updated snapshot

R/mx_snapshot.R

@@ -18,19 +18,42 @@
 #' mx_data <- mx_snapshot()
 #' }
 #'
-mx_snapshot <- function(commit = "master") {
-  mx_info(commit)
+mx_snapshot <- function(commit = "main") {
 
-  mx_data <- suppressMessages(data.table::fread(
-    paste0(
-      "https://raw.githubusercontent.com/",
-      "/mcguinlu/medrxivr-data/", commit, "/snapshot.csv"
-    ),
-    showProgress = FALSE
-  ))
+  # Get the base URL for the data repository
+  base_url <- paste0(
+    "https://github.com/YaoxiangLi/medrxivr-data/raw/refs/heads/", commit, "/"
+  )
 
+  # Generate a list of potential snapshot part files
+  # Assuming the files follow the pattern "snapshot_part1.csv", "snapshot_part2.csv", etc.
+  part_files <- paste0("snapshot_part", 1:20, ".csv")
+
+  # Initialize an empty list to store dataframes
+  df_list <- list()
+
+  # Try to read each file and add it to the list
+  for (part_file in part_files) {
+    url <- paste0(base_url, part_file)
+
+    # Attempt to read the file; skip if it doesn't exist
+    try({
+      mx_part <- suppressMessages(data.table::fread(url, showProgress = FALSE))
+      df_list[[length(df_list) + 1]] <- mx_part
+    }, silent = TRUE)
+  }
+
+
+  # Combine all the loaded parts into a single dataframe
+  if (length(df_list) == 0) {
+    stop("No data could be loaded. Please check the commit or data availability.")
+  }
+  mx_data <- dplyr::bind_rows(df_list)
+
+  # Reconstruct the link_page and link_pdf columns
   mx_data$link_page <- paste0("https://www.medrxiv.org", mx_data$link)
   mx_data$link_pdf <- paste0("https://www.medrxiv.org", mx_data$pdf)
 
+  # Return the combined dataframe
   mx_data
 }

vignettes/building-complex-search-strategies.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Building complex search strategies"
-author: "Luke A McGuinness"
+author: "Yaoxiang Li"
 date: "`r Sys.Date()`"
 output:
   rmarkdown::html_document:

vignettes/medrxiv-api.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Interacting with the Cold Spring Harbour Laboratory API"
-author: "Luke A McGuinness"
+author: "Yaoxiang Li"
 date: "`r Sys.Date()`"
 output:
   rmarkdown::html_document:

vignettes/medrxivr.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Get started"
-author: "Luke A McGuinness"
+author: "Yaoxiang Li"
 date: "`r Sys.Date()`"
 output:
   rmarkdown::html_document:
@@ -31,10 +31,10 @@ The goal of the `medrxivr` R package is two-fold. In the first instance, it prov
 
 ## Installation
 
-You can install the development version of this package using:
+You can install the stable version of this package using:
 
 ``` {r}
-devtools::install_github("mcguinlu/medrxivr")
+install.packages("medrxivr")
 library(medrxivr)
 ```