minor cleanup of metadata

teixeirak · teixeirak · commit 415de300a2a1 · 2018-01-04T05:36:09.000-05:00
diff --git a/.DS_Store b/.DS_Store
diff --git a/metadata/allometry_metadata.csv b/metadata/allometry_metadata.csv
@@ -1,5 +1,5 @@
-"Column","Field","Description","Alphanumeric.attributes..storage.type..present.data.values.","Variable.codes","n","min","max"
-"1 / A","allometric.equation","Code for allometric equation. Used in allometry and allometry2 fields in MEASUREMENTS table. When a single study presents multiple allometries (e.g., for various vegetation components or climates), the integer part refers to the study and the fractional parts refer to each individual allometry.   ","numeric (double) ","-",65,"1","35"
-"2 / B","allometry.citation","Author name and year of publication describing the allometries.","character (string) ","-",65,"-","-"
-"3 / C","allometry.citation.title","Title of reference for the allometries.","character (string) ","-",64,"-","-"
-"4 / D","allometry.notes","Description of the allometries used.","character (string) ","-",64,"-","-"
+Column,Field,Description,Storage Type,Variable Codes,n,Min ,Max
+1 / A,allometric.equation,"Code for allometric equation. Used in allometry and allometry2 fields in MEASUREMENTS table. When a single study presents multiple allometries (e.g., for various vegetation components or climates), the integer part refers to the study and the fractional parts refer to each individual allometry.   ",numeric (double) ,-,65,1,35
+2 / B,allometry.citation,Author name and year of publication describing the allometries.,character (string) ,-,65,-,-
+3 / C,allometry.citation.title,Title of reference for the allometries.,character (string) ,-,64,-,-
+4 / D,allometry.notes,Description of the allometries used.,character (string) ,-,64,-,-
diff --git a/metadata/history_metadata.csv b/metadata/history_metadata.csv
@@ -13,5 +13,5 @@ Column,Field,Description,Storage Type,Variable Codes,Units,n,Min ,Max
 12 / L,units,Level units.,character (string),-,-,955,-,-
 13 / M,percent.mortality,Percent tree mortality resulting from disturbance. 100% mortality is assumed for slash-and-burn and cultivation.,numeric (double),-,-,1595,4,100
 14 / N,hist.notes,History event details not included above.,character (string),-,-,3596,-,-
-15 / N,plothistory.ID.v1,"Original plothistory.ID, where numbers _2441 correspond to records released in the first published version of the database (Anderson-Teixeira et al., 2015)",numeric (integer),-,-,2477,1,5722
+15 / N,plothistory.ID.v1,"Original plothistory.ID, where numbers <=2441 correspond to records released in the first published version of the database (Anderson-Teixeira et al., 2015)",numeric (integer),-,-,2477,1,5722
 16 / O ,tropical.extratropical,Indicates whether data is from tropical or extratropical regions.,character (string),"tropical, extratropical",-,6159,-,-
diff --git a/metadata/histtype_metadata.csv b/metadata/histtype_metadata.csv
@@ -1,5 +1,5 @@
 Column,Field,Description,Storage Type,Variable Codes,n,Min ,Max
 1 / A,hist.cat,Plot history event categories. ,character (string),"Disturbance - includes natural and anthropogenic disturbances that directly kill or prevent establishment of trees.; Management- anthropogenic management or experimental manipulation, including chemical inputs (CO2, fertilizer, pesticides, herbicides), altered hydrology, warming, and minor mechanical disturbances; Establishment _ tree establishment, not necessarily following disturbance.; No.disturbance- Confirmed absence of major disturbance.; No.info- data not available Regrowth- vegetation regrowth following disturbance",38,-,-
-2 / B,hist.type,"Code name for plot history event types. Used HISTORY table and in regrowth.hist.type, distmrs.hisstype, dist_1.hist.type and dist_2.hist.type fileds of PLOTS table. ",character (string),-,35,-,-
+2 / B,hist.type,"Code name for plot history event types. Used HISTORY table and in regrowth.hist.type, distmrs.hisstype, dist_1.hist.type and dist_2.hist.type fields of PLOTS table. ",character (string),-,35,-,-
