Style improvements

.gitignore

@@ -3,4 +3,4 @@
 .RData
 .DS_Store
 
-docs/
+/docs/

DESCRIPTION

@@ -32,4 +32,4 @@ Suggests:
     foreach,
     doParallel,
     org.Hs.eg.db
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

NEWS.md

@@ -1,11 +1,11 @@
-# protr 1.7-0 (2023-10-30)
+# protr 1.7-0
 
 ## New features
 
 - `crossSetSim()` is added for calculating pairwise similarity between two sets
   of protein sequence based on sequence alignment (thanks, @seb-mueller, #34).
 
-# protr 1.6-3 (2023-03-05)
+# protr 1.6-3
 
 ## Bug fixes
 
@@ -21,15 +21,15 @@
 - Fixed broken or moved links in function documentation and vignettes.
 - Replaced the original logo with a new hex sticker logo.
 
-# protr 1.6-2 (2019-05-18)
+# protr 1.6-2
 
 ## Improvements
 
 - Switched to the tidyverse code style.
 - Updated GitHub repository links to reflect the handle change.
 - Removed AppVeyor CI due to the frequent Bioconductor dependency installation issues.
 
-# protr 1.6-1 (2019-02-24)
+# protr 1.6-1
 
 ## Improvements
 
@@ -53,7 +53,7 @@
 - Fixed an issue in `parGOSim()` that will create minor numerical
   inconsistencies in results due to argument matching.
 
-# protr 1.6-0 (2019-02-11)
+# protr 1.6-0
 
 ## Bug fixes
 
@@ -62,7 +62,7 @@
   Issues in the code examples are also fixed.
   We thank Denisa Duma for the feedback.
 
-# protr 1.5-2 (2018-11-21)
+# protr 1.5-2
 
 ## Bug fixes
 
@@ -76,7 +76,7 @@
 - Added floating TOC and new CSS style in the vignette to improve navigation
   and readability.
 
-# protr 1.5-1 (2018-07-12)
+# protr 1.5-1
 
 ## New features
 
@@ -85,7 +85,7 @@
   for feature extraction or sequence alignment based similarity computation.
   We thank Dr. Maisa Pinheiro for the feedback.
 
-# protr 1.5-0 (2017-11-17)
+# protr 1.5-0
 
 ## Bug fixes
 
@@ -98,64 +98,66 @@
 
 - General fixes and improvements for the package vignette.
 
-# protr 1.4-2 (2017-09-28)
+# protr 1.4-2
 
 ## Improvements
 
 - Functions are now organized into sections on the documentation website (<https://nanx.me/protr/reference/>).
 - Use system font stack instead of Google Fonts in vignettes to avoid pandoc SSL issue.
 
-# protr 1.4-1 (2017-07-08)
+# protr 1.4-1
 
 ## Improvements
 
 - Converted table images to Markdown tables in the vignette.
 - Updated the screenshot of protrweb in the vignette.
 
-# protr 1.4-0 (2017-06-06)
+# protr 1.4-0
 
 ## Improvements
 
 - Migrated from Sweave-based PDF vignette to knitr-based HTML vignette.
 
-# protr 1.3-0 (2017-05-07)
+# protr 1.3-0
 
 ## Improvements
 
 - Fix obsolete URLs.
 - Better R code formatting.
 - Better function documentation and vignette formatting.
 
-# protr 1.2-1 (2016-12-29)
+# protr 1.2-1
 
 ## Improvements
 
 - New documentation website: <https://nanx.me/protr/>.
 - Added Windows continuous integration support using AppVeyor.
 - Better R file naming scheme.
 
-# protr 1.2-0 (2016-11-12)
+# protr 1.2-0
 
 ## Improvements
 
 - Added continuous integration.
 - Code code style improvements.
 
-# protr 1.1-1 (2015-12-29)
+# protr 1.1-1
 
 ## Bug fixes
 
 - Fix URLs that cannot be accessed by `curl -I -L`:
   1. Use <http://protr.org>.
   2. Remove all inaccessible URLs.
 
-# protr 1.1-0 (2015-12-28)
+# protr 1.1-0
+
+2015-12-28
 
 ## Bug fixes
 
 - Bug fix in `extractCTDD()`.
 
-# protr 1.0-1 (2015-11-26)
+# protr 1.0-1
 
 ## Bug fixes
 
@@ -165,45 +167,51 @@
 
 - Added citation information.
 
-# protr 0.5-1 (2014-12-22)
+# protr 0.5-1
 
 ## Improvements
 
 - Minor improvements and fixes for documentation.
 
-# protr 0.5-0 (2014-12-18)
+# protr 0.5-0
+
+2014-12-18
 
 ## Improvements
 
 - Added functions allowing users to specify their own classification of the amino acid.
 - Documentation improvements.
 - Other minor improvements.
 
