Commit 82a1a01f authored by Daniel Falster's avatar Daniel Falster
Browse files

Fix metadata so that compiles. #89.

parent 13bfdac4
......@@ -10,8 +10,8 @@
"country": "Panama",
"climate": "Tropical",
"vegetation type": "Tropical rain forest",
"latitude": ,
"longitude": ,
"latitude": "" ,
"longitude": "",
"minimum tree size": "1cm dbh",
"history": "BCI: Barro Colorado Island (BCI) is a 1600 ha former hilltop in central Panama that became an island when the Chagres River was dammed, creating the main reservoir of water for the Panama Canal. The climate of BCI is strongly seasonal, with a four month dry season from late December until late April. The forest is semi-evergreen and, at 2600 mm annual rainfall, is classified as tropical moist forest by the Holdridge system. Since 1923 BCI has been a biological reserve, administered after 1946 by the Smithsonian Tropical Research Institute (STRI). A 50ha permanent plot was established in old-growth forest on the central plateau of the island, and all free-standing woody plants with a stem diameter of 1 cm dbh were tagged, identified to species, measured, and mapped.
40 0.5ha plots used in Condit et al. 2013 PNAS. All tree aboce 1cm of dbh have been measured 2 times. The plots location were selected to span a range of rainfall and geological formations. All plots were in closed forest including undisturbed old-growth forest and secondary stands",
......@@ -23,7 +23,7 @@
"Condit, R. 1998. Tropical Forest Census Plots. Springer-Verlag and R. G. Landes Company, Berlin, Germany, and Georgetown, Texas.",
"Hubbell, S.P. and R.B. Foster. (1992) 'Short-Term Dynamics of a Neotropical Forest: Why Ecological Research Matters to Tropical Conservation and Management.' Oikos 63: 48–61. doi:10.2307/3545515",
"Wright, S.J., K. Kitajima, N.J.B. Kraft, P.B. Reich, I.J. Wright, D.E. Bunker, R. Condit, et al. “Functional Traits and the Growth–mortality Trade-off in Tropical Trees.' Ecology 91: 3664–3674. doi:10.1890/09-2335.1" ,
"Condit, R., Engelbrecht, B.M.J., Pino, D., Perez, R., and Turner, B.L. (2013). Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees. Proceedings of the National Academy of Sciences 110, 5064–5068."
"Condit, R., Engelbrecht, B.M.J., Pino, D., Perez, R., and Turner, B.L. (2013). Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees. Proceedings of the National Academy of Sciences 110, 5064–5068."
],
"files":{
"Kunstler.BCI.traits.txt":{
......
......@@ -8,22 +8,22 @@
"dataset": {
"name": "Fushan",
"country": "Taiwan",
"climate": "From Lasky et al. 2013 "The forest at the site is a subtropical evergreen broad-leaved forest receiving 4271 mm year−1 rain. The soils are extremely acidic (pH 3.34.3) with low organic carbon content and fertility (for a detailed description of the plot, see Su et al. 2007)."",
"climate": "From Lasky et al. 2013 'The forest at the site is a subtropical evergreen broad-leaved forest receiving 4271 mm/yr rain. The soils are extremely acidic (pH 3.3--4.3) with low organic carbon content and fertility (for a detailed description of the plot, see Su et al. 2007).'",
"vegetation type": "subtropical evergreen broad-leaved forest",
"latitude": 24.7614,
"longitude": 121.555,
"minimum tree size": "1 cm",
"history": "",
"field methodology": "From Lasky et al. 2013. "25-ha Fushan Forest Dynamics Plot (FDP) in northern Taiwan (24o4540N, 121o3328E, 600733 m asl). Fushan FDP was established in 2004 following Centre for Tropical Forest Science protocols in which all trees with diameter at breast height (DBH, at 1.3 m height) 1 cm were mapped, tagged, identified and measured (Condit 1998). Census in 2004 and 2009."",
"field methodology": "From Lasky et al. 2013. '25-ha Fushan Forest Dynamics Plot (FDP) in northern Taiwan (24\u00B045'40''N, 121\u00B033'28''E, 600–733 m asl). Fushan FDP was established in 2004 following Centre for Tropical Forest Science protocols in which all trees with diameter at breast height (DBH, at 1.3 m height) >= 1 cm were mapped, tagged, identified and measured (Condit 1998). Census in 2004 and 2009.'",
"trait information": "Leaf trait data for a total of 99 species, maximum height data for 96 species and wood density for 75 species. See Lasky et al. 2013"
},
"references": ["Lasky, J.R., Sun, I., Su, S.-H., Chen, Z.-S., and Keitt, T.H. (2013). Trait-mediated effects of environmental filtering on tree community dynamics. Journal of Ecology.",
""],
"files":{
"fushan.rdata":{
"fushan.rdata.csv":{
"sep":"t",
"contents":"NA"},
"fs_trait_Kunstler.txt":{
"fs_trait_Kunstler.csv":{
"sep":"t",
"contents":"NA"},
"Splist_Fushan_En.csv":{
......
