diff --git a/ms/create_folders.R b/ms/create_folders.R
index af2ec0c5d65ad7e8d56de7bbf18b75f2fbc6e1cb..269a641c4c01280b27062650af0d0b0fda8d9529 100644
--- a/ms/create_folders.R
+++ b/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)
+ }
+
+
+
+
diff --git a/ms/metadata/BCI/_file_index.csv b/ms/metadata/BCI/_file_index.csv
deleted file mode 100644
index d33faadbc75192ccdabc986b1719bbc1e39d46a5..0000000000000000000000000000000000000000
--- a/ms/metadata/BCI/_file_index.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-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"
diff --git a/ms/metadata/BCI/_site_details.JSON b/ms/metadata/BCI/_site_details.JSON
index 36e242a4a796f05a9aaf63d49359b2862296229c..58b4308eb64d8792d4aa300983725a23aa0d499b 100644
--- a/ms/metadata/BCI/_site_details.JSON
+++ b/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"}
+ }
}
diff --git a/ms/metadata/Canada/_file_index.csv b/ms/metadata/Canada/_file_index.csv
deleted file mode 100644
index 111ba8a28a95840532c3c7cacada388be3f88c9e..0000000000000000000000000000000000000000
--- a/ms/metadata/Canada/_file_index.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-filename,sep,skip,contents
-Canada_Data2George_20130818.csv,c,0,
-EcoregionCodes.csv,c,0,
-FIA_REF_SPECIES.csv,c,0,
diff --git a/ms/metadata/Canada/_site_details.JSON b/ms/metadata/Canada/_site_details.JSON
index 7aa4604c8edd5d69d99908068e5cd2bf566b801e..4d7bcfe13fea528b9327b25435f46e4dfa1da910 100644
--- a/ms/metadata/Canada/_site_details.JSON
+++ b/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"}
+ }
}
diff --git a/ms/metadata/France/_file_index.csv b/ms/metadata/France/_file_index.csv
deleted file mode 100644
index 5c53d263ef4af1f1a0d0a4b14ae29644fcdfdf4b..0000000000000000000000000000000000000000
--- a/ms/metadata/France/_file_index.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-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
diff --git a/ms/metadata/France/_site_details.JSON b/ms/metadata/France/_site_details.JSON
index 17cd0ccedba7643f4b75d3482b054df367077fd1..5e94ffe9d7c648023932cf108402cb1e2601f9ed 100644
--- a/ms/metadata/France/_site_details.JSON
+++ b/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"}
+ }
+}
diff --git a/ms/metadata/Fushan/_file_index.csv b/ms/metadata/Fushan/_file_index.csv
deleted file mode 100644
index 2793286812244490c77a3d192ad7ec168f2a99bd..0000000000000000000000000000000000000000
--- a/ms/metadata/Fushan/_file_index.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-filename,sep,skip,contents
-fs_trait_Kunstler.txt,t,0,
-Splist_Fushan_En.csv,c,0,
diff --git a/ms/metadata/Fushan/_site_details.JSON b/ms/metadata/Fushan/_site_details.JSON
index b9882d0ab1ef51556b5c7f603016479b11de90c0..c108907ff5280c49c8a7d2fd5573ab32defce59d 100644
--- a/ms/metadata/Fushan/_site_details.JSON
+++ b/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" }
+ }
}
diff --git a/ms/metadata/NSW/_file_index.csv b/ms/metadata/NSW/_file_index.csv
deleted file mode 100644
index 559573d062ba3766536e372a7f251dcaab618718..0000000000000000000000000000000000000000
--- a/ms/metadata/NSW/_file_index.csv
+++ /dev/null
@@ -1,7 +0,0 @@
-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,
diff --git a/ms/metadata/NSW/_site_details.JSON b/ms/metadata/NSW/_site_details.JSON
index 44c66fc6a665c6f79ffe12b951029f0f320bc952..63f5466b165480c024587825aa501cfbe2bf62e7 100644
--- a/ms/metadata/NSW/_site_details.JSON
+++ b/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":""}
+ }
}
diff --git a/ms/metadata/NVS/_file_index.csv b/ms/metadata/NVS/_file_index.csv
deleted file mode 100644
index 2296497fab24f63ace24422dc5cbbeaa9ed38107..0000000000000000000000000000000000000000
--- a/ms/metadata/NVS/_file_index.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-filename,sep,skip,contents
-nz_plotinfo_130801.csv,c,0,
-nz_traits_130801.csv,c,0,
-nz_treedata_growth_130801.csv,c,0,
diff --git a/ms/metadata/NVS/_site_details.JSON b/ms/metadata/NVS/_site_details.JSON
index d90f3ce23db358da33f750177361150d65469901..62b809f3f9b1386047dc1ecc62f4e0cc06830af2 100644
--- a/ms/metadata/NVS/_site_details.JSON
+++ b/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":"" }
+ }
}
