Generating docs - Revision history

Chris: /* Function file Texinfo */

2021-06-03T23:44:52Z

Function file Texinfo

← Older revision		Revision as of 23:44, 3 June 2021
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	=Function file Texinfo=		=Function file Texinfo=

			Whenever a new function file is made in <code> mvapack/inst/ </code>, the following code should be copy and pasted
			to the top of the function file, with your name and email subbed in below. This first part is just the licensing
			agreement/disclaimer. It does not change from file to file but changes from user to user.

	## Copyright (C) 2021 University of Nebraska Board of Regents.		## Copyright (C) 2021 University of Nebraska Board of Regents.
	## Written by ~~Christopher Jurich~~ <~~cjurich2~~@huskers.unl.edu>.		## Written by FIRSTNAME LASTNAME <uname@huskers.unl.edu>.
	##		##
	## This program is free software; you can redistribute it and/or modify		## This program is free software; you can redistribute it and/or modify
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	## You should have received a copy of the GNU General Public License		## You should have received a copy of the GNU General Public License
	## along with this program; If not, see <http://www.gnu.org/licenses/>.		## along with this program; If not, see <http://www.gnu.org/licenses/>.

			This second part is different for each file


	## -- texinfo --		## -- texinfo --
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	##		##
	## @end deftypefn		## @end deftypefn


	=MVAPACK=		=MVAPACK=

Chris at 23:40, 3 June 2021

2021-06-03T23:40:23Z

← Older revision		Revision as of 23:40, 3 June 2021
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	=Function file Texinfo=		=Function file Texinfo=
	~~<code>~~
	## Copyright (C) 2021 University of Nebraska Board of Regents.		## Copyright (C) 2021 University of Nebraska Board of Regents.
	## Written by Christopher Jurich <cjurich2@huskers.unl.edu>.		## Written by Christopher Jurich <cjurich2@huskers.unl.edu>.
	##		##
	## This program is free software; you can redistribute it and/or modify		## This program is free software; you can redistribute it and/or modify
	## it under the terms of the GNU General Public License as published by		## it under the terms of the GNU General Public License as published by
	## the Free Software Foundation; either version 3 of the License, or		## the Free Software Foundation; either version 3 of the License, or
	## (at your option) any later version.		## (at your option) any later version.
	##		##
	## This program is distributed in the hope that it will be useful,		## This program is distributed in the hope that it will be useful,
	## but WITHOUT ANY WARRANY; without even the implied warranty of		## but WITHOUT ANY WARRANY; without even the implied warranty of
	## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the		## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	## GNU General Public License for more details.		## GNU General Public License for more details.
	##		##
	## You should have received a copy of the GNU General Public License		## You should have received a copy of the GNU General Public License
	## along with this program; If not, see <http://www.gnu.org/licenses/>.		## along with this program; If not, see <http://www.gnu.org/licenses/>.

			## -- texinfo --
			## @anchor{create_eics}
			## @deftypefn {Function File} create_eics (@var{fname}, @var{outdir}, @var{mz_min}=50, @var{mz_max}=2000, @var{eic_width}=0.05, @var{min_intensity}=1000, @var{filt_type}='base_peak', @var{cutoff}=0.001)
			##
			## Creates extracted ion chromatograms (EICs) from the data in the file specified by @var{fname}.
			## If and when multiple data points exist at the same retention time, the one with higher intensity will be kept.
			## This code relies on C++ bindings that must be compiled for this functionality to work.
			## Detail on the input parameters is provided below:
			##
			## - EICs will be made from @var{mz_min} to @var{mz_max}
			##
			## - EICs have dalton width of @var{eic_width} and are saved to the @var{outdir} directory. Note that any existing files in @var{outdir} are deleted and it is created if it does not already exist.
			##
			## - @var{min_intensity} denotes the lowest max intensity an EIC must have to be saved.
			##
			## - @var{filt_type} indicates the type of raw data filtration to be carried out. Valid options are 'base_peak' or 'absolute'.
			##
			## - @var{cutoff} indicates the cutoff that will be used to filter the raw data. For 'base_peak' mode, this decimal will be multiplied by the base peak to get a cutoff whereas for 'absolute', it is the specified value.
			##
			## @end deftypefn

