1. structToolbox
  2. Commit 4520aac348f3e26e22e531d696457bdfa9b2b92e
Browse code

minor text edits to documentation

Gavin Rhys Lloyd authored on 27/06/2024 13:06:21
Showing 19 changed files
DESCRIPTION
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@@ -122,7 +122,7 @@ Imports: ggplot2,
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     scales,
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     sp,
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     stats
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-RoxygenNote: 7.2.3
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+RoxygenNote: 7.3.1
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 Suggests: agricolae,
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  BiocFileCache,
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  BiocStyle,
man/HCA.Rd
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@@ -56,7 +56,7 @@ M = model_apply(M,D)
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 }
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 \references{
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-R Core Team (2023). \emph{R: A Language and Environment for Statistical
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+R Core Team (2024). \emph{R: A Language and Environment for Statistical
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 Computing}. R Foundation for Statistical Computing, Vienna, Austria.
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 \url{https://www.R-project.org/}.
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 }
man/HSDEM.Rd
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@@ -47,8 +47,8 @@ M = model_apply(M,D)
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 }
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 \references{
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-Lenth R (2023). \emph{emmeans: Estimated Marginal Means, aka Least-Squares
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-Means}. R package version 1.9.0,
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+Lenth R (2024). \emph{emmeans: Estimated Marginal Means, aka Least-Squares
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+Means}. R package version 1.10.1,
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 \url{https://CRAN.R-project.org/package=emmeans}.
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 Pinheiro J, Bates D, R Core Team (2023). \emph{nlme: Linear and Nonlinear
man/blank_filter.Rd
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@@ -61,8 +61,7 @@ M = blank_filter(fold_change=2,
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 M = model_apply(M,D)
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 }
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 \references{
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-Jankevics A, Lloyd GR, Weber RJM (2023). \emph{pmp: Peak Matrix Processing
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-and signal batch correction for metabolomics datasets}.
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-doi:10.18129/B9.bioc.pmp \url{https://doi.org/10.18129/B9.bioc.pmp}, R
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-package version 1.14.0, \url{https://bioconductor.org/packages/pmp}.
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+Jankevics A, Lloyd GR, Weber RJM (????). \emph{pmp: Peak Matrix Processing
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+and signal batch correction for metabolomics datasets}. R package
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+version 1.15.1.
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 }
man/corr_coef.Rd
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@@ -57,7 +57,7 @@ M = corr_coef(factor_names=c('sample_order','sample_rep'))
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 M = model_apply(M,D)
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 }
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 \references{
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-R Core Team (2023). \emph{R: A Language and Environment for Statistical
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+R Core Team (2024). \emph{R: A Language and Environment for Statistical
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 Computing}. R Foundation for Statistical Computing, Vienna, Austria.
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 \url{https://www.R-project.org/}.
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 }
man/glog_opt_plot.Rd
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@@ -40,8 +40,7 @@ C = glog_opt_plot()
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 chart_plot(C,M,D)
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 }
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 \references{
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-Jankevics A, Lloyd GR, Weber RJM (2023). \emph{pmp: Peak Matrix Processing
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-and signal batch correction for metabolomics datasets}.
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-doi:10.18129/B9.bioc.pmp \url{https://doi.org/10.18129/B9.bioc.pmp}, R
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-package version 1.14.0, \url{https://bioconductor.org/packages/pmp}.
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+Jankevics A, Lloyd GR, Weber RJM (????). \emph{pmp: Peak Matrix Processing
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+and signal batch correction for metabolomics datasets}. R package
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+version 1.15.1.
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 }
man/glog_transform.Rd
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@@ -45,10 +45,9 @@ M = glog_transform(qc_label='versicolor',factor_name='Species')
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 M = model_apply(M,D)
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 }
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 \references{
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-Jankevics A, Lloyd GR, Weber RJM (2023). \emph{pmp: Peak Matrix Processing
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-and signal batch correction for metabolomics datasets}.
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-doi:10.18129/B9.bioc.pmp \url{https://doi.org/10.18129/B9.bioc.pmp}, R
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-package version 1.14.0, \url{https://bioconductor.org/packages/pmp}.
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+Jankevics A, Lloyd GR, Weber RJM (????). \emph{pmp: Peak Matrix Processing
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+and signal batch correction for metabolomics datasets}. R package
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+version 1.15.1.
