redoc

data-raw/biorecap_data.R

@@ -1,43 +1,102 @@
 # Create vector for all bioRxiv subjects ----------------------------------
 
+subjects <- list()
+
 # https://www.biorxiv.org/alertsrss
+subjects$biorxiv <- c("all",
+                      "animal_behavior_and_cognition",
+                      "biochemistry",
+                      "bioengineering",
+                      "bioinformatics",
+                      "biophysics",
+                      "cancer_biology",
+                      "cell_biology",
+                      "clinical_trials",
+                      "developmental_biology",
+                      "ecology",
+                      "epidemiology",
+                      "evolutionary_biology",
+                      "genetics",
+                      "genomics",
+                      "immunology",
+                      "microbiology",
+                      "molecular_biology",
+                      "neuroscience",
+                      "paleontology",
+                      "pathology",
+                      "pharmacology_and_toxicology",
+                      "plant_biology",
+                      "scientific_communication_and_education",
+                      "synthetic_biology",
+                      "systems_biology",
+                      "zoology")
+
+# https://www.medrxiv.org/content/alertsrss
+subjects$medrxiv <- c("all",
+                      "Addiction_Medicine",
+                      "Allergy_and_Immunology",
+                      "Anesthesia",
+                      "Cardiovascular_Medicine",
+                      "Dentistry_and_Oral_Medicine",
+                      "Dermatology",
+                      "Dermatology",
+                      "endocrinology",
+                      "Epidemiology",
+                      "ecology",
+                      "epidemiology",
+                      "Forensic_Medicine",
+                      "Gastroenterology",
+                      "Genetic_and_Genomic_Medicine",
+                      "Geriatric_Medicine",
+                      "Health_Economics",
+                      "Health_Informatics",
+                      "Health_Policy",
+                      "Health_Systems_and_Quality_Improvement",
+                      "Hematology",
+                      "hivaids",
+                      "infectious_diseases",
+                      "Intensive_Care_and_Critical_Care_Medicine",
+                      "Medical_Education",
+                      "Medical_Ethics",
+                      "Nephrology",
+                      "Neurology",
+                      "Nursing",
+                      "Nutrition",
+                      "Obstetrics_and_Gynecology",
+                      "Occupational_and_Environmental_Health",
+                      "Oncology",
+                      "Ophthalmology",
+                      "Orthopedics",
+                      "Otolaryngology",
+                      "Pain_Medicine",
+                      "Palliative_Medicine",
+                      "Pathology",
+                      "Pediatrics",
+                      "Pharmacology_and_Therapeutics",
+                      "Primary_Care_Research",
+                      "Psychiatry_and_Clinical_Psychology",
+                      "Public_and_Global_Health",
+                      "Radiology_and_Imaging",
+                      "Rehabilitation_Medicine_and_Physical_Therapy",
+                      "Respiratory_Medicine",
+                      "Rheumatology",
+                      "Sexual_and_Reproductive_Health",
+                      "Sports_Medicine",
+                      "Surgery",
+                      "Toxicology",
+                      "Transplantation",
+                      "Urology")
 
-subjects <- c("all",
-              "animal_behavior_and_cognition",
-              "biochemistry",
-              "bioengineering",
-              "bioinformatics",
-              "biophysics",
-              "cancer_biology",
-              "cell_biology",
-              "clinical_trials",
-              "developmental_biology",
-              "ecology",
-              "epidemiology",
-              "evolutionary_biology",
-              "genetics",
-              "genomics",
-              "immunology",
-              "microbiology",
-              "molecular_biology",
-              "neuroscience",
-              "paleontology",
-              "pathology",
-              "pharmacology_and_toxicology",
-              "plant_biology",
-              "scientific_communication_and_education",
-              "synthetic_biology",
-              "systems_biology",
-              "zoology")
+subjects <- lapply(subjects, tolower)
 usethis::use_data(subjects, overwrite=TRUE)
 
 
-# Get titles, abstracts, summaries for preprints 2024-08-06 ---------------
+# Get titles, abstracts, summaries for preprints 2024-09-25 ---------------
 
 library(biorecap)
 example_preprints <-
-  get_preprints(subject=c("bioinformatics", "genomics", "synthetic_biology")) |>
+  get_preprints(subject=c("bioinformatics", "infectious_diseases")) |>
   add_prompt() |>
-  add_summary(model="llama3.1:70b")
+  add_summary(model="llama3.2")
 usethis::use_data(example_preprints, overwrite=TRUE)
 readr::write_csv(example_preprints, here::here("inst/extdata/example_preprints.csv.gz"))