diff --git a/ms/metadata/Paracou/_file_index.csv b/ms/metadata/Paracou/_file_index.csv
deleted file mode 100644
index 03dff74d962aa18337d3977f20a4979ee4fa50bf..0000000000000000000000000000000000000000
--- a/ms/metadata/Paracou/_file_index.csv
+++ /dev/null
@@ -1,8 +0,0 @@
-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,
diff --git a/ms/metadata/Paracou/_site_details.JSON b/ms/metadata/Paracou/_site_details.JSON
index eb6048c816e79dfad83dce29dd1c5c23e5203e7a..25354388131e1fd1bca47211acd04c9d05b740b8 100644
--- a/ms/metadata/Paracou/_site_details.JSON
+++ b/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":""}
+ }
}
diff --git a/ms/metadata/Spain/_file_index.csv b/ms/metadata/Spain/_file_index.csv
deleted file mode 100644
index 99a705eca480d93480958e23714d371bcea083c4..0000000000000000000000000000000000000000
--- a/ms/metadata/Spain/_file_index.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-filename,sep,skip,contents
-R_Ecoregion.csv,c,0,
-Tree_data_SFI_aug13_alldata.txt,t,0,
-Tree_data_SFI.txt,t,0,
diff --git a/ms/metadata/Spain/_site_details.JSON b/ms/metadata/Spain/_site_details.JSON
index 58f0f4ba491104ff0a03c088d9d32345f77beda4..7c18df82c607c52178bd840986d84d3b4fe39032 100644
--- a/ms/metadata/Spain/_site_details.JSON
+++ b/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":"" }
+ }
}
diff --git a/ms/metadata/Sweden/_file_index.csv b/ms/metadata/Sweden/_file_index.csv
deleted file mode 100644
index 2522b0eb0b2728f846e7e99f9a750b475a7c47ef..0000000000000000000000000000000000000000
--- a/ms/metadata/Sweden/_file_index.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-filename,sep,skip,contents
-Swe_NFI_1.csv,c,0,
-Swe_NFI_2a.csv,c,0,
-Swe_NFI_3.csv,c,0,
diff --git a/ms/metadata/Sweden/_site_details.JSON b/ms/metadata/Sweden/_site_details.JSON
index ec6e68cc3e5de3e5199d2db646143582f5caeb6b..7e5f80704123efda0e39523aa2a9ae6d1a82df30 100644
--- a/ms/metadata/Sweden/_site_details.JSON
+++ b/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":"" }
+ }
}
diff --git a/ms/metadata/Swiss/_file_index.csv b/ms/metadata/Swiss/_file_index.csv
deleted file mode 100644
index 11f35fa88d558cb2e57e3cb3b49862b7992cf41f..0000000000000000000000000000000000000000
--- a/ms/metadata/Swiss/_file_index.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-filename,sep,skip,contents
-LFI12.csv,c,0,
-LFI1to4.csv,c,0,
-LFI23.csv,c,0,
-LFI34.csv,c,0,
diff --git a/ms/metadata/Swiss/_site_details.JSON b/ms/metadata/Swiss/_site_details.JSON
index 7417415da2557c138c31daae84c9f408acffa546..a0a56d76f65e24806e1f06e204c8c57f44f52792 100644
--- a/ms/metadata/Swiss/_site_details.JSON
+++ b/ms/metadata/Swiss/_site_details.JSON
@@ -17,8 +17,14 @@
"field methodology": "",
"trait information": ""
},
- "references": [
- "",
- ""
- ]
+ "references": ["",
+ ""],
+ "files":{
+ "LFI12.csv":{
+ "sep":"c",
+ "contents":""},
+ "LFI1to4.csv":{
+ "sep":"c",
+ "contents":""}
+ }
}
diff --git a/ms/metadata/Swiss/files/LFI12.csv b/ms/metadata/Swiss/files/LFI12.csv
index 0b879946846654ed1532b9838a1c5a0e42ccf4ff..9b26745ba97206aa1db70ba1ec8571b816e5bcdc 100644
--- a/ms/metadata/Swiss/files/LFI12.csv
+++ b/ms/metadata/Swiss/files/LFI12.csv
@@ -12,7 +12,7 @@ use,var,units,description
0,BHD2,cm,"Census 2 - Diameter at breast height (derived from D13). For trees with DBH <= 60 cm it is measured by a (slide) caliper, for DBH > 60 cm it is calculated from the circumference."
0,BA1,cm2,Census 1 - Basal Area of a tree at 1.3m height (where DBH is measured)
0,BA2,cm2,Census 2 - Basal Area of a tree at 1.3m height (where DBH is measured)
-0,BAI,cm2,BA2 Ð BA1; basal area increment
+0,BAI,cm2,BA2 - BA1; basal area increment
0,BHD_DIFF,cm,BHD2 - BHD1; DBH increment
0,RPSTZ1,/ha,"Census 1 - Factor of repreentation of each tree in the two concentric circles (with differing minimum DBH to enter inventory). Each tree measured on a plot represents a certain number of trees on a hectare. The factor is not identical for all tress in a plot, but depends on diameter (larger or smaller 35cm), and may be further influenced by plot delineations that deviated from the standard plot size (e.g. when a road crosses a plot, or a forest edge reduces the plot size, etc.). The representation factor is larger the smaller the area of the plot."
