Update db/

data-raw/db/equations_metadata.csv

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+Column,Field,Description,Column_type,Field_codes,Units,Range
+1 / A,equation_id,Unique equation identification number given arbitrarely. Links to Site_Species table.,NA,NA,NA,NA
+2 / B,equation_form,Algebraic form of the biomass equation as function of DBH,character,NA,NA,NA
+3 / C,equation_allometry,Equation to calculate biomass (includes coeficients given in original publication),character,NA,NA,NA
+4 / D,dependent_variable_biomass_component,Tree component characterized by the equation,character,NA,NA,NA
+5 / E,independent_variable,Parameters included in biomass model (H: tree height (m); DBH: diameter breast heigh (1.3 m); DBA: diameter at base; WD: wood density),character,NA,NA,NA
+6 / F,allometry_specificity,"Specific taxonomic level for which the equation was developed (species, genus, family or plant group)",character,NA,NA,NA
+7 / G,proxy_species,Species used as proxy to calculate AGB when a specific-species equation was not available,character,NA,NA,NA
+8 / H,geographic_area,Geographic location from which trees were sampled to develop the original equation,character,NA,NA,NA
+9 / I,dbh_min_cm,Minimun DBH in cm sampled to develop the equation,numeric,NA,NA,NA
+10 / J,dbh_max_cm,Maximun DBH in cm sampled to develop the equation,numeric,NA,NA,NA
+11 / K,sample_size,Number of trees sampled to develop the equation,integer,NA,NA,NA
+12 / L,dbh_units_original,DBH unit used in original publication,character,NA,NA,NA
+13 / M,biomass_units_original,Mass unit used in original publication,character,NA,NA,NA
+14 / N,allometry_development_method,"Method used to develop the allometry. Traditionally, this is done by harvesting whole trees, drying, and weighing (""harvest"").  However, we anticipate that many future allometries will be developed using ground-based LiDAR (""lidar"").",character,harvest; lidar,NA,NA
+15 / O,regression_model,Regression model used in original publication,character,NA,NA,NA
+16 / P,other_equations_tested,Comparable models if reported in publication (given equation form),character,NRA - Not Readily Available,NA,NA
+17 / Q,log_biomass,Whether the regretion fit is done with biomass as the response variable (i.e log(biomass) base 10),numeric,0 - false; 1 - true,NA,NA
+18 / R,bias_corrected,Indicates if a correction factor (CF) or a relative standard error (RSE) was included in model,numeric,0 - false; 1 - true,NA,NA
+19 / S,bias_correction_factor,"Correction factor for the specific equation, pulled from original publication, if included",numeric,NA,NA,NA
+20 / T,notes_fitting_model,Other details on statistical methods,character,NA,NA,NA
+21 / U,original_data_availability,Indicates whether or not the original source data is available,character,0 - false; 1 - true,NA,NA
+22 / V,notes_to_consider,Includes any notes to consider when using selected equation,character,NA,NA,NA
+23 / W,warning,Warning or error message to indicate any pitfall that could spoil the AGB estimate based on equation selected,character,NA,NA,NA
+24 / X,ref_id,Unique reference identification number for biomass equation source. Links to Reference table.,character,NA,NA,NA

data-raw/db/missing_values_metadata.csv

@@ -0,0 +1,5 @@
+Code,Definition,Description
+NA,Not Applicable,Data does not apply to that particular case
+NAC,Not Acquired,Information may be available but has not been acquired.
+NRA,Not Readily Available,"Information was not readily available to the authors (e.g., no ready access to the publication, language barrier)."
+NI,No Information,No information available in original publication

data-raw/db/references_metadata.csv

@@ -0,0 +1,7 @@
+Column,Field,Description,Colum_type,Notes to be deleted later
+1 / A,ref_id,Unique reference identification number to our data source. Links to multiple tables.,numeric,NA
+2 / B,ref_author,Last name of first author of a cited publication,character (string),NA
+3 / C,ref_year,Year of publication,numeric,NA
+4 / D,ref_title,Title of publication,character (string),NA
+5 / E,ref_journal,"Journal, book, report where published",character (string),EG: Keep this for now 02/14/2018
+6 / F,ref_doi,Publication DOI (Digital object identifier),character (string),NA

