[CRAN-MOD] modifications for CRAN pretests

.Rbuildignore

@@ -7,3 +7,5 @@
 ^pkgdown$
 ^\.github$
 ^README\.Rmd$
+^CODE_OF_CONDUCT\.md$
+^logo\.png$

DESCRIPTION

@@ -1,13 +1,31 @@
 Package: clintrialx
 Type: Package
-Title: Connect and work with clinical trials data sources with R programming.
+Title: Connect and Work with Clinical Trials Data Sources with R Programming
 Version: 0.1.0
-Authors@R: person("Indraneel", "Chakraborty",, "hello.indraneel@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6958-8269"))
+Authors@R: 
+    person("Indraneel", "Chakraborty",, "hello.indraneel@gmail.com", 
+           role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6958-8269"))
 Maintainer: Indraneel Chakraborty <hello.indraneel@gmail.com>
-Description: Are you spending too much time fetching and managing clinical trial data? Struggling with complex queries and bulk data extraction? What if you could simplify this process with just a few lines of code? Introducing clintrialx - Fetch clinical trial data from sources like ClinicalTrials.gov and the CTTI AACT database with R, supporting pagination and bulk downloads. Also, you can generate html reports based on the data obtained from the sources!
-License: Apache License Version 2.0
+Description: Are you spending too much time fetching and managing clinical trial data? Struggling with complex queries and bulk data extraction? What if you could simplify this process with just a few lines of code? Introducing clintrialx - Fetch clinical trial data from sources like ClinicalTrials.gov and the CTTI AACT database with R, supporting pagination and bulk downloads. Also, you can generate HTML reports based on the data obtained from the sources!
+License: Apache License 2.0 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-Depends: R (>= 4.0.0), httr, lubridate, readr, dplyr, progress, RPostgreSQL
+Depends: 
+    R (>= 4.0.0)
+Imports: 
+    httr, 
+    lubridate, 
+    readr, 
+    dplyr, 
+    progress, 
+    RPostgreSQL, 
+    tibble, 
+    DBI,
+    rmarkdown
+Suggests: 
+    knitr
+VignetteBuilder: knitr
 RoxygenNote: 7.3.2
-URL: http://ineelhere.github.io/clintrialx/
+URL: http://www.indraneelchakraborty.com/clintrialx/
+ExtraLicense: LICENSE
+ExtraFiles: CODE_OF_CONDUCT.md, logo.png

NAMESPACE

@@ -1 +1,32 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(aact_check_connection)
+export(aact_connection)
+export(aact_custom_query)
+export(ctg_bulk_fetch)
+export(ctg_count)
+export(ctg_data_report)
+export(ctg_get_fields)
+export(ctg_get_nct)
+export(hello)
+export(version_info)
+import(DBI)
+import(RPostgreSQL)
+import(dplyr)
+import(httr)
+import(progress)
+import(readr)
+import(tibble)
+importFrom(dplyr,as_tibble)
+importFrom(dplyr,bind_rows)
+importFrom(grDevices,colorRampPalette)
+importFrom(httr,GET)
+importFrom(httr,content)
+importFrom(httr,status_code)
+importFrom(lubridate,ymd_hms)
+importFrom(progress,progress_bar)
+importFrom(readr,cols)
+importFrom(readr,read_csv)
+importFrom(rmarkdown,render)
+importFrom(utils,install.packages)
+importFrom(utils,installed.packages)

README.Rmd

@@ -23,7 +23,7 @@ knitr::opts_chunk$set(
 [![R-CMD-check](https://github.com/ineelhere/clintrialx/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ineelhere/clintrialx/actions/workflows/R-CMD-check.yaml)
 [![License:
 Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
-[![pkgdown](https://img.shields.io/badge/pkgdown-docs-blue.svg)](https://ineelhere.github.io/clintrialx/)
+[![pkgdown](https://img.shields.io/badge/pkgdown-docs-blue.svg)](https://www.indraneelchakraborty.com/clintrialx/)
 [![Visitors](https://api.visitorbadge.io/api/visitors?path=https%3A%2F%2Fgithub.com%2Fineelhere%2Fclintrialx&label=Visitors&labelColor=%23f47373&countColor=%2337d67a&style=flat&labelStyle=upper)](https://github.com/ineelhere/clintrialx)
 
 [![Data Sources:
@@ -146,7 +146,7 @@ print(results)
 ## Trial Data HTML Reports
 *Currently works for data from ClinicalTrials.Gov*
 