 3 / C,description,"Definition and notes about the disturbance, management, or regeneration type.",character (string),-,38,-,-
 4 / D,units,Units of the variable.,character (string),-,18,-,-
diff --git a/metadata/methodology_metadata.csv b/metadata/methodology_metadata.csv
@@ -1,5 +1,5 @@
-"Column","Field","Description","Alphanumeric.attributes..storage.type..present.data.values.","Variable.codes","n","min","max"
-"1 / A","method.ID","Code name for methodology. Used in MEASUREMENTS table. ","numeric (double) ","-",411,"1","448"
-"2 / B","method.citation","Reference for the methodology used.","character (string) ","-",411,"-","-"
-"3 / C","variables.name","The type of variable for which the methodology is described. May not exactly correspond to variables.name in VARIABLES table, as similar variables may be grouped together.","character (string) ","-",411,"-","-"
-"4 / D","method.notes","Description of the methodology used.","character (string) ","-",411,"-","-"
+Column,Field,Description,Storage Type,Variable Codes,n,Min ,Max
+1 / A,method.ID,Code name for methodology. Used in MEASUREMENTS table. ,numeric (double) ,-,411,1,448
+2 / B,method.citation,Reference for the methodology used.,character (string) ,-,411,-,-
+3 / C,variables.name,"The type of variable for which the methodology is described. May not exactly correspond to variables.name in VARIABLES table, as similar variables may be grouped together.",character (string) ,-,411,-,-
+4 / D,method.notes,Description of the methodology used.,character (string) ,-,411,-,-
diff --git a/metadata/pft_metadata.csv b/metadata/pft_metadata.csv
@@ -1,4 +1,4 @@
-"Column","Field","Description","Alphanumeric.attributes..storage.type..present.data.values.","Variable.codes","n","min","max"
-"1 / A","pftcode","Code name for plant functional traits. Used in MEASUREMENTS table. ","character (string)","-",19,"-","-"
-"2 / B","description","Definition of the pftcode.","character (string)","-",19,"-","-"
-"3 / C","notes","Details.","character (string)","-",8,"-","-"
+Column,Field,Description,Storage Type,Variable Codes,n,Min ,Max
+1 / A,pftcode,Code name for plant functional traits. Used in MEASUREMENTS table. ,character (string),-,19,-,-
+2 / B,description,Definition of the pftcode.,character (string),-,19,-,-
+3 / C,notes,Details.,character (string),-,8,-,-
diff --git a/metadata/plots_metadata.csv b/metadata/plots_metadata.csv
@@ -4,23 +4,23 @@ Column,Field,Description,Storage Type,Variable Codes,Units,n,Min ,Max
 3 / C,plot.name,"Unique plot name, sufficient to identify the plot within the original publication.",character (string),-,-,2630,-,-
 4 / D,plot.area,"Area of plot or combined area of replicate plots. For forest monitoring plots that change in area, this should be the most recent area. Note that area.sampled is recorded separately in the measurements table.",numeric (double),-,ha,760,0,50
 5 / E,establishment.ID,HistoryID (if any) detailing the establishment of oldest trees or of a keystone/ dominant tree taxa.,numeric (double),0-no record; nonzero number- history.ID,-,2731,0,2715
-6 / F,year.establishment.oldest.trees,Year of establishment of the oldest trees or of a keystone/ dominant tree taxa. Refers to the record in HISTORY that is indexted in etablishment.ID.,numeric (double),,-,1206,1013,2010
+6 / F,year.establishment.oldest.trees,Year of establishment of the oldest trees or of a keystone/ dominant tree taxa. Refers to the record in HISTORY that is indexed in etablishment.ID.,numeric (double),,-,1206,1013,2010
 7 / G,regrowth.ID,HistoryID (if any) detailing the initiation of forest (re)growth on previously non-forested land or following the most recent severe disturbance.,numeric (double),0-no record; nonzero number- history.ID,decimal years,2731,0,2715
-8 / H,regrowth.hist.type,"Type of forest (re)growth--e.g., natural succession or planted--following the most recent severe disturbance, if known. Refers to the record in HISTORY that is indexted in regrowth.ID.",character (string),Given in HISTTYPE metadata table,-,1365,-,-
