Merge pull request #94 from Meredith-Lab/release

release prep
Meredith-Lab · Dec 15, 2023 · 7483799 · 7483799
2 parents 46005bb + f1e4251
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,8 +9,8 @@ Authors@R: c(
   )
 Description: Use this package to calculate estimated relative volatility
     index values for organic compounds based on functional group
-    contributions.  Calculation uses the SIMPOL method (Prankow and Asher,
-    2008).
+    contributions.  Calculation uses the SIMPOL.1 method (Prankow and Asher,
+    2008) or modified SIMPOL.1 method as in Meredith et al. (2023).
 License: MIT + file LICENSE
 URL: https://meredith-lab.github.io/volcalc/
 BugReports: https://github.com/Meredith-Lab/volcalc/issues

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,7 @@
 # volcalc (development version)
 
 * The manuscript associated with `volcalc` is now published in Frontiers in Microbiology 🎉. DOI: 10.3389/fmicb.2023.1267234
+* There are now two vignettes available which can be viewed with `browseVignettes("volcalc")` or on the package website
 
 ## Miscelanous changes
 

diff --git a/R/calc_vol.R b/R/calc_vol.R
@@ -27,14 +27,13 @@
 #'
 #' @references Donahue, N.M., Robinson, A.L., Stanier, C.O., Pandis, S.N., 2006.
 #' Coupled Partitioning, Dilution, and Chemical Aging of Semivolatile Organics.
-#' Environ. Sci. Technol. 40, 2635–2643. <https://doi.org/10.1021/es052297c>
+#' Environ. Sci. Technol. 40, 2635–2643. \doi{10.1021/es052297c}
 #'
 #' Meredith L, Ledford S, Riemer K, Geffre P, Graves K, Honeker L, LeBauer D,
 #' Tfaily M, Krechmer J. 2023. Automating methods for estimating metabolite
-#' volatility. Frontiers in Microbiology.
-#' <https://doi.org/10.3389/fmicb.2023.1267234>.
+#' volatility. Frontiers in Microbiology. \doi{10.3389/fmicb.2023.1267234}
 #'
-#' @return A tibble with relative volatility index (`rvi`) and volatility
+#' @returns A tibble with relative volatility index (`rvi`) and volatility
 #'   category (`category`).
 #'
 #' @seealso [get_fx_groups()], [simpol1()]

diff --git a/R/get_fx_groups.R b/R/get_fx_groups.R
@@ -12,7 +12,7 @@
 #' @param compound_sdf a [ChemmineR::SDFset] object returned by
 #'   [ChemmineR::read.SDFset()] or [ChemmineR::smiles2sdf()], for example.
 #'
-#' @return A tibble with columns of basic compound info and functional group
+#' @returns A tibble with columns of basic compound info and functional group
 #'   counts.
 #' @seealso [calc_vol()]
 #' @examples

diff --git a/R/get_mol_kegg.R b/R/get_mol_kegg.R
@@ -13,7 +13,7 @@ utils::globalVariables(".data")
 #' @param force Logical; by default (`FALSE`), .mol files will not be downloaded
 #'   if they are found in `dir`. Set this to `TRUE` to download and overwrite
 #'   existing files.
-#'
+#'   
 #' @returns A tibble with the columns `compound_ids`, `pathway_ids` (if used),
 #'   and `mol_paths` (paths to downloaded .mol files).
 #' @export

diff --git a/R/mol_example.R b/R/mol_example.R
@@ -9,7 +9,7 @@
 #' - C16181: beta-2,3,4,5,6-Pentachlorocyclohexanol
 #' - C16286: Geosmin
 #' - C16521: Isoprene
-#' @return File paths to installed example .mol files.
+#' @returns File paths to installed example .mol files.
 #' @export
 #'
 #' @examples

diff --git a/R/simpol1.R b/R/simpol1.R
@@ -30,18 +30,17 @@
 #' @param meredith Logical; `FALSE`: use the original SIMPOL.1 method. `TRUE`:
 #'   use the modified version in Meredith et al. (2023).
 #'
-#' @return The `fx_groups` tibble with the additional `log10_P` column.
+#' @returns The `fx_groups` tibble with the additional `log10_P` column.
 #'
 #' @references 
 #'   Meredith L, Ledford S, Riemer K, Geffre P, Graves K, Honeker L, LeBauer D,
 #'   Tfaily M, Krechmer J. 2023. Automating methods for estimating metabolite
-#'   volatility. Frontiers in Microbiology.
-#'   <https://doi.org/10.3389/fmicb.2023.1267234>.
+#'   volatility. Frontiers in Microbiology. \doi{10.3389/fmicb.2023.1267234}
 #'   
 #'   Pankow, J.F., Asher, W.E. 2008. SIMPOL.1: a simple group
 #'   contribution method for predicting vapor pressures and enthalpies of
 #'   vaporization of multifunctional organic compounds. Atmos. Chem. Phys.
-#'   <https://doi.org/10.5194/acp-8-2773-2008>
+#'   \doi{10.5194/acp-8-2773-2008}
 #'   
 #' @seealso [calc_vol()]
 #' @export

