From b3d235b715155cb42a9d9cd4881399a12468b32e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Wed, 29 Apr 2020 07:35:42 +0200
Subject: [PATCH] man: Remove obsolete docs
---
man/RMB_EIC_prescreen_df.Rd | 29 -------------------------
man/gen_cmpd_l.Rd | 27 -----------------------
man/gen_cmpdl_and_load.Rd | 24 ---------------------
man/gen_ftable.Rd | 24 ---------------------
man/gen_stgs_and_load.Rd | 22 -------------------
man/mk_combine_file.Rd | 26 ----------------------
man/mk_sett_file.Rd | 22 -------------------
man/no_drama_mkdir.Rd | 23 --------------------
man/presc.do.Rd | 31 --------------------------
man/presc.plot.Rd | 43 -------------------------------------
man/presc.shiny.Rd | 41 -----------------------------------
man/rendersmiles2.Rd | 24 ---------------------
man/renderurl.Rd | 25 ---------------------
13 files changed, 361 deletions(-)
delete mode 100644 man/RMB_EIC_prescreen_df.Rd
delete mode 100644 man/gen_cmpd_l.Rd
delete mode 100644 man/gen_cmpdl_and_load.Rd
delete mode 100644 man/gen_ftable.Rd
delete mode 100644 man/gen_stgs_and_load.Rd
delete mode 100644 man/mk_combine_file.Rd
delete mode 100644 man/mk_sett_file.Rd
delete mode 100644 man/no_drama_mkdir.Rd
delete mode 100644 man/presc.do.Rd
delete mode 100644 man/presc.plot.Rd
delete mode 100644 man/presc.shiny.Rd
delete mode 100644 man/rendersmiles2.Rd
delete mode 100644 man/renderurl.Rd
diff --git a/man/RMB_EIC_prescreen_df.Rd b/man/RMB_EIC_prescreen_df.Rd
deleted file mode 100644
index 13016b1..0000000
--- a/man/RMB_EIC_prescreen_df.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{RMB_EIC_prescreen_df}
-\alias{RMB_EIC_prescreen_df}
-\title{Prescreen}
-\usage{
-RMB_EIC_prescreen_df(wd, RMB_mode, FileList, cmpd_list,
- ppm_limit_fine = 10, EIC_limit = 0.001)
-}
-\arguments{
-\item{wd}{Absolute path to the directory that will contain the
-resulting data frame.}
-
-\item{RMB_mode}{...}
-
-\item{FileList}{...}
-
-\item{cmpd_list}{...}
-
-\item{ppm_limit_fine}{...}
-
-\item{EIC_limit}{...}
-}
-\description{
-Prescreens. Writes data out. Adapted from ReSOLUTION
-}
-\author{
-Emma Schymanski, Todor Kondić
-}
diff --git a/man/gen_cmpd_l.Rd b/man/gen_cmpd_l.Rd
deleted file mode 100644
index e2a69af..0000000
--- a/man/gen_cmpd_l.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{gen_cmpd_l}
-\alias{gen_cmpd_l}
-\title{Generate Compound List File}
-\usage{
-gen_cmpd_l(src_fn, dest_fn)
-}
-\arguments{
-\item{src_fn}{The input compound list CSV filename.}
-
-\item{dest_fn}{The resulting compound list CSV filename.}
-}
-\value{
-Number of compounds.
-}
-\description{
-Generate the RMassBank compound list from the input compound list
-in CSV file src_fn. The input compound list format is either a
-Chemical Dashboard csv file with, at least, PREFERRED_ SMILES
-columns \emph{filled} out, or just an ordinary CSV file with columns
-SMILES and Names filled. Argument dest_fn is the destination
-filename. Returns the number of compounds.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/gen_cmpdl_and_load.Rd b/man/gen_cmpdl_and_load.Rd
deleted file mode 100644
index a782c7b..0000000
--- a/man/gen_cmpdl_and_load.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{gen_cmpdl_and_load}
-\alias{gen_cmpdl_and_load}
-\title{Generate and Load the RMassBank Compound List}
-\usage{
-gen_cmpdl_and_load(wd, fn_cmpdl)
-}
-\arguments{
-\item{wd}{Directory under which results are archived.}
-
-\item{fn_cmpdl}{The input compound list filename.}
-}
-\value{
-Named list. The key \code{fn_cmpdl} is the path of the
-generated compound list and the key \code{n} the number of
-compounds.
