Reverting to locally build documentation site.

.Rbuildignore

@@ -6,3 +6,6 @@
 ^Meta$
 ^README\.Rmd$
 ^\.travis\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.gitignore

@@ -0,0 +1,14 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store
+inst/doc
+doc
+Meta
+man/
+data-raw/
+*.svg
+R/data.R
+pkgdown/
+

DESCRIPTION

@@ -11,7 +11,7 @@ Description: This package identifies features that have altered rhythms
     single function with customizations for microarray, RNA-seq or generic 
     (prenormalized) data.
 License: GPL-3
-URL: https://github.com/bharathananth/compareRhythms
+URL: https://github.com/bharathananth/compareRhythms, https://bharathananth.github.io/compareRhythms/
 BugReports: https://github.com/bharathananth/compareRhythms/issues
 Encoding: UTF-8
 LazyData: true
@@ -32,6 +32,15 @@ Suggests:
     knitr,
     rmarkdown,
     tidyverse
+Remotes:
+    github::cran/npsm,
+    github::cran/DODR,
+    github::hadley/assertthat@>=0.2.1,
+    bioc::SummarizedExperiment@>=1.16.1, 
+    bioc::limma@>=3.38.3,
+    bioc::edgeR@>=3.28.0,
+    bioc::DESeq2@>=1.26.0,
+    bioc::rain@>=1.16.0
 VignetteBuilder: knitr
 Depends: 
     R (>= 2.10)

README.Rmd

@@ -34,7 +34,7 @@ cat(
 <!-- badges: end -->
 
 
-The goal of *compareRhythms* is to find features with altered circadian rhythm parameters (*amplitude* and *phase*) between the control and experimental groups.
+The goal of *compareRhythms* is to find features with altered circadian rhythm parameters (*amplitude* and *phase*) between the control and experimental groups. A fit of the function $A\cos(\frac{2\pi t}{24} - \phi)$ to the data defines the rhythm parameters amplitude ($A$) and phase ($\phi$). 
 
 ## Installation
 
@@ -43,7 +43,7 @@ You can install the current version of *compareRhythms* from GitHub with:
 ``` r
 if (!require("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
-BiocManager::install(version = "3.15")   # This installs bioconductor
+BiocManager::install(version = "3.19")   # This installs bioconductor, but version 3.15 onwards are also ok
 BiocManager::install(c("SummarizedExperiment", "DESeq2", "edgeR", "limma", "rain")) # Packages needed by compareRhythms
 install.packages("devtools")    # if it is not already installed
 devtools::install_github("cran/npsm")   # Package archived by CRAN
@@ -59,6 +59,7 @@ For complete examples, please refer to the vignette titled **User Guide** by run
 library(compareRhythms)
 vignette("UserGuide", package="compareRhythms")
 ```
+or view the [documentation](https://bharathananth.github.io/compareRhythms/articles/UserGuide.html).
 
 ## Citation
 

README.md

@@ -16,7 +16,9 @@ GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-pro
 
 The goal of *compareRhythms* is to find features with altered circadian
 rhythm parameters (*amplitude* and *phase*) between the control and
-experimental groups.
+experimental groups. A fit of the function
+$A\cos(\frac{2\pi t}{24} - \phi)$ to the data defines the rhythm
+parameters amplitude ($A$) and phase ($\phi$).
 
 ## Installation
 
@@ -26,7 +28,7 @@ with:
 ``` r
 if (!require("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
-BiocManager::install(version = "3.15")   # This installs bioconductor
+BiocManager::install(version = "3.19")   # This installs bioconductor, but version 3.15 onwards are also ok
 BiocManager::install(c("SummarizedExperiment", "DESeq2", "edgeR", "limma", "rain")) # Packages needed by compareRhythms
 install.packages("devtools")    # if it is not already installed
 devtools::install_github("cran/npsm")   # Package archived by CRAN
@@ -54,6 +56,9 @@ library(compareRhythms)
 vignette("UserGuide", package="compareRhythms")
 ```
 
+or view the
+[documentation](https://bharathananth.github.io/compareRhythms/articles/UserGuide.html).
+
 ## Citation
 
 Please cite *compareRhythms* in publications as:

_pkgdown.yml

@@ -0,0 +1,7 @@
+url: https://bharathananth.github.io/compareRhythms/
+template:
+  bootstrap: 5
+  bootswatch: flatly
+  bslib:
+    pkgdown-nav-height: 75px
+