address cmd notes

R/data_pmc_list.R

@@ -27,6 +27,10 @@ data_pmc_list <- function(force_install = FALSE) {
   # Local file path for storing the processed data
   df <- file.path(rappdirs::user_data_dir('pubmedr'), 'oa_file_list.rds')
 
+  # Define PMID and PMCID variables
+  PMID <- NULL
+  PMCID <- NULL
+
   # Check if the file exists, and download and process it if it doesn't or if forced
   if (!file.exists(df) | force_install) {
     # Create the directory if it doesn't exist

R/get_records.R

@@ -11,8 +11,10 @@
 #' @importFrom pbapply pblapply
 #' @importFrom data.table rbindlist
 #' @examples
+#' \donttest{
 #' pmids <- c("38136652", "31345328", "32496629")
 #' results <- get_records(pmids, endpoint = "pubmed_abstracts", cores = 1)
+#' }
 #' @export
 #' @rdname get_records
 #' 

R/search_pubmed.R

@@ -12,9 +12,18 @@
 #' @importFrom rentrez entrez_search
 #' @export
 #' @examples
+#' \donttest{
 #' ethnob1 <- search_pubmed("ethnobotany", 2010, 2012)
 #' ethnob2 <- search_pubmed("ethnobotany", use_pub_years = FALSE)
-search_pubmed <- function(x, start_year = NULL, end_year = NULL, retmax = 9999, use_pub_years = TRUE) {
+#' }
+#' 
+#' 
+search_pubmed <- function(x, 
+                          start_year = NULL, 
+                          end_year = NULL, 
+                          retmax = 9999, 
+                          use_pub_years = TRUE) {
+
   if(!is.character(x) || length(x) != 1) {
     stop("x must be a single character string.")
   }

R/source_icites.R

@@ -53,6 +53,7 @@
   data.table::setDT(pmiddf)
 
   # Clean and format the 'ref_count' column
+  ref_count <- NULL
   pmiddf[, ref_count := ifelse(is.null(references)|is.na(references), NULL, references)]
 
   # Process 'references' and 'cited_by' columns, handling empty or NA values
@@ -65,13 +66,16 @@
   rs <- strsplit(pmiddf$ref_count, split = " ")
 
   # Build a data frame for references
-  refs <- data.frame(doc_id = rep(gots, sapply(references, length)),
-                     from = rep(gots, sapply(references, length)),
-                     to = unlist(references))
+  doc_id <- NULL
+  from <- NULL
+  refs <- data.table::data.table(doc_id = rep(gots, sapply(references, length)),
+                                 from = rep(gots, sapply(references, length)),
+                                 to = unlist(references))
   # Replace placeholder '99' with NA
   refs[refs == 99] <- NA
+
   # Aggregate reference data and convert to a data.table
-  refs0 <- data.table::setDT(refs)[, list(references = .N), by = .(from)]
+  refs0 <- refs[, list(references = .N), by = list(from)]
 
   # Build a data frame for cited_by data
   cited <- data.frame(doc_id = rep(gots, sapply(cited_by, length)),
@@ -86,6 +90,7 @@
   f2 <- data.table::setDT(f1)[, list(references = list(.SD)), by = doc_id]
 
   # Add citation network data to pmiddf
+  citation_net <- NULL
   pmiddf[, citation_net := f2$references]
   # Calculate and add reference count
   pmiddf[, ref_count := sapply(rs, length)]

R/source_pubmed.R

@@ -29,6 +29,7 @@
                                content.name = 'varx')
 
   # Reshape the data into a wide format using data.table
+  id <- NULL
   sum1 <- data.table::dcast(data = sum0,
                             formula = id ~ attribute,
                             value.var = 'varx')
@@ -39,6 +40,7 @@
   sum1 <- sum1[, c('pmid', 'year', 'journal', 'articletitle', 'abstract')]
 
   # Add annotations to the data table
+  annotations <- NULL
   sum1[, annotations := list(lapply(parsed_records, '[[', 2))] 
 
   # Ensure proper encoding for compatibility

R/source_pubtations.R

@@ -76,6 +76,9 @@
     jj0$locations <- gsub("[^[:digit:],]", "", jj0$locations)
 
     # Extract start and end positions of annotations
+    start <- NULL
+    end <- NULL
+    locations <- NULL
     jj0[, c('start', 'length') := data.table::tstrsplit(locations, ",", fixed=TRUE)]
     jj0[, start := as.integer(start)]
     jj0[, end := start + as.integer(length)]

README.Rmd

@@ -9,7 +9,7 @@ always_allow_html: true
 
 # puremoe
 
-## **P**ubMed **U**niform **Re**trieval for **M**ulti-**O**utput **E**xploration (puremoe)
+> **P**ubMed **U**niform **RE**trieval for **M**ulti-**O**utput **E**xploration
 
 An R package that provides a single interface for accessing a range of NLM/PubMed databases, including [PubMed](https://pubmed.ncbi.nlm.nih.gov/) abstract records, [iCite](https://icite.od.nih.gov/) bibliometric data, [PubTator](https://www.ncbi.nlm.nih.gov/research/pubtator/) named entity annotations, and full-text entries from [PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/) (PMC).  This unified interface simplifies the data retrieval process, allowing users to interact with multiple PubMed services/APIs/output formats through a single R function.