	~~## -- texinfo --~~
	~~## @anchor{create_eics}~~
	## @deftypefn {Function File} create_eics (@var{fname}, @var{outdir}, @var{mz_min}=50, @var{mz_max}=2000, @var{eic_width}=0.05, @var{min_intensity}=1000, @var{filt_type}='base_peak', @var{cutoff}=0.001)
	##
	~~## Creates extracted ion chromatograms (EICs) from the data in the file specified by @var{fname}.~~
	~~## If and when multiple data points exist at the same retention time, the one with higher intensity will be kept.~~
	~~## This code relies on C++ bindings that must be compiled for this functionality to work.~~
	~~## Detail on the input parameters is provided below:~~
	##
	~~## - EICs will be made from @var{mz_min} to @var{mz_max}~~
	##
	~~## - EICs have dalton width of @var{eic_width} and are saved to the @var{outdir} directory. Note that any existing files in @var{outdir} are deleted and it is created if it does not already exist.~~
	##
	~~## - @var{min_intensity} denotes the lowest max intensity an EIC must have to be saved.~~
	##
	~~## - @var{filt_type} indicates the type of raw data filtration to be carried out. Valid options are 'base_peak' or 'absolute'.~~
	##
	## - @var{cutoff} indicates the cutoff that will be used to filter the raw data. For 'base_peak' mode, this decimal will be multiplied by the base peak to get a cutoff whereas for 'absolute', it is the specified value.
	##
	~~## @end deftypefn~~
	~~</code>~~

	=MVAPACK=		=MVAPACK=

Chris: /* Function file Texinfo */

2021-06-03T23:39:10Z

Function file Texinfo

← Older revision		Revision as of 23:39, 3 June 2021
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	=Function file Texinfo=		=Function file Texinfo=
	<code>		<code>
	\#\# Copyright (C) 2021 University of Nebraska Board of Regents.		## Copyright (C) 2021 University of Nebraska Board of Regents.
	## Written by Christopher Jurich <cjurich2@huskers.unl.edu>.		## Written by Christopher Jurich <cjurich2@huskers.unl.edu>.
	##		##

Chris: /* Function file Texinfo */

2021-06-03T23:38:58Z

Function file Texinfo

← Older revision		Revision as of 23:38, 3 June 2021
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	=Function file Texinfo=		=Function file Texinfo=
	<code>		<code>
	## Copyright (C) 2021 University of Nebraska Board of Regents.		\#\# Copyright (C) 2021 University of Nebraska Board of Regents.
	## Written by Christopher Jurich <cjurich2@huskers.unl.edu>.		## Written by Christopher Jurich <cjurich2@huskers.unl.edu>.
	##		##

Chris: /* Function file Texinfo */

2021-06-03T23:38:25Z

Function file Texinfo

← Older revision		Revision as of 23:38, 3 June 2021
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	=Function file Texinfo=		=Function file Texinfo=
			<code>
	## Copyright (C) 2021 University of Nebraska Board of Regents.		## Copyright (C) 2021 University of Nebraska Board of Regents.
	## Written by Christopher Jurich <cjurich2@huskers.unl.edu>.		## Written by Christopher Jurich <cjurich2@huskers.unl.edu>.
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	##		##
	## @end deftypefn		## @end deftypefn
			</code>

	=MVAPACK=		=MVAPACK=

Chris at 23:37, 3 June 2021

2021-06-03T23:37:18Z

← Older revision		Revision as of 23:37, 3 June 2021
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	=Function file Texinfo=		=Function file Texinfo=

			## Copyright (C) 2021 University of Nebraska Board of Regents.
			## Written by Christopher Jurich <cjurich2@huskers.unl.edu>.
			##
			## This program is free software; you can redistribute it and/or modify
			## it under the terms of the GNU General Public License as published by
			## the Free Software Foundation; either version 3 of the License, or
			## (at your option) any later version.
			##
			## This program is distributed in the hope that it will be useful,
			## but WITHOUT ANY WARRANY; without even the implied warranty of
			## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
			## GNU General Public License for more details.
			##
			## You should have received a copy of the GNU General Public License
			## along with this program; If not, see <http://www.gnu.org/licenses/>.