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 Durbin B, Hardin J, Hawkins D, Rocke D (2002). "A variance-stabilizing
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 transformation for gene-expression microarray data." \emph{Bioinformatics},
man/hca_dendrogram.Rd
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@@ -33,7 +33,7 @@ M = hca_dendrogram()
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 C = hca_dendrogram()
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 }
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 \references{
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-de Vries A, Ripley BD (2022). \emph{ggdendro: Create Dendrograms and Tree
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-Diagrams Using 'ggplot2'}. R package version 0.1.23,
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+de Vries A, Ripley BD (2024). \emph{ggdendro: Create Dendrograms and Tree
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+Diagrams Using 'ggplot2'}. R package version 0.2.0,
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 \url{https://CRAN.R-project.org/package=ggdendro}.
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 }
man/knn_impute.Rd
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@@ -51,8 +51,7 @@ M = knn_impute(
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 M = knn_impute()
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 }
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 \references{
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-Jankevics A, Lloyd GR, Weber RJM (2023). \emph{pmp: Peak Matrix Processing
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-and signal batch correction for metabolomics datasets}.
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-doi:10.18129/B9.bioc.pmp \url{https://doi.org/10.18129/B9.bioc.pmp}, R
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-package version 1.14.0, \url{https://bioconductor.org/packages/pmp}.
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+Jankevics A, Lloyd GR, Weber RJM (????). \emph{pmp: Peak Matrix Processing
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+and signal batch correction for metabolomics datasets}. R package
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+version 1.15.1.
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 }
man/linear_model.Rd
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@@ -50,7 +50,7 @@ M = linear_model(formula = y~Species)
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 }
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 \references{
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-R Core Team (2023). \emph{R: A Language and Environment for Statistical
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+R Core Team (2024). \emph{R: A Language and Environment for Statistical
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 Computing}. R Foundation for Statistical Computing, Vienna, Austria.
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 \url{https://www.R-project.org/}.
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 }
man/mixed_effect.Rd
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@@ -58,8 +58,8 @@ Pinheiro JC, Bates DM (2000). \emph{Mixed-Effects Models in S and S-PLUS}.
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 Springer, New York. doi:10.1007/b98882
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 \url{https://doi.org/10.1007/b98882}.
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-Lenth R (2023). \emph{emmeans: Estimated Marginal Means, aka Least-Squares
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-Means}. R package version 1.9.0,
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+Lenth R (2024). \emph{emmeans: Estimated Marginal Means, aka Least-Squares
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+Means}. R package version 1.10.1,
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 \url{https://CRAN.R-project.org/package=emmeans}.
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 Fox J, Weisberg S (2019). \emph{An R Companion to Applied Regression}, Third
man/mv_feature_filter.Rd
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@@ -54,8 +54,7 @@ M = mv_feature_filter(factor_name='Species',qc_label='versicolor')
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 M = model_apply(M,D)
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 }
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 \references{
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-Jankevics A, Lloyd GR, Weber RJM (2023). \emph{pmp: Peak Matrix Processing
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-and signal batch correction for metabolomics datasets}.
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-doi:10.18129/B9.bioc.pmp \url{https://doi.org/10.18129/B9.bioc.pmp}, R
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-package version 1.14.0, \url{https://bioconductor.org/packages/pmp}.
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+Jankevics A, Lloyd GR, Weber RJM (????). \emph{pmp: Peak Matrix Processing
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+and signal batch correction for metabolomics datasets}. R package
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+version 1.15.1.
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 }
man/mv_sample_filter.Rd
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@@ -38,8 +38,7 @@ M = mv_sample_filter(
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 C = mv_sample_filter()
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 }
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 \references{
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-Jankevics A, Lloyd GR, Weber RJM (2023). \emph{pmp: Peak Matrix Processing
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-and signal batch correction for metabolomics datasets}.
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-doi:10.18129/B9.bioc.pmp \url{https://doi.org/10.18129/B9.bioc.pmp}, R
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-package version 1.14.0, \url{https://bioconductor.org/packages/pmp}.
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+Jankevics A, Lloyd GR, Weber RJM (????). \emph{pmp: Peak Matrix Processing
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+and signal batch correction for metabolomics datasets}. R package
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+version 1.15.1.
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 }
man/plsda_feature_importance_plot.Rd
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@@ -56,7 +56,7 @@ Wickham H (2007). "Reshaping Data with the reshape Package." \emph{Journal
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 of Statistical Software}, \emph{21}(12), 1-20.
