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+.\" ========================================================================
+.\"
+.IX Title "ANALYZESDFILESDATA 1"
+.TH ANALYZESDFILESDATA 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
+.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
+.\" way too many mistakes in technical documents.
+.if n .ad l
+.nh
+.SH "NAME"
+AnalyzeSDFilesData.pl \- Analyze numerical data field values in SDFile(s)
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+AnalyzeSDFilesData.pl SDFile(s)...
+.PP
+AnalyzeSDFilesData.pl [\fB\-\-datafields\fR \*(L"fieldlabel,[fieldlabel,...]\*(R" | All]
+[\fB\-\-datafieldpairs\fR \*(L"fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]\*(R" | AllPairs] [\fB\-d, \-\-detail\fR infolevel]
+[\fB\-f, \-\-fast\fR] [\fB\-\-frequencybins\fR number | \*(L"number,number,[number,...]\*(R"]
+[\fB\-h, \-\-help\fR] [\fB\-\-klargest\fR number] [\fB\-\-ksmallest\fR number]
+[\fB\-m, \-\-mode\fR DescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | \*(L"function1, [function2,...]\*(R"]
+[\fB\-\-trimfraction\fR number] [\fB\-w, \-\-workingdir\fR dirname] SDFiles(s)...
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+Analyze numerical data field values in \fISDFile(s)\fR using a combination of various statistical
+functions; Non-numerical values are simply ignored. For \fICorrelation, RSquare, and
+Covariance\fR analysis, the count of valid values in specified data field pairs must be same;
+otherwise, column data field pair is ignored. The file names are separated by space.The valid file
+extensions are \fI.sdf\fR and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a
+current directory can be specified either by \fI*.sdf\fR or the current directory name.
+.SH "OPTIONS"
+.IX Header "OPTIONS"
+.ie n .IP "\fB\-\-datafields\fR \fI""fieldlabel,[fieldlabel,...]"" | Common | All\fR" 4
+.el .IP "\fB\-\-datafields\fR \fI``fieldlabel,[fieldlabel,...]'' | Common | All\fR" 4
+.IX Item "--datafields fieldlabel,[fieldlabel,...] | Common | All"
+Data fields to use for analysis. Possible values: list of comma separated data field
+labels, data fields common to all records, or all data fields. Default value: \fICommon\fR.
+Examples:
+.Sp
+.Vb 2
+\&    ALogP,MolWeight,EC50
+\&    "MolWeight,PSA"
+.Ve
+.ie n .IP "\fB\-\-datafieldpairs\fR \fI""fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]"" | CommonPairs | AllPairs\fR" 4
+.el .IP "\fB\-\-datafieldpairs\fR \fI``fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]'' | CommonPairs | AllPairs\fR" 4
+.IX Item "--datafieldpairs fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...] | CommonPairs | AllPairs"
+This value is mode specific and is only used for \fICorrelation, PearsonCorrelation, or
+Covariance\fR value of \fB\-m, \-\-mode\fR option. It specifies data field label pairs to use
+for data analysis during \fICorrelation\fR and \fICovariance\fR calculations. Possible values:
+comma delimited list of data field label pairs, data field label pairs common to all records,
+or all data field pairs. Default value:\fICommonPairs\fR. Example:
+.Sp
+.Vb 1
+\&    MolWeight,EC50,NumN+O,PSA
+.Ve
+.Sp
+For \fIAllPairs\fR value of \fB\-\-datafieldpairs\fR option, all data field label pairs are used for
+\&\fICorrelation\fR and \fICovariance\fR calculations.
+.IP "\fB\-d, \-\-detail\fR \fIinfolevel\fR" 4
+.IX Item "-d, --detail infolevel"
+Level of information to print about column values being ignored. Default: \fI0\fR. Possible values:
+0, 1, 2, 3, or 4.
+.IP "\fB\-f, \-\-fast\fR" 4
+.IX Item "-f, --fast"
+In this mode, all the data field values specified for analysis are assumed to contain numerical
+data and no checking is performed before analysis. By default, only numerical data is
+used for analysis; other types of column data is ignored.
+.ie n .IP "\fB\-\-frequencybins\fR \fInumber | ""number,number,[number,...]""\fR" 4
+.el .IP "\fB\-\-frequencybins\fR \fInumber | ``number,number,[number,...]''\fR" 4
+.IX Item "--frequencybins number | number,number,[number,...]"
+Specify number of bins or bin range to use for frequency analysis. Default value: \fI10\fR
+.Sp
+Number of bins value along with the smallest and largest value for a column is used to
+group the column values into different groups.
+.Sp
+The bin range list is used to group values for a column into different groups; It must contain
+values in ascending order. Examples:
+.Sp
+.Vb 2
+\&    10,20,30
+\&    0.1,0.2,0.3,0.4,0.5
+.Ve
+.Sp
+The frequency value calculated for a specific bin corresponds to all the column values
+which are greater than the previous bin value and less than or equal to the current bin value.