-}
-\description{
-Generates the RMassBank compound list and loads it.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/gen_ftable.Rd b/man/gen_ftable.Rd
deleted file mode 100644
index de5f27d..0000000
--- a/man/gen_ftable.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{gen_ftable}
-\alias{gen_ftable}
-\title{Generate and Load the RMassBank Settings File}
-\usage{
-gen_ftable(fn_data, wd, n_cmpd)
-}
-\arguments{
-\item{fn_data}{The mzML filename.}
-
-\item{wd}{Directory under which results are archived.}
-
-\item{n_cmpd}{Number of compounds.}
-}
-\value{
-File path of the file table.
-}
-\description{
-Generates file table.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/gen_stgs_and_load.Rd b/man/gen_stgs_and_load.Rd
deleted file mode 100644
index 1fb26fc..0000000
--- a/man/gen_stgs_and_load.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{gen_stgs_and_load}
-\alias{gen_stgs_and_load}
-\title{Generate and Load the RMassBank Settings File}
-\usage{
-gen_stgs_and_load(stgs, wd)
-}
-\arguments{
-\item{stgs}{Settings named list, or a settings filename.}
-
-\item{wd}{Directory under which results are archived.}
-}
-\value{
-result of RMassBank::loadRmbSettings
-}
-\description{
-Generates settings file and loads it.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/mk_combine_file.Rd b/man/mk_combine_file.Rd
deleted file mode 100644
index 9c02d2c..0000000
--- a/man/mk_combine_file.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mk_combine_file}
-\alias{mk_combine_file}
-\title{Combine RMB Settings With Different Collisional Energies}
-\usage{
-mk_combine_file(sett_fns, fname)
-}
-\arguments{
-\item{sett_fns}{A list of settings files.}
-
-\item{fname}{The name of the combined file.}
-}
-\value{
-fname
-}
-\description{
-Combine the RMB settings files
-}
-\details{
-Combine RMB settings with different collisional energies into one
-settings file with multiple collisional energy entries.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/mk_sett_file.Rd b/man/mk_sett_file.Rd
deleted file mode 100644
index cbf885a..0000000
--- a/man/mk_sett_file.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mk_sett_file}
-\alias{mk_sett_file}
-\title{Generate RMassBank settings file.}
-\usage{
-mk_sett_file(sett_alist, file)
-}
-\arguments{
-\item{sett_alist}{The named list of settings that are different
-from the RMassBank defaults.}
-
-\item{file}{The name of the YAML specification that will be merged
-with the template Rmb settings file.}
-}
-\description{
-Produce the Rmb Settings file
-}
-\details{
-Produce the Rmb Settings file based on the customisation file in
-YAML format.
-}
diff --git a/man/no_drama_mkdir.Rd b/man/no_drama_mkdir.Rd
deleted file mode 100644
index c33d17d..0000000
--- a/man/no_drama_mkdir.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{no_drama_mkdir}
-\alias{no_drama_mkdir}
-\title{Create directories without drama}
-\usage{
-no_drama_mkdir(path)
-}
-\arguments{
-\item{path}{Names of the directories.}
-}
-\value{
-The character string containing the input argument \code{path}.
-}
-\description{
-Create directories without drama.
-}
-\details{
-Create directories without drama.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/presc.do.Rd b/man/presc.do.Rd
deleted file mode 100644
index 162677c..0000000
--- a/man/presc.do.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/run.R
-\name{presc.do}
-\alias{presc.do}
-\title{Prescreening on bunch of files.}
-\usage{
-presc.do(fn_data, fn_cmpd_l, mode, dest = ".", proc = F, ...)
