Non-ontology based trait collapsing

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Last updated: 2025-09-15

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Knit directory: genomics_ancest_disease_dispar/

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html	0cd6e22	IJbeasley	2025-09-10	Build site.
Rmd	174ec54	IJbeasley	2025-09-10	Fixing + improving format of initial disease trait name harmonization

---

1 Set up

library(dplyr)
library(data.table)
library(stringr)

gwas_study_info <- fread(here::here("output/gwas_cat/gwas_study_info_trait_cat.csv"))

2 Initial summary

2.1 Objectives of this analysis:

• Collapsing and standardizing disease trait terms in GWAS study metadata without relying on ontology mappings.
• Initial harmonization of disease trait terms (fixing spelling, collapsing studies that study different aspects of the same disease)

3 Number of studies per trait - before any grouping

Let’s look at the number of studies associated with each unique disease/trait term before any grouping or collapsing.

n_studies_trait = gwas_study_info |>
  dplyr::filter(DISEASE_STUDY == T) |>
  dplyr::select(all_disease_terms, PUBMED_ID) |>
  dplyr::distinct() |>
  dplyr::group_by(all_disease_terms) |>
  dplyr::summarise(n_studies = dplyr::n()) |>
  dplyr::arrange(desc(n_studies))

head(n_studies_trait)

# A tibble: 6 × 2
  all_disease_terms         n_studies
  <chr>                         <int>
1 type 2 diabetes mellitus        144
2 major depressive disorder       108
3 alzheimer disease               104
4 asthma                           99
5 schizophrenia                    99
6 breast carcinoma                 98

dim(n_studies_trait)

[1] 3202    2

4 Disease trait collapsing and cleaning

# Basic cleaning of disease terms
# Removes trailing commas, 
gwas_study_info$all_disease_terms = sub(",$", "", gwas_study_info$all_disease_terms)

# trims whitespace
gwas_study_info$all_disease_terms = stringr::str_trim(gwas_study_info$all_disease_terms)

# remove apostrophes
gwas_study_info$all_disease_terms = stringr::str_remove_all(gwas_study_info$all_disease_terms, "'|’")

# initializes a new column (collected_all_disease_terms) to standardized traits
# collapse more traits 
gwas_study_info = gwas_study_info |> 
  mutate(collected_all_disease_terms = all_disease_terms) 

4.1 Where a study investigates a given aspect of of disease, reduce this to a study of this disease

4.1.1 Susceptibility to X measurement

4.1.1.1 Non-specific examples

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
        str_replace_all(collected_all_disease_terms, 
                    "susceptibility to (.*?) measurement(?=,|$)", "\\1")

         ) |>
    mutate(collected_all_disease_terms = 
        str_replace_all(collected_all_disease_terms, 
                    "susceptibility to (.*?) (.*?) measurement(?=,|$)", "\\1 \\2")

         ) |>
      mutate(collected_all_disease_terms = 
        str_replace_all(collected_all_disease_terms, 
                    "susceptibility to (.*?) (.*?) infection(?=,|$)", "\\1 \\2")

         ) 

4.1.2 Specific examples / changes to make

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
        str_replace_all(collected_all_disease_terms, 
                    "susceptibility to viral and mycobacterial infections",
                    "viral and mycobacterial infections")

         ) |>
    mutate(collected_all_disease_terms = 
        str_replace_all(collected_all_disease_terms, 
                    "susceptibility to strep throat",
                    "strep throat")
         ) |>    
  mutate(collected_all_disease_terms = 
        str_replace_all(collected_all_disease_terms, 
                    "decreased susceptibility to bacterial infection",
                    "bacterial infection")
  ) |> 
    mutate(collected_all_disease_terms = 
        str_replace_all(collected_all_disease_terms, 
                    "bruising susceptibility",
                    "bruisability")
    )