0,RPSTZ2,/ha,Census 2 - Factor of repreentation of each tree as per RPSTZ1
@@ -23,4 +23,4 @@ use,var,units,description
0,ALTERD2,yr,Census 2 - AGE of individual estimated from a model
0,BESTALT2,yr,"Census 2 STAND AGE: is only measured in +/- even aged forests. Is measured from tree rings, or from twig whorls, but is sometimes also estimated/guessed."
0,WTYP1,,Census 1 - FOREST TYPE in 17 classes.
-0,WTYP2,,Census 2 - FOREST TYPE in 17 classes.
\ No newline at end of file
+0,WTYP2,,Census 2 - FOREST TYPE in 17 classes.
diff --git a/ms/metadata/TRY/_file_index.csv b/ms/metadata/TRY/_file_index.csv
deleted file mode 100644
index 381b336eabb30d2697bbe3e862aa2524ba74593d..0000000000000000000000000000000000000000
--- a/ms/metadata/TRY/_file_index.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-filename,sep,skip,contents
-TRY_Proposal_177_DataRelease_2013_04_01.txt,t,0,
-TRY_Proposal_177_DataRelease_2013_07_23.txt,t,0,
diff --git a/ms/metadata/US/_file_index.csv b/ms/metadata/US/_file_index.csv
deleted file mode 100644
index de317a5945a8e62ba6a4a91a52cc4852b1ed656e..0000000000000000000000000000000000000000
--- a/ms/metadata/US/_file_index.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-filename,sep,skip,contents
-EcoregionCodes.csv,c,0,
-FIA51_trees_w_supp.csv,c,0,
-FIAspeciesCodes.csv,c,0,
-FiaSpMaxHt.csv,c,0,
diff --git a/ms/metadata/US/_site_details.JSON b/ms/metadata/US/_site_details.JSON
index a12b2b36fbed33b12cf7a551b2a3002cda688ceb..d579924abe1884f7a4bd23270da5b4ac07c122ab 100644
--- a/ms/metadata/US/_site_details.JSON
+++ b/ms/metadata/US/_site_details.JSON
@@ -17,8 +17,20 @@
"field methodology": "",
"trait information": ""
},
- "references": [
- "Vanderwel, M.C., Lyutsarev, V.S., and Purves, D.W. (2013). Climate-related variation in mortality and recruitment determine regional forest-type distributions. Global Ecology and Biogeography n/a–n/a.",
- ""
- ]
+ "references": ["Vanderwel, M.C., Lyutsarev, V.S., and Purves, D.W. (2013). Climate-related variation in mortality and recruitment determine regional forest-type distributions. Global Ecology and Biogeography n/a–n/a.",
+ ""],
+ "files":{
+ "EcoregionCodes.csv":{
+ "sep":"c",
+ "contents":""},
+ "FIA51_trees_w_supp.csv":{
+ "sep":"c",
+ "contents":""},
+ "FIAspeciesCodes.csv":{
+ "sep":"c",
+ "contents":""},
+ "FiaSpMaxHt.csv":{
+ "sep":"c",
+ "contents":""}
+ }
}
diff --git a/ms/site_description.Rmd b/ms/site_description.Rmd
index 16da38688c89da641bb402023bbc1d4030472f82..2983f2f416e2cb0ade714bd98ad06ea2c9d1dc32 100644
--- a/ms/site_description.Rmd
+++ b/ms/site_description.Rmd
@@ -3,7 +3,6 @@
opts_chunk$set(warnings = FALSE)
# LOAD SITE DETAILS
-files <- read.csv(file.path(DIR,"_file_index.csv"), stringsAsFactors=FALSE)
json_file <- file.path(DIR,"_site_details.JSON")
details <- fromJSON(paste(readLines(json_file), collapse=""))
@@ -51,14 +50,13 @@ Below is a list of the various files provided for this dataset, and the variable
```{r,results="asis",echo=FALSE}
-for(i in 1:length(files[,1])){
+for(n in names(details$files)){
writeLines("\\newpage \n")
- filename <- file.path(DIR, "files", paste0(tools::file_path_sans_ext( gsub("/", "_", files[i,1])), ".csv"))
+ filename <- file.path(DIR, "files", paste0(tools::file_path_sans_ext( gsub("/", "_", n)), ".csv"))
mytext <- pandify(read.csv(filename, stringsAsFactors=FALSE))
- writeLines(paste0("### ",files[i,"filename"],"\n"))
- writeLines(paste0(files[i,"contents"], "\n"))
+ writeLines(paste0("### ", n,"\n"))
+ writeLines(paste0( details$files[[n]]$contents, "\n"))
writeLines(mytext)
-
}
```