-9 / I,regrowth.year,"Year of forest (re)growth following the most recent severe disturbance, if known. Refers to the record in HISTORY that is indexted in regrowth.ID.",numeric (double),,decimal years,1107,1206,2008
+8 / H,regrowth.hist.type,"Type of forest (re)growth--e.g., natural succession or planted--following the most recent severe disturbance, if known. Refers to the record in HISTORY that is indexed in regrowth.ID.",character (string),Given in HISTTYPE metadata table,-,1365,-,-
+9 / I,regrowth.year,"Year of forest (re)growth following the most recent severe disturbance, if known. Refers to the record in HISTORY that is indexed in regrowth.ID.",numeric (double),,decimal years,1107,1206,2008
 10 / J,dist.mrs.ID,HistoryID (if any) detailing the most recent severe/ stand clearing disturbance or event in a disturbance sequence (see description of dist.additional.mrs.ID). ,numeric (double),0-no record; nonzero number- history.ID,-,2731,0,2710
 11 / K,dist.mrs.hist.type,"Type of the most recent severe/ stand clearing disturbance or event in a disturbance sequence, if any. Refers to event indexed in dist.mrs.ID.",character (string),Given in HISTTYPE metadata table,-,1414,-,-
-12 / L,mortality,"Percent tree mortality caused by the most recent severe/ stand clearing disturbance. Values may be approximate and are unsuitable for direct comparisons because they are not standardized by tree size threshhold. A value of 100% was automatically assigned in cases of land clearing for agricultural purposes and for clear-cuts. Values of ""<100"" indicate that at least some trees survived, but (for events listed in this field) the disturbance was confirmed severe. Refers to event indexed in dist.mrs.ID.",numeric (double) or character (string),,%,822,95,100
+12 / L,mortality,"Percent tree mortality caused by the most recent severe/ stand clearing disturbance. Values may be approximate and are unsuitable for direct comparisons because they are not standardized by tree size threshold. A value of 100% was automatically assigned in cases of land clearing for agricultural purposes and for clear-cuts. Values of ""<100"" indicate that at least some trees survived, but (for events listed in this field) the disturbance was confirmed severe. Refers to event indexed in dist.mrs.ID.",numeric (double) or character (string),,%,822,95,100
 13 / M,dist.mrs.yr,"Year of the most recent severe/ stand clearing disturbance or event in a disturbance sequence. For a multi-year disturbance (e.g., agricultural use), the starting year is given. Refers to event indexed in dist.mrs.ID.",numeric (double),0-no record; nonzero number- history.ID,decimal years,787,1013,2008
 14 / N,dist.additional.mrs.ID,"HistoryID(s), if any, detailing any additional history events in the most recent severe/ stand-clearing disturbance sequence. For example, for a disturbance sequence consisting of cutting, burning, and cultivation, cutting and burning events would be indicated here, cultivation would be indicated in dist.mrs.ID.",numeric (double),"0-no record; nonzero decimal- history.ID; nonzero integer- plot number, given if this field refers to multiple records in HISTORY.",-,2731,0,2675
 15 / O,prior.history.ID,"HistoryID(s), if any, detailing any regrowth or severe / stand clearing disturbance events prior to the most recent severe/ stand-clearing disturbance sequence. Such events are categorized as ""regrowth_prior"" or ""disturbance_prior"" in HISTORY.",numeric (double),"0-no record; nonzero decimal- history.ID; nonzero integer- plot number, given if this field refers to multiple records in HISTORY.",-,2730,0,2478