diff --git a/R/utils.R b/R/utils.R
@@ -15,7 +15,7 @@ zzz <- function() {
 #'
 #' @param atomcount output of ChemmineR::atomcount()
 #'
-#' @return a tibble
+#' @returns a tibble
 #' @noRd
 #' 
 atomcount2tibble <- function(atomcount) {

diff --git a/README.Rmd b/README.Rmd
@@ -17,22 +17,15 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/Meredith-Lab/volcalc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Meredith-Lab/volcalc/actions/workflows/R-CMD-check.yaml) [![latest-DOI](https://zenodo.org/badge/425022983.svg)](https://zenodo.org/badge/latestdoi/425022983) [![manuscript-DOI](https://img.shields.io/badge/DOI-10.3389/fmicb.2023.1267234-32a859.svg)](https://doi.org/10.3389/fmicb.2023.1267234) [![Project Status: WIP -- Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip) [![Codecov test coverage](https://codecov.io/gh/Meredith-Lab/volcalc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Meredith-Lab/volcalc?branch=master) [![volcalc status badge](https://cct-datascience.r-universe.dev/badges/volcalc)](https://cct-datascience.r-universe.dev/volcalc)
+[![R-CMD-check](https://github.com/Meredith-Lab/volcalc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Meredith-Lab/volcalc/actions/workflows/R-CMD-check.yaml) [![latest-DOI](https://zenodo.org/badge/425022983.svg)](https://zenodo.org/badge/latestdoi/425022983) [![manuscript-DOI](https://img.shields.io/badge/DOI-10.3389/fmicb.2023.1267234-32a859.svg)](https://doi.org/10.3389/fmicb.2023.1267234) [![Project Status: Active -- The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Codecov test coverage](https://codecov.io/gh/Meredith-Lab/volcalc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Meredith-Lab/volcalc?branch=master) [![volcalc status badge](https://cct-datascience.r-universe.dev/badges/volcalc)](https://cct-datascience.r-universe.dev/volcalc)
 
 <!-- badges: end -->
 
 ## Overview
 
 The `volcalc` package allows you to automate calculating estimates of volatility for chemical compounds.
 
-```{=html}
-
-> [!WARNING]
-> `volcalc` is a work in progress---use at your own risk!
-```
-For a bit of a road map of where development is headed, see our [proposal](https://cct-datascience.github.io/volcalc-isc-proposal/) for the R Consortium grant.
-
-`volcalc` is designed to support "group contribution" methods for estimating volatility that rely on molecular properties such as molecular weight, numbers of certain atoms, and counts of certain functional groups.
+`volcalc` supports "group contribution" methods for estimating volatility that rely on molecular properties such as molecular weight, numbers of certain atoms, and counts of certain functional groups.
 Currently, the only methods implemented are SIMPOL.1 (Pankow & Asher 2008) and a modified version used in Meredith et al. (2023).
 