data-raw/db/sites_info.csv

@@ -0,0 +1,64 @@
+id,Site,site,lat,long,UTM_Zone,UTM_X,UTM_Y,intertropical,size.ha,E,wsg.site.name
+42,Amacayacu,amacayacu,-3.81,-70.27,19,359223.7022,9578870.297,Tropical,25,-0.07928769,amacayacu
+51,Badagongshan,badagongshan,29.46,110.52,49,453456.2453,3259047.312,Other,25,1.011620732,NA
+52,Baotianman,baotianman,33.5,111.94,49,587323.8348,3706005.813,Other,25,1.199599082,NA
+45,Barro Colorado Island,barro colorado island,9.15,-79.85,17,626783.7403,1012114.358,Tropical,50,0.049445487,bci
+18,Bukit Timah,bukit timah,1.35,103.78,48,364271.6602,149249.8881,Tropical,4,-0.084798024,bukittimah
+53,Changbaishan,changbaishan,42.38,128.08,52,424513.4019,4692742.225,Other,25,1.834148906,changbai
+46,Cocoli,cocoli,8.99,-79.62,17,652074.2927,993779.1758,Tropical,4,0.070253499,NA
+14,Danum Valley,danum valley,5.1,117.69,50,576257.6994,563967.7964,Tropical,50,-0.044607199,NA
+7,Dinghushan,dinghushan,23.17,112.51,49,654668.0285,2563086.118,Tropical,20,0.655347094,NA
+25,Doi Inthanon,doi inthanon,18.58,98.43,47,440211,2054819,Tropical,15,0.405736946,NA
+54,Donglingshan,donglingshan,39.96,115.43,50,365470.3933,4424127.891,Other,NA,1.7615144,NA
+20,Fushan,fushan,24.76,121.56,51,353895.0124,2739300.107,Other,25,0.430479025,fushan
+55,Gutianshan,gutianshan,29.25,118.12,50,608536.5224,3236200.982,Other,24,1.055180773,gutian
+29,Haliburton,haliburton,45.29,-78.64,17,685242.9898,5017892.345,Other,13.5,1.869090628,haliburton
+31,Harvard Forest,harvard forest,42.54,-72.18,18,731942.9165,4713468.255,Other,35,1.716028059,harvardforest
+8,Heishiding,heishiding,23.27,111.53,49,554207.1143,2573508.247,Tropical,50,0.746411624,heishiding
+9,Hong Kong,hong kong,22.43,114.18,50,209917.6,2482736.6,Tropical,21,0.490748617,NA
+26,Huai Kha Khaeng,huai kha khaeng,15.63,99.22,47,523259.1915,1728286.072,Tropical,50,0.31946635,hkk
+40,Ilha do Cardoso,ilha do cardoso,-25.1,-47.96,23,201725.4144,7221210.87,Other,10.2,0.210911743,NA
+2,Ituri average (Edoro & Lenda),ituri average (edoro & lenda),1.44,28.58,35,-,-,Tropical,NA,0.003627707,ituri
+2.1,Ituri-Edoro1,ituri-edoro1,1.56,28.52,35,668563,172648,Tropical,NA,0.002745626,NA
+2.2,Ituri-Edoro2,ituri-edoro2,1.56,28.52,35,669557.0001,172645,Tropical,NA,0.002745626,NA
+2.3,Ituri-Lenda1,ituri-lenda1,1.32,28.65,35,683078.0004,145589,Tropical,NA,-0.001571496,NA
+2.4,Ituri-Lenda2,ituri-lenda2,1.31,28.65,35,683069.0005,144621,Tropical,NA,-0.001315683,NA
+10,Jianfengling,jianfengling,18.73,108.91,49,279109.9787,2072338.72,Tropical,60,0.28396406,NA
+21,Kenting,kenting,21.98,120.8,51,272526.2425,2432250.629,Tropical,10,0.097674343,kenting
+27,Khao Chong,khao chong,7.54,99.8,47,588036.7725,833908.7871,Tropical,24,0.047869472,khaochong
+1,Korup,korup,5.07,8.85,32,483894.67,560834.91,Tropical,55,-0.089526908,korup
+6,Kuala Belalong,kuala belalong,4.54,115.15,50,295190.97,501901.22,Tropical,25,-0.047395853,NA
+43,La Planada,la planada,1.16,-77.99,18,166813.2014,127926.4909,Tropical,25,-0.146312127,laplanada
