Move file list into JSON file

ms/create_folders.R

@@ -45,3 +45,19 @@ for(i in 1:length(details[,1]) )
 	l[[details[i,1]]]<- details[i,2]
 	
 	
+# Generate tables for each file
+f <- "new.JSON"
+cat("", file = f)
+	
+for(d in dir("metadata", full.names = TRUE) ){
+	cat(paste(d, "\n\n\tfiles: "), file = f, append = TRUE)
+	x<-read.csv(file.path(d,"_file_index.csv"), stringsAsFactors=FALSE)
+	l <- list()
+	for(i in 1:length(x[,1]) )
+		l[[x[i,1]]]<- as.list(x[1,2:4])
+	cat(toJSON(l), file = f, append = TRUE)
+	}
+	
+	
+	
+

ms/metadata/BCI/_file_index.csv

-filename,sep,skip,contents
-BCITRAITS_20101220.csv,c,0,"Trait data for BCI species, collected by Joe Wright and others. Available " 
-census1/PlotsDataReport.txt,t,0,"Data from a single census. There is a similar file for each census. Downlaoded from https://ctfs.arnarb.harvard.edu/webatlas/datasets/bci/"
-TaxonomyDataReport.txt,t,0,"Species codes, names, families, provided by Joe Wright"

ms/metadata/BCI/_site_details.JSON

@@ -5,7 +5,7 @@
  		"affiliation": "Centre for Tropical Science"
  	},
  	"agreement": "Census data obtained via data request from at https://ctfs.arnarb.harvard.edu/webatlas/datasets/bci/ under following agreement:\n\n * do not share the BCI data with other parties not included on the Request for Data Access Proposal.\n * Publications using BCI data should include the following citations:\n\t - Hubbell, S.P., Condit, R., and Foster, R.B. 2005. Barro Colorado Forest Census Plot Data. URL https://ctfs.arnarb.harvard.edu/webatlas/datasets/bci.\n\t - Condit, R. 1998. Tropical Forest Census Plots. Springer-Verlag and R. G. Landes Company, Berlin, Germany, and Georgetown, Texas. - Hubbell, S.P., R.B. Foster, S.T. O'Brien, K.E. Harms, R. Condit, B. Wechsler, S.J. Wright, and S. Loo de Lao. 1999. Light gap disturbances, recruitment limitation, and tree diversity in a neotropical forest. Science 283: 554-557. \n * Copies of articles should be sent to the BCI PIs prior to submission. Unless stated otherwise, the PIs will not be involved as collaborators, but reserve the right to request authorship. Once published, any manuscript making use of the BCI data should be sent to the PIs. \n * Publications should also include an acknowledgement of the support of the Center for Tropical Forest Science of the Smithsonian Tropical Research Institute and the primary granting agencies that have supported the BCI plot: *'The BCI forest dynamics research project was made possible by National Science Foundation grants to Stephen P. Hubbell: DEB-0640386, DEB-0425651, DEB-0346488, DEB-0129874, DEB-00753102, DEB-9909347, DEB-9615226, DEB-9615226, DEB-9405933, DEB-9221033, DEB-9100058, DEB-8906869, DEB-8605042, DEB-8206992, DEB-7922197, support from the Center for Tropical Forest Science, the Smithsonian Tropical Research Institute, the John D. and Catherine T. MacArthur Foundation, the Mellon Foundation, the Small World Institute Fund, and numerous private individuals, and through the hard work of over 100 people from 10 countries over the past two decades. The plot project is part the Center for Tropical Forest Science, a global network of large-scale demographic tree plots.'*\n\n Trait data supplied by Joe Wright under following agreement ????",
- 	"dataset": {
+ 	"dataset":{
 	"name": "Barro colorado island, 50 ha plot",
  	"country": "Panama",
  	"climate": "Tropical",
@@ -22,5 +22,16 @@
  				   "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" 	
- 				  ]
+ 				  ],
+	"files":{
+		"BCITRAITS_20101220.csv":{
+			"sep":"c",
+			"contents":"Trait data for BCI species, collected by Joe Wright and others."},
+		"census1/PlotsDataReport.txt":{
+			"sep":"c",
+			"contents":"Data from a single census. There is a similar file for each census."},
+		"TaxonomyDataReport.txt":{
+			"sep":"c",
+			"contents":"Species codes, names, families, provided by Joe Wright"}
+	}
 }

