From ff78e79c1451c355fe86a29fe5735aaa1cfaba80 Mon Sep 17 00:00:00 2001
From: John Elizarraras <elizarrj27@gmail.com>
Date: Thu, 13 Jun 2024 13:21:17 -0500
Subject: [PATCH] Documentation changes for CRAN compatibility

---
 .Rbuildignore |  3 +++
 DESCRIPTION   |  3 ++-
 README.Rmd    | 14 ++++++--------
 README.md     | 14 +++++++-------
 4 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index fdabd45..6e3832c 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -7,3 +7,6 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.github$
+^man\\figures\.gitkeep$
+^man/figures/\.gitkeep$
\ No newline at end of file
diff --git a/DESCRIPTION b/DESCRIPTION
index fb2e9f8..4305c8b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,10 +2,11 @@ Package: clinicalomicsdbR
 Title: Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing
 Version: 1.0.4
 Authors@R: 
-    person("John", "Elizarraras", , "john.elizarraras@bcm.edu", role = c("aut", "cre"))
+    person("John", "Elizarraras", , "john.elizarraras@bcm.edu", role = c("aut", "cre", "ctb"))
 Description: Provides an interface to the ClinicalOmicsDB API, allowing for easy data downloading and importing. ClinicalOmicsDB is a database of clinical and omics data from cancer patients. The database is accessible at <http://trials.linkedomics.org>.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Imports: httr2, R6, dplyr, utils, jsonlite
+BugReports: https://github.com/bzhanglab/clinicalomicsdbR/issues/new
diff --git a/README.Rmd b/README.Rmd
index 8e319c0..60ae473 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -25,6 +25,12 @@ Designed with the structure from https://r-pkgs.org/.
 
 ## Installation
 
+To install the latest stable release, run
+
+``` r
+install.packages("clinicalomicsdbR")
+```
+
 You can install the development version of clinicalomicsdbR from [GitHub](https://github.com/) with:
 
 ``` r
@@ -86,11 +92,3 @@ for (study in res[["study_list"]]) {
   print(ncol(res[["df"]][[study]]))
 }
 ```
-
-<!-- ```{r example} -->
-<!-- library(clinicalomicsdbR) -->
-<!-- ## basic filtering -->
-
-<!-- clinicalomicsdbR$new()$filter(drugs=c("paclitaxel"))$study_list[[1]] -->
-<!-- ``` -->
-
diff --git a/README.md b/README.md
index 8cad0bf..39b8e58 100644
--- a/README.md
+++ b/README.md
@@ -16,6 +16,12 @@ Designed with the structure from <https://r-pkgs.org/>.
 
 ## Installation
 
+To install the latest stable release, run
+
+``` r
+install.packages("clinicalomicsdbR")
+```
+
 You can install the development version of clinicalomicsdbR from
 [GitHub](https://github.com/) with:
 
@@ -48,7 +54,7 @@ See Examples below to see how to use.
   `df` that contains a list of the study data information.
 - `dataframe_from_id(study_id)` - loads a study with id from `study_id`
   into a dataframe
-- `downlaod_from_id(study_id, output_dir)` - downloads a study with id
+- `downlaod_from_id(study_id, output_dir)` - downsloads a study with id
   from `study_id` into a folder `output_dir`. `output_dir` defaults to
   `clindb`
 
@@ -100,9 +106,3 @@ for (study in res[["study_list"]]) {
 #> [1] 17145
 #> [1] 20321
 ```
-
-<!-- ```{r example} -->
-<!-- library(clinicalomicsdbR) -->
-<!-- ## basic filtering -->
-<!-- clinicalomicsdbR$new()$filter(drugs=c("paclitaxel"))$study_list[[1]] -->
-<!-- ``` -->