......@@ -20,10 +20,10 @@
"references": [
"Yakushima Forest Environment Conservation Center, Ishihara, M.I., Suzuki, S.N., Nakamura, M., Enoki, T., Fujiwara, A., Hiura, T., Homma, K., Hoshino, D., Hoshizaki, K., et al. (2011). Forest stand structure, composition, and dynamics in 34 sites over Japan. Ecological Research 26, 1007–1008.
",
""
""
],
"files":{
"TreeData/*-tree-ver1.csv":{
"TreeData-tree-ver1.csv":{
"sep":";",
"contents":"one file per plot /tree measurment data"},
"japanese_traits.csv":{
......@@ -32,10 +32,10 @@
"conversion_table.csv":{
"sep":";",
"contents":"conversion of Latin name in traits data to tree data"},
"ERDP_2011_01.5.1-SiteList.csv":{
"ERDP_2011-01.3.1-SiteList.csv":{
"sep":";",
"contents":"site data for the tree data"},
"ERDP_2011_01.3.1-SpList.csv":{
"ERDP_2011-01.3.1-SpList.csv":{
"sep":";",
"contents":"Species list for tree data"}
}
......
use var units description
0 Code Plot code.
0 Code Plot code
PlotID Alphanumeric plot code
SiteName Site name
Type Alphabetical code for forest type.
Type Alphabetical code for forest type
Status Forest age classifications
Latitude N WGS84 latitude (N)
Longitude E WGS84 longitude (E)
Altitude m Elevation above mean sea level (m).
Area ha Plot area (ha)
Latitude \u00B0N WGS84 latitude
Longitude \u00B0E WGS84 longitude
Altitude m Elevation above mean sea level
Area ha Plot area
Shape Shape of plot
Census Census year
FileName Name of tree census data file of the plot
Temp30yr C Mean of mean annual temperature during 1971 to 2000 (C).
Rain30yr mm Mean of annual precipitation during 1971 to 2000 (mm).
Snow30yr m Mean of annual maximum snow depth during 1971 to 2000 (m).
Temp30yr \u00B0C Mean of mean annual temperature during 1971 to 2000
Rain30yr mm Mean of annual precipitation during 1971 to 2000
Snow30yr m Mean of annual maximum snow depth during 1971 to 2000
......@@ -14,12 +14,12 @@
"longitude": -1,
"minimum tree size": "",
"history": "From CTFS website :'In 1990, the University of Puerto Rico established the 16-hectare Hurricane Recovery Plot in the lowland moist forest of the Luquillo Experimental Forest, a long-term research site of the U.S. Forest Service and one of the largest protected forest areas remaining in Puerto Rico. The relatively low tree diversity of this insular forest makes a 16-hectare plot adequate at this site. Hurricane Hugo struck the plot in 1989, providing an opportunity to study the impact of a major hurricane on a tropical forest. Preliminary analysis of the second census (all stems >= 1 cm) shows that mortality rates since 1991 have been low. The total number of stems for most species >= 10 cm dbh is back to pre-hurricane levels, as mortality was equal to the recruitment of stems from smaller size classes. Destruction from Hurricane Hugo provided an important opportunity for establishment and growth of pioneer trees; however, overall, it appears to have had relatively little net impact on the remainder of the tree community. Researchers are currently analyzing the effects of Hurricane George, which hit the site in 1998. Hurricane George is providing an unparalleled opportunity to reanalyze storms' impacts on the forest.'",
"field methodology": "All free-standing woody plants with diameter at breast height (dbh) > 1 cm were measured in a 16-ha plot on Luquillo. From Uriarte et al. (2005) 'All free-standing individuals greater than 10 cm d.b.h. are tagged, mapped within the LFDP, identied to species and measured for diameter at 130 cm from the ground (d.b.h.). Trees < 10 cm are assigned to a 5 × 5 m quadrat but not mapped exactly within the plot. Trees are identied by sight in the eld or from voucher specimens.'",
"trait information": "Data from Nathan G Swenson. Plant Biology Department, Michigan State University, East Lansing, Michigan, 48824. Do not redistribute the data, contact swensonn@msu.edu. Traits description from Uriarte et al. 2010: 'Trait data for all woody species present in the LFDP were derived from vegetation samples collected using standardized protocols (Cornelissen et al. 2003). Samples were collected to calculate species mean leaf traits (25 samples) and wood specific gravity (10 samples). We selected eight functional traits that are believed to represent fundamental functional trade-offs in life-history differentiation among tree species (Wright et al. 2007). These include leaf area (cm2), specific leaf area (cm2 g−1), leaf nitrogen content (%N), leaf phosphorus content (%P), leaf succulence (g H2O cm2 leaf area), wood specific gravity (g cm3), maximum tree height (m) and seed mass (g).'"