ms/metadata/Canada/_file_index.csv

-filename,sep,skip,contents
-Canada_Data2George_20130818.csv,c,0, 
-EcoregionCodes.csv,c,0, 
-FIA_REF_SPECIES.csv,c,0, 

ms/metadata/Canada/_site_details.JSON

@@ -6,19 +6,28 @@
  	},
   	"agreement": "",
  	"dataset": {
-	"name": "",
+	"name": "Candaian National Forest Inventory Dataset",
  	"country": "Canada",
  	"climate": "",
  	"vegetation type": "",
  	"latitude":  -1,
  	"longitude": -1,
- 	"minimum tree size": "variable (from ? to ?",
+ 	"minimum tree size": "variable (from ? to ?)",
  	"history": "",
  	"field methodology": "",
  	"trait information": ""
  	 },
- 	"references": [
- 				   "",
- 				   "" 	
- 				  ]
+ 	"references": ["",
+ 				   ""],
+	"files":{
+		"Canada_Data2George_20130818.csv":{
+			"sep":"c",
+			"contents":"NA"},
+		"EcoregionCodes.csv":{
+			"sep":"c",
+			"contents":"NA"},
+		"FIA_REF_SPECIES.csv":{
+			"sep":"c",
+			"contents":"NA"}
+	}
  }

ms/metadata/France/_file_index.csv

-filename,sep,skip,contents
-dataIFN.FRANCE.csv,c,0,data for IFN France with climatic variables
-species.csv,c,0,species code and species Latin name

ms/metadata/France/_site_details.JSON

@@ -20,8 +20,14 @@
 
  	"trait information": "extracted from the TRY database (http://try-db.org/)"
  	 },
- 	"references": [
- 				   "http://inventaire-forestier.ign.fr/spip/",
- 				   "Kunstler, G., S. Lavergne, B. Courbaud, W. Thuiller, G. Vieilledent, N.E. Zimmermann, J. Kattge, and D.A. Coomes. Competitive Interactions Between Forest Trees Are Driven by Species’ Trait Hierarchy, Not Phylogenetic or Functional Similarity: Implications for Forest Community Assembly. Ecology Letters 15: 831–840. doi:10.1111/j.1461-0248.2012.01803.x" 	
- 				  ]
- }
+ 	"references": ["http://inventaire-forestier.ign.fr/spip/",
+ 				   "Kunstler, G., S. Lavergne, B. Courbaud, W. Thuiller, G. Vieilledent, N.E. Zimmermann, J. Kattge, and D.A. Coomes. Competitive Interactions Between Forest Trees Are Driven by Species’ Trait Hierarchy, Not Phylogenetic or Functional Similarity: Implications for Forest Community Assembly. Ecology Letters 15: 831–840. doi:10.1111/j.1461-0248.2012.01803.x"],
+ 	"files":{
+	"dataIFN.FRANCE.csv":{
+		"sep":"c",
+		"contents":"data for IFN France with climatic variables"},
+	"species.csv":{
+		"sep":"c",
+		"contents":"species code and species Latin name"}
+	}
+}

ms/metadata/Fushan/_file_index.csv

-filename,sep,skip,contents
-fs_trait_Kunstler.txt,t,0, 
-Splist_Fushan_En.csv,c,0, 

ms/metadata/Fushan/_site_details.JSON

@@ -17,9 +17,14 @@
  	"field methodology": "",
  	"trait information": ""
  	 },
- 	"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.
-",
- 				   "" 	
- 				  ]
+ 	"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":{
+	"fs_trait_Kunstler.txt":{
+		"sep":"t",
+		"contents":"NA"},
+	"Splist_Fushan_En.csv":{
+		"sep":"t",
+		"contents":"NA"	}
+	}
  }

ms/metadata/NSW/_file_index.csv

-filename,sep,skip,contents
-NSW_data_BRcontrols.csv,c,0, 
-NSW_data_BRtreatments.csv,t,0, 
-NSW_data_BS1.csv,t,0, 
-NSW_data_BS2.csv,t,0, 
-NSW_data_TND.csv,t,0, 
-NSW_traits.csv,c,0, 

ms/metadata/NSW/_site_details.JSON

@@ -17,8 +17,26 @@
  	"field methodology": "",
  	"trait information": ""
  	 },
- 	"references": [
- 				   "",
- 				   "" 	
- 				  ]
+ 	"references": ["",
+ 				   ""],
+ 	"files":{
+	"NSW_data_BRcontrols.csv":{
+		"sep":"c",
+		"contents":""},
+	"NSW_data_BRtreatments.csv":{
+		"sep":"c",
+		"contents":""},
+	"NSW_data_BS1.csv":{
+		"sep":"c",
+		"contents":""},
+	"NSW_data_BS2.csv":{
+		"sep":"c",
+		"contents":""},
+	"NSW_data_TND.csv":{
+		"sep":"c",
+		"contents":""},
+	"NSW_traits.csv":{
+		"sep":"c",
+		"contents":""}
+	}
  }