 16 / P,dist_1.ID,"HistoryID, if any, detailing non stand-clearing disturbance events that occurred after the most recent severe/ stand-clearing disturbance (indexed in dist.mrs.ID) or in a stand with no known history of stand-clearing disturbance. When HISTORY contains multiple records of such disturbances, the first two are detailed in dist_1.ID and dist_2.ID, and any additional (subsequent) events are indexed in additional.dist.ID.",numeric (double),0-no record; nonzero number- history.ID,-,2731,0,2706
 17 / Q,dist_1.hist.type,Type of the disturbance event indexed in dist_1.ID.,character (string),Given in HISTTYPE metadata table,-,179,-,-
-18 / R,dist_1.mort,"Percent tree mortality caused by the disturbance indexed in dist_1.ID. Values may be approximate and are unsuitable for direct comparisons because they are not standardized by tree size threshhold. Values of ""<100"" indicate that at least some trees survived, but percent mortality is unknown. ",numeric (double) or character (string),-,%,158,4,100
+18 / R,dist_1.mort,"Percent tree mortality caused by the disturbance indexed in dist_1.ID. Values may be approximate and are unsuitable for direct comparisons because they are not standardized by tree size threshold. Values of ""<100"" indicate that at least some trees survived, but percent mortality is unknown. ",numeric (double) or character (string),-,%,158,4,100
 19 / S,dist_1.year,Year of the disturbance event indexed in dist_1.ID.,numeric (double) or character (string),-,decimal years,121,1617,2009
 20 / T,dist_2.ID,"HistoryID, if any, detailing non stand-clearing disturbance events that occurred after the most recent severe/ stand-clearing disturbance (indexed in dist.mrs.ID) or in a stand with no known history of stand-clearing disturbance.",numeric (double),0-no record; nonzero number- history.ID,-,2731,0,2706
 21 / U,dist_2.hist.type,Type of the disturbance event indexed in dist_2.ID.,character (string),Given in HISTTYPE metadata table,-,47,-,-
-22 / V,dist_2.mort,"Percent tree mortality caused by the disturbance indexed in dist_2.ID. Values may be approximate and are unsuitable for direct comparisons because they are not standardized by tree size threshhold. Values of ""<100"" indicate that at least some trees survived, but percent mortality is unknown. ",numeric (double) or character (string),-,%,41,4,96
+22 / V,dist_2.mort,"Percent tree mortality caused by the disturbance indexed in dist_2.ID. Values may be approximate and are unsuitable for direct comparisons because they are not standardized by tree size threshold. Values of ""<100"" indicate that at least some trees survived, but percent mortality is unknown. ",numeric (double) or character (string),-,%,41,4,96
 23 / W,dist_2.year,Year of the disturbance event indexed in dist_2.ID.,numeric (double) or character (string),-,decimal years,26,1900,2010
 24 / X,additional.dist.ID,"HistoryID(s), if any, detailing any additional non stand-clearing disturbance events that occurred after the most recent severe/ stand-clearing disturbance (indexed in dist.mrs.ID) or in a stand with no known history of stand-clearing disturbance.",numeric (double),"0-no record; nonzero decimal- history.ID; nonzero integer- plot number, given if this field refers to multiple records in HISTORY.",-,2731,0,2327
 25 / Y,management.CO2.ID,"HistoryID(s), if any, detailing experimental manipulation of atmospheric CO2.",numeric (double),"0-no record; nonzero decimal- history.ID; nonzero integer- plot number, given if this field refers to multiple records in HISTORY.",-,2731,0,2548
diff --git a/metadata/variables_metadata.csv b/metadata/variables_metadata.csv
@@ -1,15 +1,15 @@
-"Column","Field","Description","Alphanumeric.attributes..storage.type..present.data.values.","Variable.codes","n","min","max"
-"1 / A","variables.type","Variable type ","character (string) ","primary - a C cycle variable; secondary - a variable recorded because it can influence C cycle variables;  covariate - a variable required to interpret C cycle variables.",117,"-","-"
-"2 / B","variables.name","Code name for variable sampled. Used in MEASUREMENTS table.","character (string) ","-",117,"-","-"
-"3 / C","units","Units of the variable.","character (string) ","-",115,"-","-"