+.IP "\fB\-h, \-\-help\fR" 4
+.IX Item "-h, --help"
+Print this help message.
+.IP "\fB\-\-klargest\fR \fInumber\fR" 4
+.IX Item "--klargest number"
+Kth largest value to find by \fIKLargest\fR function. Default value: \fI2\fR. Valid values: positive
+integers.
+.IP "\fB\-\-ksmallest\fR \fInumber\fR" 4
+.IX Item "--ksmallest number"
+Kth smallest value to find by \fIKSmallest\fR function. Default values: \fI2\fR. Valid values: positive
+integers.
+.ie n .IP "\fB\-m, \-\-mode\fR \fIDescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | ""function1, [function2,...]""\fR" 4
+.el .IP "\fB\-m, \-\-mode\fR \fIDescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | ``function1, [function2,...]''\fR" 4
+.IX Item "-m, --mode DescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | function1, [function2,...]"
+Specify how to analyze data in SDFile(s): calculate basic or all descriptive statistics; or
+use a comma delimited list of supported statistical functions. Possible values:
+\&\fIDescriptiveStatisticsBasic | DescriptiveStatisticsAll | \*(L"function1,[function2]...\*(R"\fR. Default
+value: \fIDescriptiveStatisticsBasic\fR
+.Sp
+\&\fIDescriptiveStatisticsBasic\fR includes these functions: \fICount, Maximum, Minimum, Mean,
+Median, Sum, StandardDeviation, StandardError, Variance\fR.
+.Sp
+\&\fIDescriptiveStatisticsAll\fR, in addition to  \fIDescriptiveStatisticsBasic\fR functions, includes:
+\&\fIGeometricMean, Frequency, HarmonicMean, KLargest, KSmallest, Kurtosis, Mode, RSquare,
+Skewness, TrimMean\fR.
+.Sp
+\&\fIAll\fR uses complete list of supported functions: \fIAverage, AverageDeviation, Correlation,
+Count, Covariance, GeometricMean, Frequency, HarmonicMean, KLargest, KSmallest, Kurtosis,
+Maximum, Minimum, Mean, Median, Mode, RSquare, Skewness, Sum,
+SumOfSquares, StandardDeviation, StandardDeviationN, StandardError, StandardScores,
+StandardScoresN, TrimMean, Variance, VarianceN\fR. The function names ending with N
+calculate corresponding values assuming an entire population instead of a population sample.
+Here are the formulas for these functions:
+.Sp
+Average: See Mean
+.Sp
+AverageDeviation: \s-1SUM\s0( \s-1ABS\s0(x[i] \- Xmean) ) / n
+.Sp
+Correlation: See Pearson Correlation
+.Sp
+Covariance: \s-1SUM\s0( (x[i] \- Xmean)(y[i] \- Ymean) ) / n
+.Sp
+GeometricMean: NthROOT( \s-1PRODUCT\s0(x[i]) )
+.Sp
+HarmonicMean: 1 / ( \s-1SUM\s0(1/x[i]) / n )
+.Sp
+Mean: \s-1SUM\s0( x[i] ) / n
+.Sp
+Median: Xsorted[(n \- 1)/2 + 1] for even values of n; (Xsorted[n/2] + Xsorted[n/2 + 1])/2
+for odd values of n.
+.Sp
+Kurtosis: [ {n(n + 1)/(n \- 1)(n \- 2)(n \- 3)}  SUM{ ((x[i] \- Xmean)/STDDEV)^4 } ] \-
+{3((n \- 1)^2)}/{(n \- 2)(n\-3)}
+.Sp
+PearsonCorrelation: \s-1SUM\s0( (x[i] \- Xmean)(y[i] \- Ymean) ) / \s-1SQRT\s0( \s-1SUM\s0( (x[i] \- Xmean)^2 )
+(\s-1SUM\s0( (y[i] \- Ymean)^2 ))   )
+.Sp
+RSquare: PearsonCorrelation^2
+.Sp
+Skewness: {n/(n \- 1)(n \- 2)} SUM{ ((x[i] \- Xmean)/STDDEV)^3 }
+.Sp
+StandardDeviation: \s-1SQRT\s0 ( \s-1SUM\s0( (x[i] \- Mean)^2 ) / (n \- 1) )
+.Sp
+StandardDeviationN: \s-1SQRT\s0 ( \s-1SUM\s0( (x[i] \- Mean)^2 ) / n )
+.Sp
+StandardError: StandardDeviation / \s-1SQRT\s0( n )
+.Sp
+StandardScore: (x[i] \- Mean) / (n \- 1)
+.Sp
+StandardScoreN: (x[i] \- Mean) / n
+.Sp
+Variance: \s-1SUM\s0( (x[i] \- Xmean)^2  / (n \- 1) )
+.Sp
+VarianceN: \s-1SUM\s0( (x[i] \- Xmean)^2  / n )
+.IP "\fB\-o, \-\-overwrite\fR" 4
+.IX Item "-o, --overwrite"
+Overwrite existing files.