ms/metadata/NVS/_file_index.csv

-filename,sep,skip,contents
-nz_plotinfo_130801.csv,c,0, 
-nz_traits_130801.csv,c,0, 
-nz_treedata_growth_130801.csv,c,0, 

ms/metadata/NVS/_site_details.JSON

@@ -17,8 +17,16 @@
  	"field methodology": "",
  	"trait information": ""
  	 },
- 	"references": [
- 				   "",
- 				   "" 	
- 				  ]
+ 	"references": ["",""],
+ 	"files":{
+	"nz_plotinfo_130801.csv":{
+		"sep":"c",
+		"contents":""},
+	"nz_traits_130801.csv":{
+		"sep":"c",
+		"contents":""},
+	"nz_treedata_growth_130801.csv":{
+		"sep":"c",
+		"contents":""	}
+	}
  }

ms/metadata/Paracou/_file_index.csv

-filename,sep,skip,contents
-20130717_paracou_1984_2012.csv,;,0, 
-20130717_paracou_codes_mesure.csv,;,0, 
-20130717_paracou_taxonomie.csv,;,0, 
-Autour-de-Paracou-Releves-par-trait-et-taxon,t,0, 
-bridge.csv,t,0, 
-BridgeDATA.g.csv,;,0, 
-WD-Species-Paracou-Ervan_GV.csv, " ",0, 

ms/metadata/Paracou/_site_details.JSON

@@ -20,5 +20,28 @@
  	"references": [
  				   "",
  				   "" 	
- 				  ]
+ 				  ],
+ 	"files":{
+		"20130717_paracou_1984_2012.csv":{
+			"sep":";",
+			"contents":""},
+		"20130717_paracou_codes_mesure.csv":{
+			"sep":";",
+			"contents":""},
+		"20130717_paracou_taxonomie.csv":{
+			"sep":";",
+			"contents":""},
+		"Autour-de-Paracou-Releves-par-trait-et-taxon":{
+			"sep":";",
+			"contents":""},
+		"bridge.csv":{
+			"sep":";",
+			"contents":""},
+		"BridgeDATA.g.csv":{
+			"sep":";",
+			"contents":""},
+		"WD-Species-Paracou-Ervan_GV.csv":{
+			"sep":";",
+			"contents":""}
+	}
  }

ms/metadata/Spain/_file_index.csv

-filename,sep,skip,contents
-R_Ecoregion.csv,c,0, 
-Tree_data_SFI_aug13_alldata.txt,t,0, 
-Tree_data_SFI.txt,t,0, 

ms/metadata/Spain/_site_details.JSON

@@ -20,5 +20,16 @@
  	"references": [
  				   "",
  				   "" 	
- 				  ]
+ 				  ],
+ 	"files":{
+		"R_Ecoregion.csv":{
+			"sep":"c",
+			"contents":""},
+		"Tree_data_SFI_aug13_alldata.txt":{
+			"sep":"c",
+			"contents":""},
+		"Tree_data_SFI.txt":{
+			"sep":"c",
+			"contents":""	}
+	}
  }

ms/metadata/Sweden/_file_index.csv

-filename,sep,skip,contents
-Swe_NFI_1.csv,c,0, 
-Swe_NFI_2a.csv,c,0, 
-Swe_NFI_3.csv,c,0, 

ms/metadata/Sweden/_site_details.JSON

@@ -19,5 +19,16 @@
  	"references": [
  				   "",
  				   "" 	
- 				  ]
+ 				  ],
+ 	"files":{
+		"Swe_NFI_1.csv":{
+			"sep":"c",
+			"contents":""},
+		"Swe_NFI_2a.csv":{
+			"sep":"c",
+			"contents":""},
+		"Swe_NFI_3.csv":{
+			"sep":"c",
+			"contents":""	}
+	}
  }

ms/metadata/Swiss/_file_index.csv

-filename,sep,skip,contents
-LFI12.csv,c,0, 
-LFI1to4.csv,c,0, 
-LFI23.csv,c,0, 
-LFI34.csv,c,0,