-}
-\arguments{
-\item{fn_data}{The mzML files. Basis for the out directory name
-generation.}
-
-\item{fn_cmpd_l}{The compound list.}
-
-\item{mode}{RMB mode.}
-
-\item{dest}{Destination directory.}
-
-\item{proc}{Amount of processors, or FALSE.}
-
-\item{fn_cmpd_list}{The compound list CSV.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Do the prescreening.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/presc.plot.Rd b/man/presc.plot.Rd
deleted file mode 100644
index fb9939d..0000000
--- a/man/presc.plot.Rd
+++ /dev/null
@@ -1,43 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{presc.plot}
-\alias{presc.plot}
-\title{Plot the Output of Prescreen}
-\usage{
-presc.plot(prescdf, mode, out = "prescreen.pdf", fn_cmpd_l,
- pal = "Dark2", cex = 0.75, rt_digits = 2, m_digits = 4)
-}
-\arguments{
-\item{prescdf}{File table data-frame. See presc.shiny for details.}
-
-\item{mode}{RMB mode.}
-
-\item{out}{The name of the output file.}
-
-\item{fn_cmpd_l}{The compound list name.}
-
-\item{pal}{ColorBrewer palette name.}
-
-\item{cex}{As in legend.}
-
-\item{rt_digits}{Number of digits after the point for the retention time.}
-
-\item{m_digits}{Number of digits after the point for the mass.}
-
-\item{wd}{Sequence of data dirs containing the prescreen subdir.}
-
-\item{digits}{Number of significant digits for peak ret times.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Plot the output of prescreen.
-}
-\author{
-Todor Kondić
-
-Mira Narayanan
-
-Anjana Elapavalore
-}
diff --git a/man/presc.shiny.Rd b/man/presc.shiny.Rd
deleted file mode 100644
index d2f0e5d..0000000
--- a/man/presc.shiny.Rd
+++ /dev/null
@@ -1,41 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{presc.shiny}
-\alias{presc.shiny}
-\title{Prescreening with Shiny}
-\usage{
-presc.shiny(prescdf, mode, fn_cmpd_l, pal = "Dark2", cex = 0.75,
- rt_digits = 2, m_digits = 4)
-}
-\arguments{
-\item{prescdf}{File table data-frame. Columns: Files,ID,wd,tag,set_name ...}
-
-\item{mode}{RMassBank mode.}
-
-\item{fn_cmpd_l}{Compound list file name.}
-
-\item{pal}{ColorBrewer palette.}
-
-\item{cex}{Size of fonts.}
-
-\item{rt_digits}{Number of decimal places for the retention time.}
-
-\item{m_digits}{Number of decimal places for the mass.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Prescreening using shiny interface.
-}
-\author{
-Jessy Krier
-
-Mira Narayanan
-
-Hiba Mohammed Taha
-
-Anjana Elapavalore
-
-Todor Kondić
-}
diff --git a/man/rendersmiles2.Rd b/man/rendersmiles2.Rd
deleted file mode 100644
index f9bf7ab..0000000
--- a/man/rendersmiles2.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{rendersmiles2}
-\alias{rendersmiles2}
-\title{Turn SMILES to an Image Using Online Resource}
-\usage{
-rendersmiles2(smiles, style = "cow", ...)
-}
-\arguments{
-\item{smiles}{The SMILES string.}
-
-\item{style}{Structure style.}
-
-\item{...}{Hand over to renderurl.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Render smiles from an online resource.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/renderurl.Rd b/man/renderurl.Rd
deleted file mode 100644
index b1a143f..0000000
--- a/man/renderurl.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{renderurl}
-\alias{renderurl}
-\title{Render Compound from an Online Resource}
-\usage{
-renderurl(depictURL, coords = c(0, 0, 100, 100),
- filename = tempfile(fileext = ".svg"))
-}
-\arguments{
-\item{depictURL}{The URL of the object to plot.}
-
-\item{coords}{The positioning of the image (in data coords).}
-
-\item{filename}{Temp filename.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Helper function for rendersmiles2
-}
-\author{
-Todor Kondić
-}
--
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