Merge pull request #10 from phiguera/dev

R package v2.0.0 beta — initial release

Author: phiguera

CharAnalysis_2_0_MATLAB/RA07_charData.csv

@@ -0,0 +1,302 @@
+cmTop  (cm),cmBot      (cm),ageTop        (yr BP),ageBot        (yr BP),charVol        (cm3),charCount      (#)
+0,0.39,-57,-56.31,3,0
+0.39,1.16,-56.31,-50.7,3,1
+1.16,1.54,-50.7,-49.04,3,0
+1.54,1.93,-49.04,-46.41,3,1
+1.93,2.31,-46.41,-43.03,3,0
+2.31,2.7,-43.03,-39.8,3,1
+2.7,3.08,-39.8,-36.73,3,0
+3.08,3.47,-36.73,-33.64,3,0
+3.47,3.85,-33.64,-30.61,3,1
+3.85,4.24,-30.61,-27.71,3,0
+4.24,4.62,-27.71,-24.73,3,2
+4.62,5.01,-24.73,-21.43,3,0
+5.01,5.39,-21.43,-17.83,3,0
+5.39,5.78,-17.83,-13.94,3,0
+5.78,6.16,-13.94,-9.55,3,0
+6.16,6.55,-9.55,-4.43,3,0
+6.55,6.93,-4.43,1.33,3,0
+6.93,7.32,1.33,7.66,3,0
+7.32,7.7,7.66,14.55,3,1
+7.7,8.09,14.55,22.04,3,0
+8.09,8.47,22.04,30.16,3,0
+8.47,8.86,30.16,38.79,3,0
+8.86,9.24,38.79,47.24,3,1
+9.24,9.63,47.24,54.8,3,0
+9.63,10.01,54.8,61.24,3,3
+10.01,10.4,61.24,66.56,3,2
+10.4,10.78,66.56,71.37,3,1
+10.78,11.17,71.37,76.25,3,2
+11.17,11.55,76.25,81.23,3,2
+11.55,11.94,81.23,99.82,3,0
+11.94,12.32,99.82,117.79,3,0
+12.32,12.71,117.79,135.77,3,0
+12.71,13.09,135.77,153.74,3,1
+13.09,13.48,153.74,171.71,3,1
+13.48,13.86,171.71,189.68,3,1
+13.86,14.25,189.68,207.64,3,1
+14.25,14.63,207.64,225.61,3,3
+14.63,15.02,225.61,243.58,3,1
+15.02,15.4,243.58,261.54,3,1
+15.4,15.5,261.54,266.21,3,1
+15.5,15.75,266.21,277.87,3,1
+15.75,16,277.87,289.53,3,0
+16,16.25,289.53,301.2,3,0
+16.25,16.5,301.2,312.86,3,0
+16.5,16.75,312.86,324.52,3,6
+16.75,17,324.52,336.18,3,3
+17,17.25,336.18,347.83,3,5
+17.25,17.5,347.83,359.49,3,5
+17.5,17.75,359.49,371.15,3,2
+17.75,18,371.15,382.8,3,0
+18,18.25,382.8,394.46,3,0
+18.25,18.5,394.46,406.11,3,0
+18.5,18.75,406.11,417.76,3,0
+18.75,19,417.76,429.41,3,1
+19,19.25,429.41,441.06,3,3
+19.25,19.5,441.06,452.7,3,3
+19.5,19.75,452.7,464.35,3,1
+19.75,20,464.35,475.99,3,1
+20,20.25,475.99,487.63,3,0
+20.25,20.5,487.63,499.27,3,0
+20.5,20.75,499.27,510.91,3,1
+20.75,21,510.91,522.55,3,2
+21,21.25,522.55,534.18,3,1
+21.25,21.5,534.18,545.81,3,2
+21.5,21.75,545.81,557.44,3,0
+21.75,22,557.44,569.07,3,1
+22,22.25,569.07,580.7,3,3
+22.25,22.5,580.7,592.32,2,0
+22.5,22.75,592.32,603.95,3,3
+22.75,23,603.95,615.57,3,1
+23,23.25,615.57,627.19,3,1
+23.25,23.5,627.19,638.8,3,0
+23.5,23.75,638.8,650.41,3,1
+23.75,24,650.41,662.03,3,1
+24,24.25,662.03,673.63,3,0
+24.25,24.5,673.63,685.24,3,2
+24.5,24.75,685.24,696.84,3,0
+24.75,25,696.84,708.45,3,2
+25,25.25,708.45,720.04,3,3
+25.25,25.5,720.04,731.64,3,0
+25.5,25.75,731.64,743.23,3,1
+25.75,26,743.23,754.82,3,0
+26,26.25,754.82,766.41,3,1
+26.25,26.5,766.41,778,3,1
+26.5,26.75,778,789.58,3,1
+26.75,27,789.58,801.16,3,1
+27,27.25,801.16,812.73,3,0
+27.25,27.5,812.73,824.31,2,0
+27.5,27.75,824.31,835.88,2,1
+27.75,28,835.88,847.44,2,0
+28,28.25,847.44,859.01,3,2
+28.25,28.5,859.01,870.57,3,0
+28.5,28.75,870.57,882.12,3,2
+28.75,29,882.12,893.68,3,3
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+29.25,29.5,905.23,916.77,3,2
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+30.5,30.75,962.92,974.45,3,5
+30.75,31,974.45,985.98,3,8
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+33.25,33.5,1089.53,1101.01,3,1
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+34,34.25,1123.97,1135.44,3,0
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+34.5,34.75,1146.91,1158.37,3,0
+34.75,35,1158.37,1169.83,3,1
+35,35.25,1169.83,1181.28,3,6
+35.25,35.5,1181.28,1192.73,3,0
+35.5,35.75,1192.73,1204.17,3,9
+35.75,36,1204.17,1215.61,3,0
+36,36.25,1215.61,1227.04,3,6
+36.25,36.5,1227.04,1238.46,3,6
+36.5,36.75,1238.46,1249.88,3,9
+36.75,37,1249.88,1261.29,3,15
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+37.25,37.5,1272.69,1284.09,3,9
+37.5,37.75,1284.09,1295.47,2.5,2
+37.75,38,1295.47,1306.85,3,1
+38,38.25,1306.85,1318.23,3,9
+38.25,38.5,1318.23,1329.59,3,2
+38.5,38.75,1329.59,1340.95,3,2
+38.75,39,1340.95,1352.29,3,0
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+39.5,39.75,1374.96,1386.28,3,1
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+53.5,53.75,1988.44,1998.94,3,1
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+54,54.25,2009.43,2019.89,3,8
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CharAnalysis_2_0_MATLAB/RA07_charParams.csv