 `volcalc` works with either .mol files or [SMILES](https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system) strings as input, and supports downloading .mol files directly from [KEGG](https://www.kegg.jp/).
@@ -58,7 +51,7 @@ You can install the 'legacy' version used in Meredith et al. (2023) with
 pak::pkg_install("Meredith-Lab/volcalc@v1.0.2")
 ```
 
-Installation of `volcalc` requires the system libraries [OpenBabel](https://openbabel.org/wiki/Main_Page) and Eigen3 (requirements of the `ChemmineOB` package, which `volcalc` depends on).
+Installation of `volcalc` requires the system libraries [OpenBabel](https://open-babel.readthedocs.io/) and Eigen3 (requirements of the `ChemmineOB` package, which `volcalc` depends on).
 `pak` will take care of the installation of these libraries for you on some systems, but you may need to install them manually on some operating systems.
 
 For macOS, they can be installed via homebrew by running the following shell command:
@@ -76,7 +69,7 @@ sudo apt-get install libeigen3-dev
 
 For windows, `OpenBabel` is included in the `ChemmineOB` binary and does not need to be installed separately.
 
-For other installation options see the [OpenBabel documentation](https://openbabel.org/docs/dev/Installation/install.html) and `ChemmineOB` [install guide](https://github.com/girke-lab/ChemmineOB/blob/master/INSTALL)
+For other installation options see the [OpenBabel documentation](https://open-babel.readthedocs.io/en/latest/Installation/install.html) and `ChemmineOB` [install guide](https://github.com/girke-lab/ChemmineOB/blob/master/INSTALL)
 
 ## Basic Usage
 

diff --git a/README.md b/README.md
@@ -8,9 +8,9 @@
 [![R-CMD-check](https://github.com/Meredith-Lab/volcalc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Meredith-Lab/volcalc/actions/workflows/R-CMD-check.yaml)
 [![latest-DOI](https://zenodo.org/badge/425022983.svg)](https://zenodo.org/badge/latestdoi/425022983)
 [![manuscript-DOI](https://img.shields.io/badge/DOI-10.3389/fmicb.2023.1267234-32a859.svg)](https://doi.org/10.3389/fmicb.2023.1267234)
-[![Project Status: WIP – Initial development is in progress, but there
-has not yet been a stable, usable release suitable for the
-public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+[![Project Status: Active – The project has reached a stable, usable
+state and is being actively
+developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Codecov test
 coverage](https://codecov.io/gh/Meredith-Lab/volcalc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Meredith-Lab/volcalc?branch=master)
 [![volcalc status
@@ -23,19 +23,11 @@ badge](https://cct-datascience.r-universe.dev/badges/volcalc)](https://cct-datas
 The `volcalc` package allows you to automate calculating estimates of
 volatility for chemical compounds.
 
-> [!WARNING]
-> `volcalc` is a work in progress---use at your own risk!
-
-For a bit of a road map of where development is headed, see our
-[proposal](https://cct-datascience.github.io/volcalc-isc-proposal/) for
-the R Consortium grant.
-
-`volcalc` is designed to support “group contribution” methods for
-estimating volatility that rely on molecular properties such as
-molecular weight, numbers of certain atoms, and counts of certain
-functional groups. Currently, the only methods implemented are SIMPOL.1
-(Pankow & Asher 2008) and a modified version used in Meredith et
-al. (2023).
+`volcalc` supports “group contribution” methods for estimating
+volatility that rely on molecular properties such as molecular weight,
+numbers of certain atoms, and counts of certain functional groups.
+Currently, the only methods implemented are SIMPOL.1 (Pankow & Asher
+2008) and a modified version used in Meredith et al. (2023).
 
 `volcalc` works with either .mol files or
 [SMILES](https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system)
@@ -64,11 +56,11 @@ pak::pkg_install("Meredith-Lab/volcalc@v1.0.2")
 ```
 
 Installation of `volcalc` requires the system libraries
-[OpenBabel](https://openbabel.org/wiki/Main_Page) and Eigen3
-(requirements of the `ChemmineOB` package, which `volcalc` depends on).
-`pak` will take care of the installation of these libraries for you on
-some systems, but you may need to install them manually on some
-operating systems.
+[OpenBabel](https://open-babel.readthedocs.io/) and Eigen3 (requirements
+of the `ChemmineOB` package, which `volcalc` depends on). `pak` will
+take care of the installation of these libraries for you on some
+systems, but you may need to install them manually on some operating
+systems.
 
 For macOS, they can be installed via homebrew by running the following
 shell command:
@@ -88,7 +80,7 @@ For windows, `OpenBabel` is included in the `ChemmineOB` binary and does
 not need to be installed separately.
 
 For other installation options see the [OpenBabel
-documentation](https://openbabel.org/docs/dev/Installation/install.html)
+documentation](https://open-babel.readthedocs.io/en/latest/Installation/install.html)
 and `ChemmineOB` [install
 guide](https://github.com/girke-lab/ChemmineOB/blob/master/INSTALL)
 

diff --git a/man/calc_vol.Rd b/man/calc_vol.Rd
diff --git a/man/simpol1.Rd b/man/simpol1.Rd
diff --git a/man/volcalc-package.Rd b/man/volcalc-package.Rd
diff --git a/vignettes/volcalc.Rmd b/vignettes/volcalc.Rmd
@@ -71,6 +71,6 @@ calc_vol("CC/C=C\\C[C@@H]1[C@H](CCC1=O)CC(=O)O", from = "smiles")
 
 ### References
 
-Donahue, N.M., Robinson, A.L., Stanier, C.O., Pandis, S.N., 2006. Coupled Partitioning, Dilution, and Chemical Aging of Semivolatile Organics. Environ. Sci. Technol. 40, 2635–2643. <https://doi.org/10.1021/es052297c>
+Donahue, N.M., Robinson, A.L., Stanier, C.O., Pandis, S.N., 2006. Coupled Partitioning, Dilution, and Chemical Aging of Semivolatile Organics. Environ. Sci. Technol. 40, 2635–2643. DOI: 10.1021/es052297c
 
-Meredith L, Ledford S, Riemer K, Geffre P, Graves K, Honeker L, LeBauer D, Tfaily M, Krechmer J, 2023. Automating methods for estimating metabolite volatility. Frontiers in Microbiology. <https://doi.org/10.3389/fmicb.2023.1267234>.
+Meredith L, Ledford S, Riemer K, Geffre P, Graves K, Honeker L, LeBauer D, Tfaily M, Krechmer J, 2023. Automating methods for estimating metabolite volatility. Frontiers in Microbiology. DOI: 10.3389/fmicb.2023.1267234