"field methodology": "All free-standing woody plants with diameter at breast height (dbh) > 1 cm were measured in a 16-ha plot on Luquillo. From Uriarte et al. (2005) 'All free-standing individuals greater than 10 cm d.b.h. are tagged, mapped within the LFDP, identified to species and measured for diameter at 130 cm from the ground (d.b.h.). Trees < 10 cm are assigned to a 5x5 m quadrat but not mapped exactly within the plot. Trees are identified by sight in the field or from voucher specimens.'",
"trait information": "Data from Nathan G Swenson. Plant Biology Department, Michigan State University, East Lansing, Michigan, 48824. Do not redistribute the data, contact swensonn@msu.edu. Traits description from Uriarte et al. 2010: 'Trait data for all woody species present in the LFDP were derived from vegetation samples collected using standardized protocols (Cornelissen et al. 2003). Samples were collected to calculate species mean leaf traits (25 samples) and wood specific gravity (10 samples). We selected eight functional traits that are believed to represent fundamental functional trade-offs in life-history differentiation among tree species (Wright et al. 2007). These include leaf area (cm2), specific leaf area (cm2/g), leaf nitrogen content (%N), leaf phosphorus content (%P), leaf succulence (g H2O /cm2 leaf area), wood specific gravity (g/cm3), maximum tree height (m) and seed mass (g).'"
},
"references": [
"http://www.ctfs.si.edu/data/pdf/CTFSbook_PDF/LuquilloChapt.pdf",
""
""
],
"files":{
"luq_traits2georges.9sept2013.csv":{
......
......@@ -14,14 +14,14 @@
"longitude": -1,
"minimum tree size": "10cm",
"history": "",
"field methodology": "Taken from Ouedraogo et al. (2013) J Ecol'The site contains ten 4-ha permanent sample plots (200 × 200 m), each surrounded by a 50-m-wide buffer zone (Bedel et al. 1998). Three different silvicultural treatments of increasing intensity were implemented in the plots. Three plots have been left untouched (control treatment). The other seven plots were selectively logged in 198485 (logging treatment), and four of these were thinned 2 years later (logging + thinning treatment). All live trees 10 cm dbh (diameter at breast height) in the plots were botanically identified (229 tree species or morphospecies) and geo-referenced, and their girth measured annually between 1982 and 2008 to the nearest 0.5 cm using a metal tape measure.'",
"field methodology": "Taken from Ouedraogo et al. (2013) J Ecol'The site contains ten 4-ha permanent sample plots (200x200 m), each surrounded by a 50-m-wide buffer zone (Bedel et al. 1998). Three different silvicultural treatments of increasing intensity were implemented in the plots. Three plots have been left untouched (control treatment). The other seven plots were selectively logged in 1984--85 (logging treatment), and four of these were thinned 2 years later (logging + thinning treatment). All live trees >= 10 cm dbh (diameter at breast height) in the plots were botanically identified (229 tree species or morphospecies) and geo-referenced, and their girth measured annually between 1982 and 2008 to the nearest 0.5 cm using a metal tape measure.'",
"trait information": "Take from different data base from Cirad (see Gourlet-Fleury et al. 2011)"
},
"references": [
"Ouédraogo, D.-Y., Mortier, F., Gourlet-Fleury, S., Freycon, V., and Picard, N. (2013). Slow-growing species cope best with drought: evidence from long-term measurements in a tropical semi-deciduous moist forest of Central Africa. Journal of Ecology 101, 14591470.
"Ouédraogo, D.-Y., Mortier, F., Gourlet-Fleury, S., Freycon, V., and Picard, N. (2013). Slow-growing species cope best with drought: evidence from long-term measurements in a tropical semi-deciduous moist forest of Central Africa. Journal of Ecology 101, 1459--1470.