			## -- texinfo --
			## @anchor{create_eics}
			## @deftypefn {Function File} create_eics (@var{fname}, @var{outdir}, @var{mz_min}=50, @var{mz_max}=2000, @var{eic_width}=0.05, @var{min_intensity}=1000, @var{filt_type}='base_peak', @var{cutoff}=0.001)
			##
			## Creates extracted ion chromatograms (EICs) from the data in the file specified by @var{fname}.
			## If and when multiple data points exist at the same retention time, the one with higher intensity will be kept.
			## This code relies on C++ bindings that must be compiled for this functionality to work.
			## Detail on the input parameters is provided below:
			##
			## - EICs will be made from @var{mz_min} to @var{mz_max}
			##
			## - EICs have dalton width of @var{eic_width} and are saved to the @var{outdir} directory. Note that any existing files in @var{outdir} are deleted and it is created if it does not already exist.
			##
			## - @var{min_intensity} denotes the lowest max intensity an EIC must have to be saved.
			##
			## - @var{filt_type} indicates the type of raw data filtration to be carried out. Valid options are 'base_peak' or 'absolute'.
			##
			## - @var{cutoff} indicates the cutoff that will be used to filter the raw data. For 'base_peak' mode, this decimal will be multiplied by the base peak to get a cutoff whereas for 'absolute', it is the specified value.
			##
			## @end deftypefn


	=MVAPACK=		=MVAPACK=

Chris at 23:28, 3 June 2021

2021-06-03T23:28:14Z

← Older revision		Revision as of 23:28, 3 June 2021
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	=Function file Texinfo=		=Function file Texinfo=

	=~~VAPACK~~=		=MVAPACK=
			=extra=

	[[Category:Sysadmin]]		[[Category:Sysadmin]]

Chris at 23:18, 3 June 2021

2021-06-03T23:18:18Z

← Older revision		Revision as of 23:18, 3 June 2021
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	==Making the pdf==		=Making the pdf=

	To make the documentation, first <code> cd </code> into your <code> mvapack/ </code> directory. Next, you will run the following command:		To make the documentation, first <code> cd </code> into your <code> mvapack/ </code> directory. Next, you will run the following command:
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	This will build the documentation and save it to <code> mvapack/doc/mvapack.pdf </code>, assuming the build finished successfully.		This will build the documentation and save it to <code> mvapack/doc/mvapack.pdf </code>, assuming the build finished successfully.

			=Function file Texinfo=

	~~==Function file Texinfo==~~		=VAPACK=

	==VAPACK==

	[[Category:Sysadmin]]		[[Category:Sysadmin]]

Chris at 23:18, 3 June 2021

2021-06-03T23:18:04Z

← Older revision		Revision as of 23:18, 3 June 2021
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	== Making the pdf ==		==Making the pdf==

	To make the documentation, first <code> cd </code> into your <code> mvapack/ </code> directory. Next, you will run the following command:		To make the documentation, first <code> cd </code> into your <code> mvapack/ </code> directory. Next, you will run the following command:
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	== Function file Texinfo ==		==Function file Texinfo==

	== ~~MVAPACK~~ ==		==VAPACK==

	[[Category:Sysadmin]]		[[Category:Sysadmin]]

Chris at 23:16, 3 June 2021

2021-06-03T23:16:44Z

← Older revision		Revision as of 23:16, 3 June 2021
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	== ~~Section 2~~ ==		== Function file Texinfo ==

			== MVAPACK ==

	[[Category:Sysadmin]]		[[Category:Sysadmin]]