4.1.3 Severity measurement / symptom severity measurement / exacerbation measurement

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
          stringr::str_remove(collected_all_disease_terms, " symptom severity measurement")
         ) |>
  mutate(collected_all_disease_terms = 
          stringr::str_remove(collected_all_disease_terms, " severity measurement| exacerbation measurement")
         ) 

4.1.4 Other kinds of measurement

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
        str_replace_all(collected_all_disease_terms, 
                    "(.*?) (.*?) measurement(?=,|$)", "\\1 \\2")
  )

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms =
           str_replace_all(collected_all_disease_terms,
                           "\\bdependence\\s+measurement(?=,|$)",
                           "dependence")) |> 
  mutate(collected_all_disease_terms =
           str_replace_all(collected_all_disease_terms,
                           "\\ballergy\\s+measurement(?=,|$)",
                           "allergy")) |> 
  mutate(collected_all_disease_terms =
           str_replace_all(collected_all_disease_terms,
                           "\\baddiction\\s+measurement(?=,|$)",
                           "addiction")) |> 
      mutate(collected_all_disease_terms =
           str_replace_all(collected_all_disease_terms,
                           "\\bsyndrome\\s+measurement(?=,|$)",
                           "syndrome")) |> 
      mutate(collected_all_disease_terms =
           str_replace_all(collected_all_disease_terms,
                           "\\bdisorder\\s+measurement(?=,|$)",
                           "disorder")) 

4.1.5 Age of onset of

4.1.5.1 Non-specific correction

gwas_study_info = gwas_study_info |>
      mutate(collected_all_disease_terms = 
         stringr::str_remove(collected_all_disease_terms,
                              pattern = "age of onset of ")
         )

4.1.5.2 Specific corrections

gwas_study_info = 
gwas_study_info |> 
 mutate(collected_all_disease_terms  = 
          stringr::str_replace_all(collected_all_disease_terms ,
                                  pattern = "age of onset of type 2 diabetes mellitus",
                                   "type 2 diabetes mellitus"
                          )  
        )


gwas_study_info = 
gwas_study_info |> 
 mutate(collected_all_disease_terms  = 
          stringr::str_replace_all(collected_all_disease_terms ,
                                  pattern = "age of onset of alzheimer disease",
                                   "alzheimers disease"
                          )  
        )


# febrile seizure (within the age range of 3 months to 6 years)
gwas_study_info = gwas_study_info |> 
 mutate(collected_all_disease_terms  = 
          stringr::str_replace_all(collected_all_disease_terms ,
                                  pattern = "febrile seizure \\(within the age range of 3 months to 6 years\\)",
                                   "febrile seizure"
                          )  
        )

4.1.6 Family history of

4.1.6.1 Non-specific example

gwas_study_info = gwas_study_info |>
      mutate(collected_all_disease_terms = 
         stringr::str_remove(collected_all_disease_terms,
                         pattern = "family history of "))

4.1.6.2 Speciic example: Alzheimer’s disease

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "family history of alzheimer’s disease",
                          "alzheimers disease"
         ))

4.1.7 Disease progression

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
         stringr::str_remove_all(collected_all_disease_terms,
                          "^disease progression, |"
         )) |> 
    mutate(collected_all_disease_terms = 
         stringr::str_remove_all(collected_all_disease_terms,
                          ", disease progression$"
         ))   


gwas_study_info = gwas_study_info |>
      mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          ", disease progression, ",
                          ", "
         ))

4.1.8 Time to remission

4.1.8.1 COVID

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "time to remission of covid-19 symptoms",
                          "covid-19"
         ))

4.1.9 Symptom measurement

4.1.9.1 ADHD

gwas_study_info = gwas_study_info |> 
  mutate(collected_all_disease_terms = 
           stringr::str_replace_all(collected_all_disease_terms,
                            "adhd symptom",
                            "adhd")
         )

4.1.9.2 Agoraphobia

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "agoraphobia symptom",
                          "agoraphobia"
         ))