",
"Gourlet-Fleury, S., Rossi, V., Rejou-Mechain, M., Freycon, V., Fayolle, A., Saint-André, L., Cornu, G., Gérard, J., Sarrailh, J.-M., Flores, O., et al. (2011). Environmental filtering of dense-wooded species controls above-ground biomass stored in African moist forests. Journal of Ecology 99, 981990.
"
"Gourlet-Fleury, S., Rossi, V., Rejou-Mechain, M., Freycon, V., Fayolle, A., Saint-André, L., Cornu, G., Gérard, J., Sarrailh, J.-M., Flores, O., et al. (2011). Environmental filtering of dense-wooded species controls above-ground biomass stored in African moist forests. Journal of Ecology 99, 981--990.
"
],
"files":{
"Mbaiki_1995_2000_2005.csv":{
......@@ -41,4 +41,3 @@
"contents":""}
}
}
......@@ -9,19 +9,19 @@
"name": "Paracou",
"country": "France, French Guiana",
"climate": "Taken from Herault et al. (2011) J Ecol 'The site receives nearly two-thirds of the annual 3041 mm of precipitation between mid-March and mid-June, and <50 mm per month in September and October (Gourlet-Fleury, Guehl & Laroussinie 2004)'",
"vegetation type": "Taken from Herault et al. (2011) J Ecol 'the Paracou experimental site (5°18N, 52°55W), a lowland tropical rain forest near Sinnamary, French Guiana.'",
"vegetation type": "Taken from Herault et al. (2011) J Ecol 'the Paracou experimental site (5\u00B018'N, 52\u00B055'W), a lowland tropical rain forest near Sinnamary, French Guiana.'",
"latitude": -1,
"longitude": -1,
"minimum tree size": "2cm",
"history": "Taken from Herault et al. (2011) J Ecol 'In 1984, 12 plots of 6·25 ha each were established at the Paracou site for a complete annual inventory of all trees 10 cm DBH. From October 1986 to May 1987, the plots underwent three logging treatments, with three plots assigned as controls. An average of 10 trees 50 or 60 cm DBH (treatment 1, 3 plots), 32 trees 40 cm DBH (treatment 2, 3 plots) and 40 trees 40 cm DBH (treatment 3, 3 plots) were removed per hectare. Three new additional control plots of 6·25 ha were established in 1990.'",
"field methodology": "Taken from Herault et al. (2011) J Ecol 'More than 550 woody species attaining 2 cm DBH (diameter at breast height) have been described at the site, with 150180 species of trees 10 cm DBH per hectare. The floristic composition is typical of Guianan rainforests (Ter Steege et al. 2003) with dominant families including Leguminoseae, Chrysobalanaceae, Lecythidaceae, Sapotaceae and Burseraceae. First, all trees 10 cm in DBH (diameter at 1·3 m height) have been mapped and measured annually from 1984 to 1995 and every 2 years thereafter in fifteen 6·25 ha permanent plots (Gourlet-Fleury, Guehl & Laroussinie 2004; Rutishauser et al. in press). '",
"history": "Taken from Herault et al. (2011) J Ecol 'In 1984, 12 plots of 6.25 ha each were established at the Paracou site for a complete annual inventory of all trees >=10 cm DBH. From October 1986 to May 1987, the plots underwent three logging treatments, with three plots assigned as controls. An average of 10 trees >=50 or 60 cm DBH (treatment 1, 3 plots), 32 trees >=40 cm DBH (treatment 2, 3 plots) and 40 trees >=40 cm DBH (treatment 3, 3 plots) were removed per hectare. Three new additional control plots of 6.25 ha were established in 1990.'",
"field methodology": "Taken from Herault et al. (2011) J Ecol 'More than 550 woody species attaining 2 cm DBH (diameter at breast height) have been described at the site, with 150--180 species of trees >=10 cm DBH per hectare. The floristic composition is typical of Guianan rainforests (Ter Steege et al. 2003) with dominant families including Leguminoseae, Chrysobalanaceae, Lecythidaceae, Sapotaceae and Burseraceae. First, all trees >=10 cm in DBH (diameter at 1.3 m height) have been mapped and measured annually from 1984 to 1995 and every 2 years thereafter in fifteen 6.25 ha permanent plots (Gourlet-Fleury, Guehl & Laroussinie 2004; Rutishauser et al. in press). '",
"trait information": "Taken from Herault et al. (2011) J Ecol 'information on seven functional traits for which (i) information was available for the 43 focal species and (ii) trait values do not change with ontogeny, was extracted from a trait data base (Appendix S1) developed for the Guiana Shield region (Digital Appendix A,Ollivier, Baraloto & Marcon 2007). These seven key-traits have been often proposed to be important for plant performance and to represent complementary axes of tree ecological strategies in tropical forests (Westoby 1998; Weiher et al. 1999; Poorter et al. 2008): tree position in forest layers and stem architecture play a pivotal role in access to light, height and DBH at tree maturity indicate the place for volume expansion in tree bole, wood density represents the biomass invested per unit wood volume, and seed mass and seedling morphology influence reproduction, dispersal and establishment. Complete details on the methods used to estimate trait values are given in Appendix S1.'"