+.IP "\fB\-\-outdelim\fR \fIcomma | tab | semicolon\fR" 4
+.IX Item "--outdelim comma | tab | semicolon"
+Output text file delimiter. Possible values: \fIcomma, tab, or semicolon\fR
+Default value: \fIcomma\fR.
+.IP "\fB\-p, \-\-precision\fR \fInumber\fR" 4
+.IX Item "-p, --precision number"
+Precision of calculated values in the output file. Default: up to \fI2\fR decimal places.
+Valid values: positive integers.
+.IP "\fB\-q, \-\-quote\fR \fIyes | no\fR" 4
+.IX Item "-q, --quote yes | no"
+Put quotes around column values in output text file. Possible values: \fIyes or
+no\fR. Default value: \fIyes\fR.
+.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4
+.IX Item "-r, --root rootname"
+New text file name is generated using the root: <Root>.<Ext>. Default new file
+name: <InitialSDFileName><Mode>.<Ext>. Based on the specified analysis,
+<Mode> corresponds to one of these values: DescriptiveStatisticsBasic,
+DescriptiveStatisticsAll, AllStatistics, SpecifiedStatistics, Covariance, Correlation,
+Frequency, or StandardScores. The csv, and tsv <Ext> values are used for
+comma/semicolon, and tab delimited text files respectively. This option is ignored for
+multiple input files.
+.IP "\fB\-\-trimfraction\fR \fInumber\fR" 4
+.IX Item "--trimfraction number"
+Fraction of data to exclude from the top and bottom of the data set during
+\&\fITrimMean\fR calculation. Default value: \fI0.1\fR Valid values: > 0 and < 1.
+.IP "\fB\-w \-\-workingdir\fR \fItext\fR" 4
+.IX Item "-w --workingdir text"
+Location of working directory. Default: current directory.
+.SH "EXAMPLES"
+.IX Header "EXAMPLES"
+To calculate basic statistics for data in all common data fields and generate a
+NewSample1DescriptiveStatisticsBasic.csv file, type:
+.PP
+.Vb 1
+\&    % AnalyzeSDFilesData.pl \-o \-r NewSample1 Sample1.sdf
+.Ve
+.PP
+To calculate basic statistics for MolWeight data field and generate a
+NewSample1DescriptiveStatisticsBasic.csv file, type:
+.PP
+.Vb 2
+\&    % AnalyzeSDFilesData.pl \-\-datafields MolWeight \-o \-r NewSample1
+\&    Sample1.sdf
+.Ve
+.PP
+To calculate all available statistics for MolWeight data field and all data field pairs,
+and generate NewSample1DescriptiveStatisticsAll.csv, NewSample1CorrelationMatrix.csv,
+NewSample1CorrelationMatrix.csv, and NewSample1MolWeightFrequencyAnalysis.csv
+files, type:
+.PP
+.Vb 2
+\&    % AnalyzeSDFilesData.pl \-m DescriptiveStatisticsAll \-\-datafields
+\&    MolWeight \-o \-\-datafieldpairs AllPairs \-r NewSample1 Sample1.sdf
+.Ve
+.PP
+To compute frequency distribution of MolWeight data field into five bins and
+generate NewSample1MolWeightFrequencyAnalysis.csv, type:
+.PP
+.Vb 2
+\&    % AnalyzeSDFilesData.pl \-m Frequency \-\-frequencybins 5 \-\-datafields
+\&    MolWeight \-o \-r NewSample1 Sample1.sdf
+.Ve
+.PP
+To compute frequency distribution of data in MolWeight data field into specified bin range
+values, and generate NewSample1MolWeightFrequencyAnalysis.csv, type:
+.PP
+.Vb 2
+\&    % AnalyzeSDFilesData.pl \-m Frequency \-\-frequencybins "100,200,400"
+\&    \-\-datafields MolWeight \-o \-r NewSample1 Sample1.sdf
+.Ve
+.PP
+To calculate all available statistics for data in all data fields and pairs, type:
+.PP
+.Vb 2
+\&    % AnalyzeSDFilesData.pl \-m All \-\-datafields  All \-\-datafieldpairs
+\&    AllPairs \-o \-r NewSample1 Sample1.sdf
+.Ve
+.SH "AUTHOR"
+.IX Header "AUTHOR"
+Manish Sud <[e-mail]>
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, MergeTextFilesWithSD.pl
+.SH "COPYRIGHT"
+.IX Header "COPYRIGHT"
+Copyright (C) 2015 Manish Sud. All rights reserved.
+.PP
+This file is part of MayaChemTools.
+.PP
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.