From d709380164dde6e2e68707686d90c7a52c14a7ac Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Wed, 13 Dec 2023 16:37:14 -0700 Subject: [PATCH 1/7] update development to "active" and remove warning --- README.Rmd | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/README.Rmd b/README.Rmd index 0e96e08..9f60f34 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,7 +17,7 @@ knitr::opts_chunk$set( -[![R-CMD-check](https://github.com/Meredith-Lab/volcalc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Meredith-Lab/volcalc/actions/workflows/R-CMD-check.yaml) [![latest-DOI](https://zenodo.org/badge/425022983.svg)](https://zenodo.org/badge/latestdoi/425022983) [![manuscript-DOI](https://img.shields.io/badge/DOI-10.3389/fmicb.2023.1267234-32a859.svg)](https://doi.org/10.3389/fmicb.2023.1267234) [![Project Status: WIP -- Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip) [![Codecov test coverage](https://codecov.io/gh/Meredith-Lab/volcalc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Meredith-Lab/volcalc?branch=master) [![volcalc status badge](https://cct-datascience.r-universe.dev/badges/volcalc)](https://cct-datascience.r-universe.dev/volcalc) +[![R-CMD-check](https://github.com/Meredith-Lab/volcalc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Meredith-Lab/volcalc/actions/workflows/R-CMD-check.yaml) [![latest-DOI](https://zenodo.org/badge/425022983.svg)](https://zenodo.org/badge/latestdoi/425022983) [![manuscript-DOI](https://img.shields.io/badge/DOI-10.3389/fmicb.2023.1267234-32a859.svg)](https://doi.org/10.3389/fmicb.2023.1267234) [![Project Status: Active -- The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Codecov test coverage](https://codecov.io/gh/Meredith-Lab/volcalc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Meredith-Lab/volcalc?branch=master) [![volcalc status badge](https://cct-datascience.r-universe.dev/badges/volcalc)](https://cct-datascience.r-universe.dev/volcalc) @@ -25,14 +25,7 @@ knitr::opts_chunk$set( 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/). From 52340e5a5572bffd78bd4845d31192e8a7d68b54 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Wed, 13 Dec 2023 16:39:29 -0700 Subject: [PATCH 2/7] update description --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b9812da..eba79ce 100644 --- 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 From 704eb21400aeafdc3c9de7781d858e3209186d29 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Wed, 13 Dec 2023 16:49:26 -0700 Subject: [PATCH 3/7] add vignettes to news --- NEWS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/NEWS.md b/NEWS.md index 0dc9862..2b898e1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -12,6 +12,7 @@ * New example .mol files were added. See `?mol_example()`. * `mol_example()` no longer takes any arguments and just returns file paths to all example .mol files. * 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 # volcalc 2.0.0 From dcbed1f3ed4203f69fd2239361a2e514dc2f4df2 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Thu, 14 Dec 2023 14:37:48 -0700 Subject: [PATCH 4/7] use @returns instead of @return --- R/calc_vol.R | 2 +- R/get_fx_groups.R | 2 +- R/get_mol_kegg.R | 2 +- R/mol_example.R | 2 +- R/simpol1.R | 2 +- R/utils.R | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/R/calc_vol.R b/R/calc_vol.R index 87d1e44..e494d37 100644 --- a/R/calc_vol.R +++ b/R/calc_vol.R @@ -34,7 +34,7 @@ #' volatility. Frontiers in Microbiology. #' . #' -#' @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 index eeb4e75..fa6c84d 100644 --- 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 index 6784a7f..8aad590 100644 --- 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 index c15531b..8d8d0b1 100644 --- 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 index ec3c7ec..00fb7e7 100644 --- a/R/simpol1.R +++ b/R/simpol1.R @@ -30,7 +30,7 @@ #' @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, diff --git a/R/utils.R b/R/utils.R index 2eed14e..a944e1b 100644 --- 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) { From 757995c616d08721a042b1dfdc8970315a0d2add Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Thu, 14 Dec 2023 14:37:56 -0700 Subject: [PATCH 5/7] document() --- man/volcalc-package.