-"4 / D","description","Definition and notes about the variable.","character (string) ","-",117,"-","-"
-"5 / E","equations","Equations describing relationships among variables. Parentheses indicate variables that are not included in the current database version.","character (string) ","-",55,"-","-"
-"6 / F","requires.allometry","Indicates whether covariate allometric.equation should (generally) be recorded in association with the measurement. Covariate is defined in this table. ","number (binary)","0- false; 1- true",89,"0","1"
-"7 / G","requires.min.dbh","Indicates whether covariate min.dbh should (generally) be recorded in association with the measurement. Covariate is defined in this table.","number (binary)","0- false; 1- true",89,"0","1"
-"8 / H","requires.depth","Indicates whether covariate depth should (generally) be recorded in association with the measurement. Covariate is defined in this table.","number (binary)","0- false; 1- true",89,"0","1"
-"9 / I","associated.covariate_1","Other covariate associated with the variable listed. Parentheses indicate non-required covariate. Order listed here does not necessarily match the order listed in the MEASUREMENTS table). These covariates are also defined in this table.","character (string) ","-",52,"-","-"
-"10 / J","associated.covariate_2","Same as above.","character (string) ","-",10,"-","-"
-"11 / K","n.records","Number of records in the database (at the time of most recent update)","numeric (double)","-",117,"0","2079"
-"12 / L","Min","Minimum value in current version of the database.","numeric (double)","-",117,"-25","53"
-"13 / M","Max","Maximum value in current version of the database.","numeric (double)","-",117,"0","1533"
-"14 / N","notes","Notes of relevance to interpreting variables. ","character (string) ","-",31,"-","-"
+Column,Field,Description,Storage Type,Variable Codes,n,Min ,Max
+1 / A,variables.type,Variable type ,character (string) ,primary - a C cycle variable; secondary - a variable recorded because it can influence C cycle variables;  covariate - a variable required to interpret C cycle variables.,117,-,-
+2 / B,variables.name,Code name for variable sampled. Used in MEASUREMENTS table.,character (string) ,-,117,-,-
+3 / C,units,Units of the variable.,character (string) ,-,115,-,-
+4 / D,description,Definition and notes about the variable.,character (string) ,-,117,-,-
+5 / E,equations,Equations describing relationships among variables. Parentheses indicate variables that are not included in the current database version.,character (string) ,-,55,-,-
+6 / F,requires.allometry,Indicates whether covariate allometric.equation should (generally) be recorded in association with the measurement. Covariate is defined in this table. ,number (binary),0- false; 1- true,89,0,1
+7 / G,requires.min.dbh,Indicates whether covariate min.dbh should (generally) be recorded in association with the measurement. Covariate is defined in this table.,number (binary),0- false; 1- true,89,0,1
+8 / H,requires.depth,Indicates whether covariate depth should (generally) be recorded in association with the measurement. Covariate is defined in this table.,number (binary),0- false; 1- true,89,0,1
+9 / I,associated.covariate_1,Other covariate associated with the variable listed. Parentheses indicate non-required covariate. Order listed here does not necessarily match the order listed in the MEASUREMENTS table). These covariates are also defined in this table.,character (string) ,-,52,-,-
+10 / J,associated.covariate_2,Same as above.,character (string) ,-,10,-,-
+11 / K,n.records,Number of records in the database (at the time of most recent update),numeric (double),-,117,0,2079
+12 / L,min,Minimum value in current version of the database.,numeric (double),-,117,-25,53
+13 / M,max,Maximum value in current version of the database.,numeric (double),-,117,0,1533
+14 / N,notes,Notes of relevance to interpreting variables. ,character (string) ,-,31,-,-
