Merge pull request #47 from nanxstats/chores

Improve code and documentation style

Author: nanxstats

.Rbuildignore

@@ -4,6 +4,6 @@
 ^_pkgdown\.yml$
 ^pkgdown$
 ^docs$
-^CONDUCT\.md$
+^CODE_OF_CONDUCT\.md$
 ^CONTRIBUTING\.md$
 ^\.github$

CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at me@nanx.me. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

CONDUCT.md

@@ -32,4 +32,4 @@ Suggests:
     foreach,
     doParallel,
     org.Hs.eg.db
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

DESCRIPTION

@@ -930,8 +930,8 @@ extractTC <- function(x) {
   n <- nchar(x)
   TC <- summary(factor(
     paste(paste(xSplitted[-c(n, n - 1)], xSplitted[-c(1, n)], sep = ""),
-          xSplitted[-c(1, 2)],
-          sep = ""
+      xSplitted[-c(1, 2)],
+      sep = ""
     ),
     levels = TCDict
   ), maxsum = 8001) / (n - 2)

R/desc-03-TC.R

@@ -101,11 +101,11 @@
 #'   )
 #' )
 extractMoreauBroto <- function(
-  x, props = c(
-    "CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102",
-    "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"
-  ),
-  nlag = 30L, customprops = NULL) {
+    x, props = c(
+      "CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102",
+      "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"
+    ),
+    nlag = 30L, customprops = NULL) {
   if (protcheck(x) == FALSE) {
     stop("x has unrecognized amino acid type")
   }

R/desc-04-MoreauBroto.R

@@ -101,11 +101,11 @@
 #'   )
 #' )
 extractMoran <- function(
-  x, props = c(
-    "CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102",
-    "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"
-  ),
-  nlag = 30L, customprops = NULL) {
+    x, props = c(
+      "CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102",
+      "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"
+    ),
+    nlag = 30L, customprops = NULL) {
   if (protcheck(x) == FALSE) {
     stop("x has unrecognized amino acid type")
   }

R/desc-05-Moran.R

@@ -101,11 +101,11 @@
 #'   )
 #' )
 extractGeary <- function(
-  x, props = c(
-    "CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102",
-    "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"
-  ),
-  nlag = 30L, customprops = NULL) {
+    x, props = c(
+      "CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102",
+      "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"
+    ),
+    nlag = 30L, customprops = NULL) {
   if (protcheck(x) == FALSE) {
     stop("x has unrecognized amino acid type")
   }

R/desc-06-Geary.R

@@ -72,8 +72,8 @@ extractCTDCClass <- function(x, aagroup1, aagroup2, aagroup3) {
   if (protcheck(x) == FALSE) stop("x has unrecognized amino acid type")
 
   if ((length(aagroup1) != length(aagroup2) |
-       length(aagroup1) != length(aagroup3)) |
-      (length(aagroup2) != length(aagroup3))) {
+    length(aagroup1) != length(aagroup3)) |
+    (length(aagroup2) != length(aagroup3))) {
     stop("The three groups must have the same property numbers")
   }
 

R/desc-07-CTDCClass.R

@@ -88,12 +88,13 @@ extractCTDT <- function(x) {
   # Combine single amino acids by a 2-length step
 
   for (i in 1:7) G[[i]] <- paste(G[[i]][-n], G[[i]][-1], sep = "")
-  G <- lapply(G, function(x)
+  G <- lapply(G, function(x) {
     factor(x, levels = c(
       "G1G2", "G2G1", "G1G3",
       "G3G1", "G2G3", "G3G2",
       "G1G1", "G2G2", "G3G3"
-    )))
+    ))
+  })
 
   GSummary <- lapply(G, summary)