+15,Lambir,lambir,4.19,114.02,50,168797.5144,463372.1445,Tropical,52,-0.105606113,lambir
+49,Laupahoehoe,laupahoehoe,19.93,-155.29,5,260613.292,2205375.382,Tropical,4,NA,NA
+22,Lienhuachih,lienhuachih,23.91,120.88,51,284093.6913,2646281.327,Other,25,0.223115583,lienhuachih
+32,Lilly Dickey Woods,lilly dickey woods,39.24,-86.22,16,567481.1184,4343246.441,Other,25,1.686475838,lillydickey
+48,Luquillo,luquillo,18.33,-65.82,20,202346.9856,2028576.873,Tropical,16,0.096506178,luquillo
+41,Manaus,manaus,-2.44,-59.79,21,190167.2928,9729796.059,Tropical,25,-0.116549646,manaus
+28,Mo Singto,mo singto,14.43,101.35,47,753358.2549,1596943.59,Tropical,30.5,0.352063637,mosingto
+4,Mpala,mpala,0.29,36.88,37,264146.1264,32274.8907,Tropical,150,0.540809412,mpala
+13,Mudumalai,mudumalai,11.6,76.53,43,667229.3428,1282651.532,Tropical,50,0.20541107,mudumalai
+23,Nanjenshan,nanjenshan,22.06,120.85,51,278542.3832,2440915.528,Tropical,6,0.013545828,nanjenshan
+11,Nonggang,nonggang,22.43,106.95,48,700691.1024,2482092.06,Tropical,15,0.572216054,NA
+50,Palamanui,palamanui,19.74,-155.99,5,186188.785,2185414.698,Tropical,4,NA,NA
+17,Palanan,palanan,17.04,122.39,51,434869.6106,1884104.104,Tropical,16,-0.019430539,palanan
+16,Pasoh,pasoh,2.98,102.31,48,201296.6791,329968.1588,Tropical,50,-0.094024937,pasoh
+3,Rabi,rabi,-1.92,9.88,32,597875.4122,9787247.824,Tropical,25,0.01258341,rabi
+47,San Lorenzo/ Sherman,san lorenzo/ sherman,9.28,-79.97,17,612688.965,1026137.017,Tropical,6,-0.04491691,NA
+33,Santa Cruz,santa cruz,37.01,-122.08,10,582290.4887,4096647.841,Other,16,0.6355596,NA
+34,SCBI,scbi,38.89,-78.15,17,747576.8353,4308832.418,Other,NA,1.571394901,NA
+30,Scotty Creek,scotty creek,61.3,-121.3,10,591070.3047,6797388.659,Other,21,2.646941295,scotty
+35,SERC,serc,38.89,-76.56,18,364754.7104,4305625.637,Other,NA,1.631266437,serc
+19,Sinharaja,sinharaja,6.4,80.4,44,433901.8141,707714.4623,Tropical,25,-0.118385938,sinharaja
+58,Speulderbos,speulderbos,52.25,5.7,31,684429.1599,5792617.953,Other,27,0.951916465,NA
+56,Tiantongshan,tiantongshan,29.81,121.78,51,382397.5835,3298530.392,Other,20,1.110867343,NA
+36,Tyson Research Center,tyson research center,38.52,-90.56,15,712942.9979,4266096.106,Other,20,1.838340028,NA
+37,Wabikon,wabikon,45.55,-88.79,16,359937.4361,5046128.58,Other,25.6,1.731811064,wabikon
+5,Wanang,wanang,-5.25,145.27,55,307935.092,9419435.135,Tropical,50,-0.176488947,NA
+38,Wind River,wind river,45.82,-121.96,10,581116.9193,5074545.366,Other,25.6,0.8436695,windriver
+59,Wytham Woods,wytham woods,51.77,-1.34,30,614673.2627,5737242.505,Other,18,0.90247604,wytham
+12,Xishuangbanna,xishuangbanna,21.61,101.57,47,766473.4356,2392054.222,Tropical,20,0.33522321,xtbg
+44,Yasuni,yasuni,-0.69,-76.4,18,344544.4378,9924164.715,Tropical,50,-0.02645997,yasuni
+39,Yosemite National Park,yosemite national park,37.77,-119.82,11,251690.3705,4183617.761,Other,25.6,1.360057948,yosemite
+24,Zenlun,zenlun,23.42,120.55,51,249752.1018,2592662.301,Tropical,12,0.211963255,NA
+57,Zofin,zofin,48.66,14.71,33,478447.4731,5390124.453,Other,25,1.002541365,zofin