-Visit here for an exqample report - https://ineelhere.github.io/clintrialx/report.html
+Visit here for an exqample report - https://www.indraneelchakraborty.com/clintrialx/report.html
 ```{r example6, eval = FALSE}
 #first get the data in a R dataframe
 my_clinical_trial_data <- ctg_bulk_fetch(condition="cancer")

README.md

@@ -8,7 +8,7 @@
 [![R-CMD-check](https://github.com/ineelhere/clintrialx/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ineelhere/clintrialx/actions/workflows/R-CMD-check.yaml)
 [![License:
 Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
-[![pkgdown](https://img.shields.io/badge/pkgdown-docs-blue.svg)](https://ineelhere.github.io/clintrialx/)
+[![pkgdown](https://img.shields.io/badge/pkgdown-docs-blue.svg)](https://www.indraneelchakraborty.com/clintrialx/)
 [![Visitors](https://api.visitorbadge.io/api/visitors?path=https%3A%2F%2Fgithub.com%2Fineelhere%2Fclintrialx&label=Visitors&labelColor=%23f47373&countColor=%2337d67a&style=flat&labelStyle=upper)](https://github.com/ineelhere/clintrialx)
 
 [![Data Sources:
@@ -130,7 +130,7 @@ print(results)
 *Currently works for data from ClinicalTrials.Gov*
 
 Visit here for an exqample report -
-<https://ineelhere.github.io/clintrialx/report.html>
+<https://www.indraneelchakraborty.com/clintrialx/report.html>
 
 ``` r
 #first get the data in a R dataframe

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: http://ineelhere.github.io/clintrialx/
+url: http://www.indraneelchakraborty.com/clintrialx/
 
 template:
   bootstrap: 5

clintrialx.Rproj

@@ -18,3 +18,5 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
+PackageRoxygenize: rd,collate,namespace,vignette

tests/testthat/test-aact_query.R

@@ -1,9 +1,16 @@
 # Test for aact_connection function
 test_that("aact_connection function works correctly", {
+  skip_on_cran() # Skip on CRAN
+
   # Mock credentials
   user <- Sys.getenv('user')
   password <- Sys.getenv('password')
 
+  # Skip if credentials are not set
+  if (user == "" || password == "") {
+    skip("Database credentials are not set in the environment.")
+  }
+
   # Test connection
   con <- aact_connection(user, password)
 
@@ -16,10 +23,17 @@ test_that("aact_connection function works correctly", {
 
 # Test for aact_check_connection function
 test_that("aact_check_connection function works correctly", {
+  skip_on_cran() # Skip on CRAN
+
   # Mock credentials
   user <- Sys.getenv('user')
   password <- Sys.getenv('password')
 
+  # Skip if credentials are not set
+  if (user == "" || password == "") {
+    skip("Database credentials are not set in the environment.")
+  }
+
   # Establish connection
   con <- aact_connection(user, password)
 
@@ -38,10 +52,17 @@ test_that("aact_check_connection function works correctly", {
 
 # Test for aact_custom_query function
 test_that("aact_custom_query function works correctly", {
+  skip_on_cran() # Skip on CRAN
+
   # Mock credentials
   user <- Sys.getenv('user')
   password <- Sys.getenv('password')
 
+  # Skip if credentials are not set
+  if (user == "" || password == "") {
+    skip("Database credentials are not set in the environment.")
+  }
+
   # Establish connection
   con <- aact_connection(user, password)
 

tests/testthat/test-hello.R

@@ -3,5 +3,5 @@ library(clintrialx)
 
 test_that("hello function works correctly", {
   output <- hello()
-  expect_equal(output, "👋 Welcome to ClinTrialX!")
+  expect_equal(output, "Welcome to ClinTrialX!")
 })