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/volcalc-package.Rd b/man/volcalc-package.Rd index 2eae577..5367094 100644 --- a/man/volcalc-package.Rd +++ b/man/volcalc-package.Rd @@ -8,7 +8,7 @@ \description{ \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} -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). +Use this package to calculate estimated relative volatility index values for organic compounds based on functional group contributions. Calculation uses the SIMPOL.1 method (Prankow and Asher, 2008) or modified SIMPOL.1 method as in Meredith et al. (2023). } \seealso{ Useful links: From 5c845c036b2835e1082d1a66a39a46a988895b15 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Thu, 14 Dec 2023 14:46:39 -0700 Subject: [PATCH 6/7] fix URLs --- R/calc_vol.R | 5 ++--- README.Rmd | 4 ++-- README.md | 36 ++++++++++++++---------------------- man/calc_vol.Rd | 5 ++--- vignettes/volcalc.Rmd | 4 ++-- 5 files changed, 22 insertions(+), 32 deletions(-) diff --git a/R/calc_vol.R b/R/calc_vol.R index e494d37..610138a 100644 --- a/R/calc_vol.R +++ b/R/calc_vol.R @@ -27,12 +27,11 @@ #' #' @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. +#' 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. -#' . +#' volatility. Frontiers in Microbiology. DOI: 10.3389/fmicb.2023.1267234 #' #' @returns A tibble with relative volatility index (`rvi`) and volatility #' category (`category`). diff --git a/README.Rmd b/README.Rmd index 9f60f34..b57eccf 100644 --- a/README.Rmd +++ b/README.Rmd @@ -51,7 +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: @@ -69,7 +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 index d904f5c..06f8351 100644 --- 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 index 39fc048..ddcb9e9 100644 --- a/man/calc_vol.Rd +++ b/man/calc_vol.Rd @@ -64,12 +64,11 @@ calc_vol(mol_paths, return_calc_steps = TRUE) \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. \url{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. -\url{https://doi.org/10.3389/fmicb.2023.1267234}. +volatility. Frontiers in Microbiology. DOI: 10.3389/fmicb.2023.1267234 } \seealso{ \code{\link[=get_fx_groups]{get_fx_groups()}}, \code{\link[=simpol1]{simpol1()}} diff --git a/vignettes/volcalc.Rmd b/vignettes/volcalc.Rmd index 33fbf03..6b9e700 100644 --- 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. +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. . +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 From f1e4251023e43ea1ab280291425255cba74cde72 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Fri, 15 Dec 2023 09:31:00 -0700 Subject: [PATCH 7/7] TIL you can use \doi{} in roxygen2 --- R/calc_vol.R | 4 ++-- R/simpol1.R | 5 ++--- man/calc_vol.Rd | 4 ++-- man/simpol1.Rd | 5 ++--- 4 files changed, 8 insertions(+), 10 deletions(-) diff --git a/R/calc_vol.R b/R/calc_vol.R index 610138a..e6e941d 100644 --- a/R/calc_vol.R +++ b/R/calc_vol.R @@ -27,11 +27,11 @@ #' #' @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. DOI: 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. DOI: 10.3389/fmicb.2023.1267234 +#' volatility. Frontiers in Microbiology. \doi{10.3389/fmicb.2023.1267234} #' #' @returns A tibble with relative volatility index (`rvi`) and volatility #' category (`category`). diff --git a/R/simpol1.R b/R/simpol1.R index 00fb7e7..dbd824f 100644 --- a/R/simpol1.R +++ b/R/simpol1.R @@ -35,13 +35,12 @@ #' @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. -#' . +#' 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. -#' +#' \doi{10.5194/acp-8-2773-2008} #' #' @seealso [calc_vol()] #' @export diff --git a/man/calc_vol.Rd b/man/calc_vol.Rd index ddcb9e9..06b425f 100644 --- a/man/calc_vol.Rd +++ b/man/calc_vol.Rd @@ -64,11 +64,11 @@ calc_vol(mol_paths, return_calc_steps = TRUE) \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. DOI: 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. DOI: 10.3389/fmicb.2023.1267234 +volatility. Frontiers in Microbiology. \doi{10.3389/fmicb.2023.1267234} } \seealso{ \code{\link[=get_fx_groups]{get_fx_groups()}}, \code{\link[=simpol1]{simpol1()}} diff --git a/man/simpol1.Rd b/man/simpol1.Rd index 2282720..1e0f461 100644 --- a/man/simpol1.Rd +++ b/man/simpol1.Rd @@ -54,13 +54,12 @@ simpol1(fx_groups) \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. -\url{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. -\url{https://doi.org/10.5194/acp-8-2773-2008} +\doi{10.5194/acp-8-2773-2008} } \seealso{ \code{\link[=calc_vol]{calc_vol()}}