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 \url{http://www.jstatsoft.org/v21/i12/}.
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-Wilke C (2023). \emph{cowplot: Streamlined Plot Theme and Plot Annotations
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-for 'ggplot2'}. R package version 1.1.2,
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+Wilke C (2024). \emph{cowplot: Streamlined Plot Theme and Plot Annotations
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+for 'ggplot2'}. R package version 1.1.3,
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 \url{https://CRAN.R-project.org/package=cowplot}.
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 }
man/pqn_norm.Rd
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@@ -63,8 +63,7 @@ M = model_apply(M,D)
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 }
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 \references{
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-Jankevics A, Lloyd GR, Weber RJM (2023). \emph{pmp: Peak Matrix Processing
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-and signal batch correction for metabolomics datasets}.
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-doi:10.18129/B9.bioc.pmp \url{https://doi.org/10.18129/B9.bioc.pmp}, R
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-package version 1.14.0, \url{https://bioconductor.org/packages/pmp}.
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+Jankevics A, Lloyd GR, Weber RJM (????). \emph{pmp: Peak Matrix Processing
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+and signal batch correction for metabolomics datasets}. R package
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+version 1.15.1.
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 }
man/rsd_filter.Rd
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@@ -45,8 +45,7 @@ M = rsd_filter(factor_name='Class')
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 }
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 \references{
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-Jankevics A, Lloyd GR, Weber RJM (2023). \emph{pmp: Peak Matrix Processing
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-and signal batch correction for metabolomics datasets}.
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-doi:10.18129/B9.bioc.pmp \url{https://doi.org/10.18129/B9.bioc.pmp}, R
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-package version 1.14.0, \url{https://bioconductor.org/packages/pmp}.
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+Jankevics A, Lloyd GR, Weber RJM (????). \emph{pmp: Peak Matrix Processing
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+and signal batch correction for metabolomics datasets}. R package
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+version 1.15.1.
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 }
man/sb_corr.Rd
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@@ -71,10 +71,9 @@ M = sb_corr(
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 M = sb_corr(order_col='run_order',batch_col='batch_no',qc_col='class')
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 }
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 \references{
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-Jankevics A, Lloyd GR, Weber RJM (2023). \emph{pmp: Peak Matrix Processing
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-and signal batch correction for metabolomics datasets}.
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-doi:10.18129/B9.bioc.pmp \url{https://doi.org/10.18129/B9.bioc.pmp}, R
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-package version 1.14.0, \url{https://bioconductor.org/packages/pmp}.
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+Jankevics A, Lloyd GR, Weber RJM (????). \emph{pmp: Peak Matrix Processing
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+and signal batch correction for metabolomics datasets}. R package
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+version 1.15.1.
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 Kirwan JA, Broadhurst DI, Davidson RL, Viant MR (2013). "Characterising
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 and correcting batch variation in an automated direct infusion mass
man/structToolbox-package.Rd
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new file mode 100644
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@@ -0,0 +1,28 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/structToolbox.R
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+\docType{package}
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+\name{structToolbox-package}
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+\alias{structToolbox}
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+\alias{structToolbox-package}
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+\title{structToolbox: Examples of tools built using the Statistics in R Using Class Templates (struct) package}
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+\description{
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+This package extends the classes defined in the struct package
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+}
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+\seealso{
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+Useful links:
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+\itemize{
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+  \item \url{https://github.com/computational-metabolomics/structToolbox}
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+  \item \url{https://computational-metabolomics.github.io/structToolbox/}
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+}
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+
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+}
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+\author{
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+\strong{Maintainer}: Gavin Rhys Lloyd \email{[email protected]} (\href{https://orcid.org/0000-0001-7989-6695}{ORCID})
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+
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+Authors:
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+\itemize{
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+  \item Ralf Johannes Maria Weber \email{[email protected]}
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+}
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+
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+}
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+\keyword{internal}
man/structToolbox.Rd
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deleted file mode 100644
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@@ -1,9 +0,0 @@
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-% Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/structToolbox.R
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-\docType{package}
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-\name{structToolbox}
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-\alias{structToolbox}
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-\title{structToolbox: Examples of tools built using the Statistics in R Using Class Templates (struct) package}
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-\description{
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-This package extends the classes defined in the struct package
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-}