@@ -0,0 +1,26 @@
+Stage,Variable,Parameters,Units,Description and Options,,Parameter Log: use these columns to store parameters from previous analyses:
+Pretreatment,zoneDiv,-57,cal. yr BP,"Years defining beginning and end of record and any zone divisions. Zone divisions are used for plotting and for analyzing fire return intervals. You must input at least two values, the beginning and end of your record, in ascending order (i.e. youngest age on top). You may leave the spaces you don't use blank. ",,
+,,6274,,,,
+,,-9999,,,,
+,,-9999,,,,
+,,-9999,,,,
+,,-9999,,,,
+,,-9999,,,,
+,,-9999,,,,
+,yrInterpolate,15,yr,"Years to interpolate record to. Charcoal counts, sample volume, and sample depths are all interpolated before calculating charcoal accumulation rates. Enter 0 here is you want to interpolate to the median sample resolution (yr sample-1) of the selected record.",,
+,transform,0,index,"Do you want to transform the record before analysis?  0 == No;  1 == base-10 log transform;  2 == natural log transform. For 1-2, all charcoal accumulation rates have 1 added to them before transformation.",,
+Smoothing,method,2,index,"How do you want to estimate low-frequency CHAR (aka Cbackground)? 1 == Lowess smoother;  2 == Lowess smoother, robust to outliers;  3 == moving average;  4 == moving median;  5 == moving mode.",,
+,yr,750,yr,Years to smooth record over for estimating Cbackground.,,
+Peak Analysis,cPeak,1,index,How do you want to calculate high-frequency CHAR (aka Cpeak)? 1 == residuals (Cpeak = Cinterpolated - Cbackground);  2 == ratios (Cpeak = Cinterpolated / Cbackground).,,
+,threshType,2,index,What type of threshold do you want to use? 1 == Globally defined; 2 == Locally defined.,,
+,threshMethod,3,index,"How do you want to determine the threshold values for peak identification? 1 == user defines threshold values in threshValues (below), 2 == base threshold values on a percentile cut-off of a noise distribution, modeled with a 0- or 1-mean Gaussian (for cPeak method = 1 or 2, respectively); 3 == same as 2, but noise distribution is determined by a Gaussian mixture model.",,
+,threshValues,0.95,variable,"What threshold values do you want to evaluate? If threshMethod == 1, these values are in Cpeak units (i.e. either a residual or ratio value). If threshMethod == 2-3, these values are percentiles of the noise distribution (e.g. 0.95). In both cases, the last value (row 20) will be used for peak plotting and peak analysis.",,
+,,0.99,,,,
+,,0.999,,,,
+,,0.99,,,,
+,minCountP,0.25,probability,"Cut-off probability for minimum count analysis. E.g. if minCountP = 0.05, then the minimum charcoal count within 75 years before a peak has to have < 5% chance of coming from the same Poisson distribution as the maximum charcoal count associated with the peak. Peaks with a probability > 5% will be flagged and displayed but not included in peak analysis. Set this value to 0.99 to turn it off.",,
+Peak Analysis Results,peakFrequ,1000,yr,Years to smooth fire frequency and fire return intervals over. ,,
+,Cbackground sensitivity,0,index,Do you want to evaluate the sensitivity of your results to varying smoothing windows? 0 == no; 1 == yes.,,
+,saveFigures,0,index,Do you want to save the plots as .tiff and .pdf files? 0 == no; 1 == yes.,,
+,saveData,1,index,Do you want to save the output data by appending it to this file? 0 == no; 1 == yes.,,
+,allFigures,0,index,Do you want to display all (diagnostic) figures or only figures related to peak analysis results? 0 == no; 1 == yes.,,