALF) e.V. https://doi.org/10.4228/ZALF.2007.290.
Hiroki, Mikiya, and Makoto M. Watanabe. 1996. “Microbial Community and Rate of Cellulose Decomposition in Peat Soils in a Mire.” Soil Science and Plant Nutrition 42 (4): 893–903. https://doi.org/10.1080/00380768.1996.10416636.
Hogg, Edward H., Victor J. Lieffers, and Ross W. Wein. 1992. “Potential Carbon Losses from Peat Profiles: Effects of Temperature, Drought Cycles, and Fire.” Ecological Applications 2 (3): 298–306. https://doi.org/10.2307/1941863.
Hoorens, Bart, Martin Stroetenga, and Rien Aerts. 2010. “Litter Mixture Interactions at the Level of Plant Functional Types Are Additive.” Ecosystems 13 (1): 90–98. https://doi.org/10.1007/s10021-009-9301-1.
Johnson, Loretta C., and Antoni W. H. Damman. 1991. “Species-Controlled Sphagnum Decay on a South Swedish Raised Bog.” Oikos 61 (2): 234. https://doi.org/10.2307/3545341.
Lieffers, V. J. 1988. “Sphagnum and Cellulose Decomosition in Drained and Natural Areas of an Alberta Peatland.” Canadian Journal of Soil Science 68 (4): 755–61. https://doi.org/10.4141/cjss88-073.
Limpens, Juul, and Frank Berendse. 2003. “How Litter Quality Affects Mass Loss and N Loss from Decomposing Sphagnum.” Oikos 103 (3): 537–47. https://doi.org/10.1034/j.1600-0706.2003.12707.x.
Mäkilä, M., H. Säävuori, A. Grundström, and T. Suomi. 2018. “Sphagnum Decay Patterns and Bog Microtopography in South-Eastern Finland.” Mires and Peat, no. 21 (July): 1–12. https://doi.org/10.19189/MaP.2017.OMB.283.
Manninen, S., S. Kivimäki, I. D. Leith, S. R. Leeson, and L. J. Sheppard. 2016. “Nitrogen Deposition Does Not Enhance Sphagnum Decomposition.” Science of The Total Environment 571 (November): 314–22. https://doi.org/10.1016/j.scitotenv.2016.07.152.
Orwin, Kate H., and Nicholas J. Ostle. 2012. “Moss Species Effects on Peatland Carbon Cycling After Fire: Moss Species Effects on C Cycling After Fire.” Functional Ecology 26 (4): 829–36. https://doi.org/10.1111/j.1365-2435.2012.01991.x.
Piatkowski, Bryan T., Joseph B. Yavitt, Merritt R. Turetsky, and A. Jonathan Shaw. 2021. “Natural Selection on a Carbon Cycling Trait Drives Ecosystem Engineering by Sphagnum (Peat Moss).” Proceedings of the Royal Society B: Biological Sciences 288 (1957): 20210609. https://doi.org/10.1098/rspb.2021.0609.
Piatkowski, Bryan, Joseph B. Yavitt, Merritt Turetsky, and A. Jonathan Shaw. 2021. “Online Data for "Natural Selection on a Carbon Cycling Trait Drives Ecosystem Engineering by Sphagnum (Peat Moss).",” August. https://doi.org/10.6084/m9.figshare.14109725.v2.
Prevost, Marcel, Pierre Belleau, and André P. Plamondon. 1997. “Substrate Conditions in a Treed Peatland: Responses to Drainage.” Écoscience 4 (4): 543–54. https://doi.org/10.1080/11956860.1997.11682434.
Sanger, L. J., M. F. Billett, and M. S. Cresser. 1994. “The Effects of Acidity on Carbon Fluxes from Ombrotrophic Peat.” Chemistry and Ecology 8 (4): 249–64. https://doi.org/10.1080/02757549408038552.
Scheffer, R. A., R. S. P Van Logtestijn, and J. T. A. Verhoeven. 2001. “Decomposition of Carex and Sphagnum Litter in Two Mesotrophic Fens Differing in Dominant Plant Species.” Oikos 92 (1): 44–54. https://doi.org/10.1034/j.1600-0706.2001.920106.x.
Scheffer, Robbert A., and Rien Aerts. 2000. “Root Decomposition and Soil Nutrient and Carbon Cycling in Two Temperate Fen Ecosystems.” Oikos 91 (3): 541–49. https://doi.org/10.1034/j.1600-0706.2000.910316.x.
Straková, Petra, Jani Anttila, Peter Spetz, Veikko Kitunen, Tarja Tapanila, and Raija Laiho. 2010. “Litter Quality and Its Response to Water Level Drawdown in Boreal Peatlands at Plant Species and Community Level.” Plant and Soil 335 (1-2): 501–20. https://doi.org/10.1007/s11104-010-0447-6.
Straková, Petra, Timo Penttilä, Jukka Laine, and Raija Laiho. 2012. “Disentangling Direct and Indirect Effects of Water Table Drawdown on Above- and Belowground Plant Litter Decomposition: Consequences for Accumulation of Organic Matter in Boreal Peatlands.” Global Change Biology 18 (1): 322–35. https://doi.org/10.1111/j.1365-2486.2011.02503.x.
Szumigalski, Anthony R., and Suzanne E. Bayley. 1996. “Decomposition Along a Bog to Rich Fen Gradient in Central Alberta, Canada.” Canadian Journal of Botany 74 (4): 573–81. https://doi.org/10.1139/b96-073.
Teickner, Henning, and Klaus-Holger Knorr. 2024. “Peatland Decomposition Database (1.0.0).” Zenodo. https://doi.org/10.5281/ZENODO.11276065.
Thormann, Markus N, Suzanne E Bayley, and Randolph S Currah. 2001. “Comparison of Decomposition of Belowground and Aboveground Plant Litters in Peatlands of Boreal Alberta, Canada.” Canadian Journal of Botany 79 (1): 9–22. https://doi.org/10.1139/b00-138.
Trinder, Clare J., David Johnson, and Rebekka R. E. Artz. 2008. “Interactions Among Fungal Community Structure, Litter Decomposition and Depth of Water Table in a Cutover Peatland.” FEMS Microbiology Ecology 64 (3): 433–48. https://doi.org/10.1111/j.1574-6941.2008.00487.x.
———. 2009. “Litter Type, but Not Plant Cover, Regulates Initial Litter Decomposition and Fungal Community Structure in a Recolonising Cutover Peatland.” Soil Biology and Biochemistry 41 (3): 651–55. https://doi.org/10.1016/j.soilbio.2008.12.006.
Vitt, Dale H. 1990. “Growth and Production Dynamics of Boreal Mosses over Climatic, Chemical and Topographic Gradients.” Botanical Journal of the Linnean Society 104 (1-3): 35–59. https://doi.org/10.1111/j.1095-8339.1990.tb02210.x.
Waddington, J. M., L. Rochefort, and S. Campeau. 2003. “Sphagnum Production and Decomposition in a Restored Cutover Peatland.” Wetlands Ecology and Management 11 (1): 85–95. https://doi.org/10.1023/A:1022009621693.
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