4.1.9.3 Autism

gwas_study_info = gwas_study_info |> 
  mutate(collected_all_disease_terms = 
           stringr::str_replace_all(collected_all_disease_terms,
                            "autism spectrum disorders symptom",
                            "autism")
         ) |>
    mutate(collected_all_disease_terms = 
           stringr::str_replace_all(collected_all_disease_terms,
                            "autism spectrum disorder symptom",
                            "autism")
         ) 


gwas_study_info = gwas_study_info |> 
  mutate(collected_all_disease_terms = 
           stringr::str_replace_all(collected_all_disease_terms,
                            "autism symptom",
                            "autism")
         ) 


gwas_study_info = gwas_study_info |> 
  mutate(collected_all_disease_terms = 
           stringr::str_replace_all(collected_all_disease_terms,
                            "autism symptom",
                            "autism")
         ) 

4.1.9.4 Agoraphobia

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "agoraphobia symptom measurement",
                          "agoraphobia"
         ))

4.1.9.5 Alzheimer’s disease - neuropathological change

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "alzheimer disease neuropathological change",
                          "alzheimers disease"
         ))


gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "alzheimers disease neuropathologic change",
                          "alzheimers disease"
         ))

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "alzheimers disease biomarker",
                          "alzheimers disease"
         ))

4.1.9.6 Asthma

gwas_study_info = gwas_study_info |> 
  mutate(collected_all_disease_terms = 
           stringr::str_replace_all(collected_all_disease_terms,
                            "asthma symptoms",
                            "asthma"
           )) 

4.1.9.7 Covid-19

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "covid-19 symptoms",
                          "covid-19"
         ))

4.1.9.8 Irritable bowel syndrome

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "irritable bowel syndrome symptom",
                          "irritable bowel syndrome"
         ))

4.1.9.9 Multiple sclerosis

gwas_study_info = gwas_study_info |> 
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "multiple sclerosis symptom",
                          "multiple sclerosis"
         ))

4.1.9.10 Obsessive-compulsive disorder

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "obsessive-compulsive symptom",
                          "obsessive-compulsive disorder"
         ))

4.1.9.11 Parkinson’s disease

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "parkinsons disease symptom",
                          "parkinsons disease"
         ))

4.1.9.12 PTSD

gwas_study_info = gwas_study_info |> 
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "post-traumatic stress disorder symptom",
                          "post-traumatic stress disorder"
         ))

4.1.9.13 Respiratory symptom change

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "respiratory symptom change",
                          "respiratory symptom" 
         ))

4.1.10 Measurement

4.1.10.1 Anxiety

gwas_study_info = gwas_study_info |> 
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "anxiety measurement",
                          "anxiety"
         ))

4.1.10.2 Insomnia

gwas_study_info = gwas_study_info |> 
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "insomnia measurement",
                          "insomnia"
         ))

4.1.10.3 Lewy body dementia

gwas_study_info = gwas_study_info |> 
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "lewy body dementia measurement",
                          "lewy body dementia"
         ))

4.1.11 Substance abuse measurement

4.1.11.1 Cocaine

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "cocaine use disorder|cocaine dependence",
                          "cocaine-related disorders"
         ))

4.1.11.2 Nicotine

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "nicotine dependence symptom count",
                          "nicotine dependence"
         ))

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "nicotine withdrawal symptom count|nicotine withdrawal measurement",
                          "nicotine withdrawal"
         ))

4.2 Deal with basic synonyms

4.2.1 ADHD = attention deficit hyperactivity disorder

gwas_study_info = gwas_study_info |> 
    mutate(collected_all_disease_terms = 
           stringr::str_replace_all(collected_all_disease_terms,
                            "attention deficit hyperactivity disorder",
                            "adhd"
         ))

4.2.2 Anemia (phenotype) -> anemia

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms =
         stringr::str_replace_all(collected_all_disease_terms,
                          "anemia \\(phenotype\\)",
                          "anemia"
         ))

