From de89c763c281cdc88e2a65ba4986c8a0ec3e5461 Mon Sep 17 00:00:00 2001 From: Amandine Gillet Date: Mon, 29 Jul 2024 19:01:57 +0200 Subject: [PATCH] Documentation update --- DESCRIPTION | 102 +++++++++++++++++------------------ man/MorphoRegions-package.Rd | 4 +- man/alligator.Rd | 2 +- man/dolphin.Rd | 4 +- man/musm.Rd | 2 +- man/porpoise.Rd | 2 +- 6 files changed, 59 insertions(+), 57 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7e7ff19..cdce65b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,51 +1,51 @@ -Package: MorphoRegions -Type: Package -Title: Analysis of Regionalization Patterns in Serially Homologous Structures -Version: 0.1.0 -Authors@R: c( - person("Amandine", "Gillet", role = c("cre", "aut"), - email = "gillet.aman@gmail.com", - comment = c(ORCID = "0000-0001-9763-6061")), - person("Katrina", "Jones", role = c("aut"), - email = "katrina.jones@manchester.ac.uk", - comment = c(ORCID="0000-0003-1088-0497")), - person("Noah", "Greifer", role = c("aut"), - email = "ngreifer@iq.harvard.edu", - comment = c(ORCID="0000-0003-3067-7154")), - person("Stephanie", "Pierce", role = c("aut"), - email = "spierce@oeb.harvard.edu", - comment = c(ORCID = "0000-0003-0717-1841")) - ) -Description: Computes the optimal number of regions (or subdivisions) and - their position in serial structures without a priori assumptions and to visualize - the results. After reducing data dimensionality with the built-in function for - data ordination, regions are fitted as segmented linear regressions - along the serial structure. Every region boundary - position and increasing number of regions are iteratively fitted and - the best model (number of regions and boundary positions) is selected - with an information criterion. This package expands on the previous - 'regions' package (Jones et al., Science 2018) with improved - computation and more fitting and plotting options. -License: GPL (>= 2) -Encoding: UTF-8 -Depends: - R (>= 4.0.0) -Imports: - stats, parallel, utils, grDevices, - RColorBrewer (>= 1.1-3), - cluster (>= 2.1.4), - scales (>= 1.3.0), - ggplot2 (>= 3.5.1), - chk (>= 0.9.0), - pbapply (>= 1.7-2) -Suggests: - viridisLite, - patchwork (>= 1.1.0), - knitr, - rmarkdown -VignetteBuilder: knitr -LazyData: true -Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 -URL: https://aagillet.github.io/MorphoRegions/, https://github.com/aagillet/MorphoRegions -BugReports: https://github.com/aagillet/MorphoRegions/issues +Package: MorphoRegions +Type: Package +Title: Analysis of Regionalization Patterns in Serially Homologous Structures +Version: 0.1.0 +Authors@R: c( + person("Amandine", "Gillet", role = c("cre", "aut"), + email = "gillet.aman@gmail.com", + comment = c(ORCID = "0000-0001-9763-6061")), + person("Katrina", "Jones", role = c("aut"), + email = "katrina.jones@manchester.ac.uk", + comment = c(ORCID="0000-0003-1088-0497")), + person("Noah", "Greifer", role = c("aut"), + email = "ngreifer@iq.harvard.edu", + comment = c(ORCID="0000-0003-3067-7154")), + person("Stephanie", "Pierce", role = c("aut"), + email = "spierce@oeb.harvard.edu", + comment = c(ORCID = "0000-0003-0717-1841")) + ) +Description: Computes the optimal number of regions (or subdivisions) and + their position in serial structures without a priori assumptions and to visualize + the results. After reducing data dimensionality with the built-in function for + data ordination, regions are fitted as segmented linear regressions + along the serial structure. Every region boundary + position and increasing number of regions are iteratively fitted and + the best model (number of regions and boundary positions) is selected + with an information criterion. This package expands on the previous + 'regions' package (Jones et al., Science 2018) with improved + computation and more fitting and plotting options. +License: GPL (>= 2) +Encoding: UTF-8 +Depends: + R (>= 4.0.0) +Imports: + stats, parallel, utils, grDevices, + RColorBrewer (>= 1.1-3), + cluster (>= 2.1.4), + scales (>= 