-# protr 0.4-1 (2014-10-10)
+# protr 0.4-1
 
 ## Improvements
 
 - General documentation improvements.
 
-# protr 0.4-0 (2014-09-20)
+# protr 0.4-0
+
+2014-09-20
 
 ## New features
 
 - Added profile-based descriptors derived by PSSM.
 
-# protr 0.3-0 (2014-06-20)
+# protr 0.3-0
+
+2014-06-20
 
 ## Improvements
 
 - Added an example workflow using protr in the vignette.
 
-# protr 0.2-1 (2014-01-25)
+# protr 0.2-1
 
 ## Improvements
 
 - Added a `LICENSE` file according to CRAN policies.
 
-# protr 0.2-0 (2013-12-10)
+# protr 0.2-0
 
 ## New features
 
@@ -221,7 +229,7 @@
 - Initial version of Auto Cross Covariance (ACC) for generating scales-based descriptors of the same length.
 - Introducing ProtWeb, the web service based on protr: <http://protr.org>.
 
-# protr 0.1-0 (2012-11-18)
+# protr 0.1-0
 
 ## New features
 

README.md

@@ -31,7 +31,7 @@ BibTeX entry:
 
 ## Installation
 
-To install `protr` from CRAN:
+To install protr from CRAN:
 
 ```r
 install.packages("protr")

_pkgdown.yml

@@ -6,9 +6,9 @@ template:
     preset: "bootstrap"
 
 reference:
-  - title: "Protein/Peptide Sequence Descriptors"
+  - title: "Protein and peptide sequence descriptors"
     desc: >
-      Functions for calculating protein/peptide sequence descirptors.
+      Functions for calculating protein/peptide sequence descriptors.
     contents:
     - extractAAC
     - extractDC
@@ -28,15 +28,15 @@ reference:
     - extractQSO
     - extractPAAC
     - extractAPAAC
-  - title: "Profile-Based Protein/Peptide Sequence Descriptors"
+  - title: "Profile-based protein and peptide sequence descriptors"
     desc: >
-      Functions for calculating the profile-based (PSSM) descirptors.
+      Functions for calculating the profile-based (PSSM) descriptors.
     contents:
     - extractPSSM
     - extractPSSMAcc
     - extractPSSMFeature
     - acc
-  - title: "Proteochemometric Modeling (PCM) Descriptors"
+  - title: "Proteochemometric Modeling (PCM) descriptors"
     desc: >
       Functions for calculating proteochemometric modeling (PCM) descriptors.
     contents:
@@ -48,7 +48,7 @@ reference:
     - extractFAScales
     - extractMDSScales
     - extractBLOSUM
-  - title: "Similarity Measures between Proteins"
+  - title: "Similarity measures between proteins"
     desc: >
       Functions for calculating protein sequence alignment based
       similarity measures and GO-based semantic similarity measures.
@@ -59,9 +59,9 @@ reference:
     - twoSeqSim
     - parGOSim
     - twoGOSim
-  - title: "Helper Functions for Pre-Processing Protein Sequences"
+  - title: "Pre-process protein sequences"
     desc: >
-      Functions for pre-processing protein sequences.
+      Helper Functions for pre-processing protein sequences.
     contents:
     - getUniProt
     - readFASTA
@@ -70,7 +70,7 @@ reference:
     - protseg
     - removeGaps
     - protr-package
-  - title: "Precomputed Molecular Descriptors for the 20 Amino Acids"
+  - title: "Precomputed molecular descriptors for the 20 amino acids"
     desc: >
       Precomputed molecular descriptors for the 20 amino acids.
     contents:
@@ -100,7 +100,7 @@ reference:
     - AATopoChg
     - AAWalk
     - AAWHIM
-  - title: "BLOSUM and PAM matrices for the 20 Amino Acids"
+  - title: "BLOSUM and PAM matrices for the 20 amino acids"
     desc: >
       BLOSUM and PAM matrices for the 20 amino acids.
     contents:

vignettes/protr.Rmd

@@ -12,8 +12,9 @@ output:
     highlight: "textmate"
     css: "custom.css"
 vignette: >
-  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{protr: R package for generating various numerical representation schemes of protein sequences}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r, include=FALSE}
@@ -283,7 +284,7 @@ The protr package integrates the function of parallelized similarity score
 computation derived by local or global protein sequence alignment between
 a list of protein sequences, the sequence alignment computation is
 provided by `Biostrings`, the corresponding functions listed in the
-`protr` package include:
+protr package include:
 
 - `twoSeqSim()` - Similarity calculation derived by sequence alignment
   between two protein sequences