4.2.3 Autism = Autism Spectrum Disorder = Asperger Syndrome

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
        stringr::str_replace_all(collected_all_disease_terms,
                         "autism spectrum disorder",
                         "autism")
        ) |>
    mutate(collected_all_disease_terms = 
        stringr::str_replace_all(collected_all_disease_terms,
                         "asperger syndrome",
                         "autism")
        )

4.2.4 Carcinoma = Cancer

gwas_study_info = gwas_study_info |>
      mutate(collected_all_disease_terms = 
           stringr::str_replace_all(collected_all_disease_terms,
                            "\\bcarcinoma",
                            "cancer")
         )

4.2.5 Coronary artery disease = coronary atherosclerosis

https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001645

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "coronary atherosclerosis",
                          "coronary artery disease"
         ))

4.2.6 Head and neck cancer = head and neck malignant neoplasia

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "head and neck malignant neoplasia",
                          "head and neck cancer"
         ))

4.2.7 Hepatitis virus infection = hepatitis infection

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "hepatitis a virus infection",
                          "hepatitis a infection"
         )) |>
      mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "hepatitis b virus infection",
                          "hepatitis b infection"
         )) |>
        mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "hepatitis c virus infection",
                          "hepatitis c infection"
         ))

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "chronic hepatitis c virus infection",
                          "chronic hepatitis, hepatitis c infection"
         )) |>
      mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "chronic hepatitis b virus infection",
                          "chronic hepatitis, hepatitis b infection"
         ))

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "hepatitis virus-related liver cancer",
                          "hepatitis, liver cancer"
         ))

4.2.8 Narcolepsy = Narcolepsy without cataplexy

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "narcolepsy without cataplexy",
                          "narcolepsy"
         ))

4.2.9 Mumps virus infection = mumps

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "mumps virus infectious disease",
                          "mumps"
         ))

4.2.10 Renal cancer = kidney cancer

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "renal cancer",
                          "kidney cancer"
         ))

4.2.11 Rubella infect = rubella

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "rubella infection",
                          "rubella"
         ))

gwas_study_info = gwas_study_info |> 
    mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "multiple sclerosis symptom measurement",
                          "multiple sclerosis"
         ))  

4.2.12 Type 1 diabetes = type 1 diabetes mellitus

gwas_study_info = gwas_study_info |>
    mutate(collected_all_disease_terms = 
        stringr::str_replace_all(collected_all_disease_terms,
                         "type 1 diabetes(?=,|$)",
                         "type 1 diabetes mellitus")
        )

gwas_study_info = gwas_study_info |>
      mutate(collected_all_disease_terms = 
        stringr::str_replace_all(collected_all_disease_terms,
                         "type 1 diabetes(?=,|$)",
                         "type 1 diabetes mellitus")
        )

4.2.13 Type 1 diabetes mellitus nephropathy = type 1 diabetes nephropathy

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
        stringr::str_replace_all(collected_all_disease_terms,
                         "type 1 diabetes mellitus nephropathy",
                         "type 1 diabetes nephropathy")
        )

4.2.14 Von willebrand disease (hereditary or acquired) = von willebrand disease

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms =
         stringr::str_replace_all(collected_all_disease_terms,
                          "von willebrand disease \\(hereditary or acquired\\)",
                          "von willebrand disease"
         ))

4.3 Typos

4.3.1 Alzheimer -> alzheimers

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms =
         stringr::str_replace_all(collected_all_disease_terms,
                          "alzheimer disease",
                          "alzheimers disease"
         ))

4.3.2 Parkinson -> parkinsons

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms =
         stringr::str_replace_all(collected_all_disease_terms,
                          "parkinson disease",
                          "parkinsons disease"
         ))

5 Other

5.1 Decreased susceptibility to hepatitis c infection -> decreased hepatitis c -> hepatitis c

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          "decreased hepatitis c",
                          "hepatitis c"
         ))