1.3.0), + ggplot2 (>= 3.5.1), + chk (>= 0.9.0), + pbapply (>= 1.7-2) +Suggests: + viridisLite, + patchwork (>= 1.1.0), + knitr, + rmarkdown +VignetteBuilder: knitr +LazyData: true +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.3.2 +URL: https://aagillet.github.io/MorphoRegions/, https://github.com/aagillet/MorphoRegions +BugReports: https://github.com/aagillet/MorphoRegions/issues diff --git a/man/MorphoRegions-package.Rd b/man/MorphoRegions-package.Rd index d5acbbd..1b14977 100644 --- a/man/MorphoRegions-package.Rd +++ b/man/MorphoRegions-package.Rd @@ -4,7 +4,7 @@ \name{MorphoRegions-package} \alias{MorphoRegions} \alias{MorphoRegions-package} -\title{MorphoRegions: Analysis of Regionalization Patterns in Serially-Homologous Structures} +\title{MorphoRegions: Analysis of Regionalization Patterns in Serially Homologous Structures} \description{ Computes the optimal number of regions (or subdivisions) and their position in serial structures without a priori assumptions and to visualize the results. After reducing data dimensionality with the built-in function for data ordination, regions are fitted as segmented linear regressions along the serial structure. Every region boundary position and increasing number of regions are iteratively fitted and the best model (number of regions and boundary positions) is selected with an information criterion. This package expands on the previous 'regions' package (Jones et al., Science 2018) with improved computation and more fitting and plotting options. } @@ -12,6 +12,8 @@ Computes the optimal number of regions (or subdivisions) and their position in s Useful links: \itemize{ \item \url{https://aagillet.github.io/MorphoRegions/} + \item \url{https://github.com/aagillet/MorphoRegions} + \item Report bugs at \url{https://github.com/aagillet/MorphoRegions/issues} } } diff --git a/man/alligator.Rd b/man/alligator.Rd index f7a23d3..5a32620 100644 --- a/man/alligator.Rd +++ b/man/alligator.Rd @@ -3,7 +3,7 @@ \docType{data} \name{alligator} \alias{alligator} -\title{Measurements from the vertebral column of Alligator} +\title{Measurements from the vertebral column of an alligator} \format{ A matrix with 22 vertebrae and 19 measurements. Column 1, vertebra, is the positional information. diff --git a/man/dolphin.Rd b/man/dolphin.Rd index 3643d13..657429b 100644 --- a/man/dolphin.Rd +++ b/man/dolphin.Rd @@ -3,7 +3,7 @@ \docType{data} \name{dolphin} \alias{dolphin} -\title{Measurements from the vertebral column of Dolphin} +\title{Measurements from the vertebral column of a dolphin} \format{ A matrix with 40 vertebrae and 16 measurements. Column 1, vertebra, is the positional information. @@ -12,6 +12,6 @@ information. dolphin } \description{ -Linear and angular measurements from FIXME +Linear and angular measurements from Platanista gangetica SMNS 45653 } \keyword{datasets} diff --git a/man/musm.Rd b/man/musm.Rd index bb5e3b5..41edcb0 100644 --- a/man/musm.Rd +++ b/man/musm.Rd @@ -3,7 +3,7 @@ \docType{data} \name{musm} \alias{musm} -\title{Measurements from the vertebral column of Mus} +\title{Measurements from the vertebral column of a mouse} \format{ A matrix with 23 vertebrae and 19 measurements. Column 1, vertebra, is the positional information. diff --git a/man/porpoise.Rd b/man/porpoise.Rd index 548ce6a..71de3dc 100644 --- a/man/porpoise.Rd +++ b/man/porpoise.Rd @@ -14,7 +14,7 @@ Each is a data frame with 58, 56, and 59 vertebrae (respectively) and 16 measure data("porpoise") } \description{ -Linear and angular measurements from NRM 815072 (\code{porpoise1}), NRM 835011 (\code{porpoise2}), and NRM 855083 (\code{porpoise3}). +Linear and angular measurements from Phocoena phocoena NRM 815072 (\code{porpoise1}), NRM 835011 (\code{porpoise2}), and NRM 855083 (\code{porpoise3}). } \references{ Gillet, A., Frederich, B., Pierce, S. E., & Parmentier, E. (2022). Iterative habitat transitions are associated with morphological convergence of the backbone in delphinoids. Journal of Mammalian Evolution, 29(4), 931-946.