vignettes/usecase-doc.R

@@ -0,0 +1,74 @@
+## ----eval=FALSE---------------------------------------------------------------
+#  # Load required libraries
+#  invisible(suppressPackageStartupMessages({
+#    library(clintrialx)  # For fetching clinical trial data
+#    library(ggplot2)     # For data visualization
+#    library(plotly)      # For interactive plots
+#    library(dplyr)       # For data manipulation
+#    library(lubridate)   # For date handling
+#  }))
+
+## ----eval=FALSE---------------------------------------------------------------
+#  # Fetch cancer study data in India
+#  df <- ctg_bulk_fetch(condition = "cancer", location = "India")
+
+## ----eval=FALSE---------------------------------------------------------------
+#  # Create a table of study statuses
+#  status_counts <- table(df$`Study Status`)
+#  
+#  # Convert the table to a data frame
+#  status_df <- data.frame(status = names(status_counts), count = as.numeric(status_counts))
+#  
+#  # Generate the bar plot
+#  ggplotly(ggplot(status_df, aes(x = reorder(status, -count), y = count)) +
+#    geom_bar(stat = "identity", fill = "orange") +
+#    theme_minimal() +
+#    labs(title = "Distribution of Study Statuses",
+#         x = "Study Status",
+#         y = "Count") +
+#    theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
+#    geom_text(aes(label = count), vjust = -0.5))
+
+## ----eval=FALSE---------------------------------------------------------------
+#  # Create an interactive box plot of enrollment by study phase
+#  ggplotly(ggplot(df, aes(x = Phases, y = Enrollment)) +
+#    geom_boxplot(fill = "lightblue", outlier.colour = "red", outlier.shape = 1) +
+#    geom_jitter(color = "darkblue", size = 0.5, alpha = 0.5, width = 0.2) +
+#    theme_minimal(base_size = 14) +
+#    labs(title = "Enrollment by Study Phase",
+#         x = "Study Phase",
+#         y = "Enrollment") +
+#    theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 12),
+#          plot.title = element_text(hjust = 0.5)))
+
+## ----eval=FALSE---------------------------------------------------------------
+#  # Convert date strings to Date objects
+#  df$start_date <- as.Date(df$`Start Date`, format = "%Y-%m-%d")
+#  df$completion_date <- as.Date(df$`Completion Date`, format = "%Y-%m-%d")
+#  
+#  # Create a scatter plot with a horizontal line at 2024
+#  ggplot(df, aes(x = start_date, y = completion_date, color = `Study Status`)) +
+#    geom_point(alpha = 0.6) +
+#    geom_hline(yintercept = as.Date("2024-01-01"), linetype = "dashed", color = "blue") +
+#    theme_minimal() +
+#    labs(title = "Study Duration Timeline",
+#         x = "Start Date",
+#         y = "Completion Date") +
+#    scale_color_brewer(palette = "Set1")
+
+## ----eval=FALSE---------------------------------------------------------------
+#  # Summarize and plot funding sources by study type
+#  df_summary <- df %>%
+#    count(`Funder Type`, `Study Type`) %>%
+#    group_by(`Funder Type`) %>%
+#    mutate(prop = n / sum(n))
+#  
+#  ggplotly(ggplot(df_summary, aes(x = `Funder Type`, y = prop, fill = `Study Type`)) +
+#    geom_bar(stat = "identity", position = "dodge") +
+#    theme_minimal() +
+#    labs(title = "Funding Sources and Study Types",
+#         x = "Funder Type",
+#         y = "Proportion") +
+#    scale_fill_brewer(palette = "Set2") +
+#    theme(axis.text.x = element_text(angle = 45, hjust = 1)))
+

vignettes/usecase-doc.Rmd

@@ -2,12 +2,11 @@
 title: "Exploring Clinical Trial Data with clintrialx"
 author: "Indraneel Chakraborty"
 date: "`r Sys.Date()`"
-output: 
-  html_document:
-    theme: cerulean
-    highlight: tango
-    toc: true
-    toc_float: true
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Exploring Clinical Trial Data with clintrialx}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ## Introduction
@@ -18,7 +17,7 @@ Welcome to the `clintrialx` vignette! This package simplifies the process of fet
 
 To start, load the necessary libraries. We use `suppressPackageStartupMessages` to keep the output clean:
 
-```{r}
+```{r, eval=FALSE}
 # Load required libraries
 invisible(suppressPackageStartupMessages({
   library(clintrialx)  # For fetching clinical trial data
@@ -33,7 +32,7 @@ invisible(suppressPackageStartupMessages({
 
 Retrieve clinical trial data related to cancer studies in India using the `ctg_bulk_fetch` function:
 
-```{r}
+```{r, eval=FALSE}
 # Fetch cancer study data in India
 df <- ctg_bulk_fetch(condition = "cancer", location = "India")
 ```
@@ -42,7 +41,7 @@ df <- ctg_bulk_fetch(condition = "cancer", location = "India")
 
 Understand the distribution of study statuses by creating a bar plot:
 
-```{r}
+```{r, eval=FALSE}
 # Create a table of study statuses
 status_counts <- table(df$`Study Status`)
 
@@ -66,7 +65,7 @@ This plot provides an overview of the number of studies in each status category.
 
 Compare enrollment numbers across different study phases using an interactive box plot:
 
-```{r}
+```{r, eval=FALSE}
 # Create an interactive box plot of enrollment by study phase
 ggplotly(ggplot(df, aes(x = Phases, y = Enrollment)) +
   geom_boxplot(fill = "lightblue", outlier.colour = "red", outlier.shape = 1) +
@@ -85,7 +84,7 @@ This interactive plot allows you to explore enrollment numbers across different
 
 Examine the timeline of studies with a scatter plot:
 
-```{r}
+```{r, eval=FALSE}
 # Convert date strings to Date objects
 df$start_date <- as.Date(df$`Start Date`, format = "%Y-%m-%d")
 df$completion_date <- as.Date(df$`Completion Date`, format = "%Y-%m-%d")
@@ -107,7 +106,7 @@ This scatter plot helps visualize study durations and their statuses, providing
 
 Examine the relationship between funding sources and study types using a stacked bar plot:
 
-```{r}
+```{r, eval=FALSE}
 # Summarize and plot funding sources by study type
 df_summary <- df %>%
   count(`Funder Type`, `Study Type`) %>%