},
"references": [
"Herault, B., Bachelot, B., Poorter, L., Rossi, V., Bongers, F., Chave, J., Paine, C.E., Wagner, F., and Baraloto, C. (2011). Functional traits shape ontogenetic growth trajectories of rain forest tree species. Journal of Ecology 99, 14311440.
"Herault, B., Bachelot, B., Poorter, L., Rossi, V., Bongers, F., Chave, J., Paine, C.E., Wagner, F., and Baraloto, C. (2011). Functional traits shape ontogenetic growth trajectories of rain forest tree species. Journal of Ecology 99, 1431--1440.
",
"Herault, B., Ouallet, J., Blanc, L., Wagner, F., and Baraloto, C. (2010). Growth responses of neotropical trees to logging gaps. Journal of Applied Ecology 47, 821831.
"
"Herault, B., Ouallet, J., Blanc, L., Wagner, F., and Baraloto, C. (2010). Growth responses of neotropical trees to logging gaps. Journal of Applied Ecology 47, 821--831.
"
],
"files":{
"20130717_paracou_1984_2012.csv":{
......@@ -39,7 +39,7 @@
"seed.Rdata":{
"sep":"",
"contents":""},
"BridgeDATA.g.csv":{
"BridgeDATA.csv":{
"sep":";",
"contents":""}
}
......
......@@ -10,16 +10,15 @@
"country": "Sweden",
"climate": "temperate and subartic.",
"vegetation type": "Temperate and boreal forests",
"latitude": NA,
"longitude": NA,
"latitude": "",
"longitude": "",
"minimum tree size": "10cm",
"history": "The NFI is an annual sparse stratified sample plot inventory with partial replacement (Ranneby et al. 1987). Permanent sample plots (radius 10 m) were established between 1983 and 1987 and remeasured for the first time after 5 yrs, i.e. between 1988 and 1992.",
"field methodology": "Only trees with a diameter at breast height (DBH, 1.3 m) of at least 10 cm, on plots with mean stand height of at least 7 m and plot area of at least 157 m 2 (at least half the 10 m radius plot), were used. Mortality of single trees was identified as trees that were alive in the beginning of the period but dead at the remeasurement. ",
"trait information": "Maximum height from France NFI and other traits from TRY."
},
"references": [
"Fridman, J., and Stahl, G. (2001). A three-step approach for modelling tree mortality in Swedish forests. Scandinavian Journal of Forest Research 16, 455–466.",
""
"Fridman, J., and Stahl, G. (2001). A three-step approach for modelling tree mortality in Swedish forests. Scandinavian Journal of Forest Research 16, 455–466."
],
"files":{
"Swe_NFI_all.csv":{
......
......@@ -10,15 +10,14 @@
"country": "Switzerland",
"climate": "Temperate, mountain to subalpine.",
"vegetation type": "Temperate and mountain forests",
"latitude": NA,
"longitude": NA,
"latitude": "",
"longitude": "",
"minimum tree size": "12cm",
"history": "The first survey (LFI1) took place from 1983–85, the second survey followed in 1993–95 and the third inventory was carried out 2004–2006. Since 2009, the continuous survey of the fourth NFI (2009–2017) has been in progress.",
"field methodology": "The Swiss Forest Inventory, comprised plots on a 1km regular grid and has been reameasured three times. Each plot is based on two concentric plot of 200m2 (for tree dbh>12cm) and 500m2 (fro tree dbh >3^cm).",
"field methodology": "The Swiss Forest Inventory, comprised plots on a 1km regular grid and has been reameasured three times. Each plot is based on two concentric plot of 200m2 (for tree dbh>12cm) and 500m2 (fro tree dbh >3cm).",
"trait information": "TRY"
},
"references": ["http://www.lfi.ch/index-en.php",
""],
"references": ["http://www.lfi.ch/index-en.php"],
"files":{
"LFI12.csv":{
"sep":"c",
......
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