6 Putting it all together

gwas_study_info = gwas_study_info |>
  rowwise() |>
  mutate(
    collected_all_disease_terms = paste0(
      unique(unlist(stringr::str_split(collected_all_disease_terms, ", "))),
      collapse = ", "
    )
  ) |>
  ungroup()

           
gwas_study_info$collected_all_disease_terms = stringr::str_trim(gwas_study_info$collected_all_disease_terms)
gwas_study_info$collected_all_disease_terms = sub(",$", "", gwas_study_info$collected_all_disease_terms)



gwas_study_info$collected_all_disease_terms = stringr::str_replace_all(gwas_study_info$collected_all_disease_terms, "^, ", "")

6.1 Final summary - number of studies per trait - after harmonization

n_studies_trait = gwas_study_info |>
  dplyr::filter(DISEASE_STUDY == T) |>
  dplyr::select(collected_all_disease_terms, PUBMED_ID) |>
  dplyr::distinct() |>
  dplyr::group_by(collected_all_disease_terms) |>
  dplyr::summarise(n_studies = dplyr::n()) |>
  dplyr::arrange(desc(n_studies))

head(n_studies_trait)

# A tibble: 6 × 2
  collected_all_disease_terms n_studies
  <chr>                           <int>
1 type 2 diabetes mellitus          145
2 alzheimers disease                116
3 breast cancer                     112
4 asthma                            110
5 major depressive disorder         108
6 schizophrenia                     103

dim(n_studies_trait)

[1] 3065    2

6.2 Number of unique disease terms after harmonization

diseases <- stringr::str_split(pattern = ", ", 
                               gwas_study_info$collected_all_disease_terms[gwas_study_info$collected_all_disease_terms != ""])  |> 
            unlist() |>
            stringr::str_trim()

length(unique(diseases))

[1] 2194

6.3 Frequency of unique disease terms after harmonization

# make frequency table
freq <- table(as.factor(diseases))

# sort in decreasing order
freq_sorted <- sort(freq, decreasing = TRUE)

# show top N, e.g. top 10
head(freq_sorted, 10)

   chronic kidney disease              hypertension  type 2 diabetes mellitus 
                    10828                      6991                       922 
major depressive disorder   coronary artery disease        alzheimers disease 
                      471                       456                       406 
            schizophrenia                  covid-19                    asthma 
                      356                       305                       283 
            breast cancer 
                      270 

6.4 Save the updated gwas_study_info with repaired / harmonized disease terms

fwrite(gwas_study_info,
here::here("output/gwas_cat/gwas_study_info_disease_trait_simplified.csv"))

Session information

sessionInfo()

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.6.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] stringr_1.5.1     data.table_1.17.8 dplyr_1.1.4       workflowr_1.7.1  

loaded via a namespace (and not attached):
 [1] jsonlite_2.0.0    compiler_4.3.1    renv_1.0.3        promises_1.3.3   
 [5] tidyselect_1.2.1  Rcpp_1.1.0        git2r_0.36.2      callr_3.7.6      
 [9] later_1.4.2       jquerylib_0.1.4   yaml_2.3.10       fastmap_1.2.0    
[13] here_1.0.1        R6_2.6.1          generics_0.1.4    knitr_1.50       
[17] tibble_3.3.0      rprojroot_2.1.0   bslib_0.9.0       pillar_1.11.0    
[21] rlang_1.1.6       utf8_1.2.6        cachem_1.1.0      stringi_1.8.7    
[25] httpuv_1.6.16     xfun_0.52         getPass_0.2-4     fs_1.6.6         
[29] sass_0.4.10       cli_3.6.5         withr_3.0.2       magrittr_2.0.3   
[33] ps_1.9.1          digest_0.6.37     processx_3.8.6    rstudioapi_0.17.1
[37] lifecycle_1.0.4   vctrs_0.6.5       evaluate_1.0.4    glue_1.8.0       
[41] whisker_0.4.1     rmarkdown_2.29    httr_1.4.7        tools_4.3.1      
[45] pkgconfig_2.0.3   htmltools_0.5.8.1