From 758c07dd33d3ba1beaec7a8d985fb1c90257499c Mon Sep 17 00:00:00 2001
From: Daniel Falster <daniel.falster@mq.edu.au>
Date: Mon, 9 Sep 2013 10:44:38 +1000
Subject: [PATCH] Move file list into JSON file
---
ms/create_folders.R | 16 ++++++++++++++++
ms/metadata/BCI/_file_index.csv | 4 ----
ms/metadata/BCI/_site_details.JSON | 15 +++++++++++++--
ms/metadata/Canada/_file_index.csv | 4 ----
ms/metadata/Canada/_site_details.JSON | 21 +++++++++++++++------
ms/metadata/France/_file_index.csv | 3 ---
ms/metadata/France/_site_details.JSON | 16 +++++++++++-----
ms/metadata/Fushan/_file_index.csv | 3 ---
ms/metadata/Fushan/_site_details.JSON | 15 ++++++++++-----
ms/metadata/NSW/_file_index.csv | 7 -------
ms/metadata/NSW/_site_details.JSON | 26 ++++++++++++++++++++++----
ms/metadata/NVS/_file_index.csv | 4 ----
ms/metadata/NVS/_site_details.JSON | 16 ++++++++++++----
ms/metadata/Paracou/_file_index.csv | 8 --------
ms/metadata/Paracou/_site_details.JSON | 25 ++++++++++++++++++++++++-
ms/metadata/Spain/_file_index.csv | 4 ----
ms/metadata/Spain/_site_details.JSON | 13 ++++++++++++-
ms/metadata/Sweden/_file_index.csv | 4 ----
ms/metadata/Sweden/_site_details.JSON | 13 ++++++++++++-
ms/metadata/Swiss/_file_index.csv | 5 -----
ms/metadata/Swiss/_site_details.JSON | 14 ++++++++++----
ms/metadata/Swiss/files/LFI12.csv | 4 ++--
ms/metadata/TRY/_file_index.csv | 3 ---
ms/metadata/US/_file_index.csv | 5 -----
ms/metadata/US/_site_details.JSON | 20 ++++++++++++++++----
ms/site_description.Rmd | 10 ++++------
26 files changed, 179 insertions(+), 99 deletions(-)
delete mode 100644 ms/metadata/BCI/_file_index.csv
delete mode 100644 ms/metadata/Canada/_file_index.csv
delete mode 100644 ms/metadata/France/_file_index.csv
delete mode 100644 ms/metadata/Fushan/_file_index.csv
delete mode 100644 ms/metadata/NSW/_file_index.csv
delete mode 100644 ms/metadata/NVS/_file_index.csv
delete mode 100644 ms/metadata/Paracou/_file_index.csv
delete mode 100644 ms/metadata/Spain/_file_index.csv
delete mode 100644 ms/metadata/Sweden/_file_index.csv
delete mode 100644 ms/metadata/Swiss/_file_index.csv
delete mode 100644 ms/metadata/TRY/_file_index.csv
delete mode 100644 ms/metadata/US/_file_index.csv
diff --git a/ms/create_folders.R b/ms/create_folders.R
index af2ec0c..269a641 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 d33faad..0000000
--- 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 36e242a..58b4308 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 111ba8a..0000000
--- 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 7aa4604..4d7bcfe 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 5c53d26..0000000
--- 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 17cd0cc..5e94ffe 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 2793286..0000000
--- 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 b9882d0..c108907 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 559573d..0000000
--- 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 44c66fc..63f5466 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 2296497..0000000
--- 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 d90f3ce..62b809f 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 03dff74..0000000
--- 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 eb6048c..2535438 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 99a705e..0000000
--- 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 58f0f4b..7c18df8 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 2522b0e..0000000
--- 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 ec6e68c..7e5f807 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 11f35fa..0000000
--- 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 7417415..a0a56d7 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 0b87994..9b26745 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 381b336..0000000
--- 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 de317a5..0000000
--- 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 a12b2b3..d579924 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 16da386..2983f2f 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)
-
}
```
--
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