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library(dplyr)
library(data.table)
library(ggplot2)
library(stringr)source(here::here("code/get_term_descendants.R"))gwas_study_info <- fread(here::here("output/gwas_cat/gwas_study_info_group_l1_v2.csv"))gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms = l1_all_disease_terms)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "acne",
"acne vulgaris"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "adhd",
"attention-deficit/hyperactivity disorder"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "alcohol-related disorders|alcohol and nicotine codependence",
"alcohol use disorders"
)
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "alcohol use disorder",
"alcohol use disorders"
)
)dementia <- c("alzheimers disease biomarker measurement",
"alzheimers disease neuropathologic change",
"aids dementia",
"dementia",
"frontotemporal dementia",
"lewy body dementia",
"vascular dementia",
"alzheimers disease"
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(dementia, collapse = "(?=,|$)|\\b"),
"alzheimer's disease and other dementias"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mesh/terms/http%253A%252F%252Fid.nlm.nih.gov%252Fmesh%252FD001008/descendants"
anxiety_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 15
[1] "\n Some example terms"
[1] "obsessive-compulsive disorder" "generalized anxiety disorder"
[3] "neurocirculatory asthenia" "excoriation disorder"
[5] "anxiety, separation" anxiety_terms <- c(anxiety_terms, "obsessive-compulsive symptom measurement")
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(anxiety_terms, collapse = "(?=,|$)|\\b"),
"anxiety disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "anxiety disorder|anxiety measurement",
"anxiety disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "anxiety",
"anxiety disorders"
)
)afib_terms <- c("atrial fibrillation",
"atrial flutter",
"post-operative atrial fibrillation")
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(afib_terms, collapse = "(?=,|$)|\\b"),
"atrial fibrillation and flutter"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "methamphetamine",
"amphetamine"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/cvdo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_3627/descendants"
aortic_aneurysm_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 6
[1] "\n Some example terms"
[1] "ruptured thoracoabdominal aortic aneurysm"
[2] "ruptured abdominal aortic aneurysm"
[3] "ruptured thoracic aortic aneurysm"
[4] "abdominal aortic aneurysm"
[5] "ruptured aortic aneurysm" gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(aortic_aneurysm_terms, collapse = "(?=,|$)|\\b"),
"aortic aneurysm"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "autism",
"autism spectrum disorders"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "blindness|color vision disorder|vision disorder|myopia|refractive error|hyperopia|astigmatism|corneal astigmatism|presbyopia|anisometropia|esotropia|on-accomodative esotropia|ccommodative esotropia",
"blindness and vision loss"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "cannabis dependence",
"cannabis use disorders"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "urinary bladder cancer, disease progression measurement|b;adder tumor",
"bladder cancer"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "colorectal cancer",
"colon and rectum cancer"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "ocular melanoma|ocular cancer",
"eye cancer"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "hodgkins lymphoma",
"hodgkin lymphoma"
)
)skin_melanoma <- c("cutaneous melanoma",
"melanoma")gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "non-hodgkins lymphoma",
"non-hodgkin lymphoma"
)
)resp_cancer_terms = c("lung cancer",
"bronchus cancer",
"respiratory system cancer"
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(resp_cancer_terms, collapse = "(?=,|$)|\\b"),
"tracheal bronchus and lung cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F328383001/descendants"
chronic_liver_disease_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 114
[1] "\n Some example terms"
[1] "hepatic ascites co-occurrent with chronic active hepatitis due to toxic liver disease"
[2] "cirrhosis of liver co-occurrent and due to primary sclerosing cholangitis (disorder)"
[3] "chronic hepatitis c co-occurrent with human immunodeficiency virus infection"
[4] "primary biliary cirrhosis co-occurrent with systemic scleroderma (disorder)"
[5] "pulmonary fibrosis, hepatic hyperplasia, bone marrow hypoplasia syndrome" chronic_liver_disease_terms <- c("primary biliary cirrhosis",
"alcoholic liver cirrhosis",
"chronic hepatitis B virus infection",
"acute-on-chronic liver failure",
chronic_liver_disease_terms)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(chronic_liver_disease_terms, collapse = "(?=,|$)|\\b"),
"cirrhosis and other chronic liver diseases"
)
)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "liver disease",
"cirrhosis and other chronic liver diseases"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "cocaine-related disorders",
"cocaine use disorders"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "depressive symptom measurement|major depressive disorder",
"depressive disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "depressive disorder",
"depressive disorders"
)
)gal_bile_terms = c("gallbladder disease",
"bile duct disorder",
"biliary tract disease")
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(gal_bile_terms, collapse = "(?=,|$)|\\b"),
"gallbladder and biliary diseases"
)
)diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l2_all_disease_terms) |>
unlist() |>
stringr::str_trim()
pregnancy_terms <- grep("pregnancy", diseases, value = T)
gyno_terms <- c("endometriosis","placenta disease", pregnancy_terms)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(gyno_terms, collapse = "(?=,|$)|\\b"),
"gynecological diseases"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "bulimia nervosa|anorexia nervosa|binge eating|eating disorder",
"eating disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "anorexia",
"eating disorders"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "headache disorder|cluster headache|migraine",
"headache disorders"
)
)== coronary artery disease (https://www.ncbi.nlm.nih.gov/books/NBK209964/)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "coronary artery disease",
"ischemic heart disease"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "opioid dependence|opioid use disorder",
"opioid use disorders"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "parkinsons disease",
"parkinson's disease"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0002028/descendants"
personality_disorders <- get_descendants(url)[1] "Number of terms collected:"
[1] 10
[1] "\n Some example terms"
[1] "obsessive-compulsive personality disorder"
[2] "narcissistic personality disorder"
[3] "schizotypal personality disorder"
[4] "histrionic personality disorder"
[5] "antisocial personality disorder" gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(personality_disorders, collapse = "(?=,|$)|\\b"),
"personality disorders"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "heroin dependence|drug dependence|nictone dependence|substance abuse|drug misuse|alcohol use disorders delirium",
"other drug use disorders"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_535/descendants"
sleep_disorders <- get_descendants(url)[1] "Number of terms collected:"
[1] 16
[1] "\n Some example terms"
[1] "periodic limb movement disorder" "advanced sleep phase syndrome 3"
[3] "advanced sleep phase syndrome 2" "advanced sleep phase syndrome 1"
[5] "advanced sleep phase syndrome 4"url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0008568/descendants"
other_sleep_disorders <- get_descendants(url)[1] "Number of terms collected:"
[1] 26
[1] "\n Some example terms"
[1] "autosomal dominant cerebellar ataxia, deafness and narcolepsy"
[2] "hereditary sensory neuropathy-deafness-dementia syndrome"
[3] "rapid eye movement sleep disorder"
[4] "substance-induced sleep disorder"
[5] "drug induced central sleep apnea" sleep_disorders <- c(sleep_disorders,
other_sleep_disorders)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(sleep_disorders, collapse = "(?=,|$)|\\b"),
"sleep disorders"
)
)and remove alz, parks, dementia
other_mental_disorders <- c("schizophrenia",
"manic or hypomanic episode",
"mental or behavioural disorder",
"mental disorder"
)other_neuro <- c("mild neurocognitive disorder",
"hiv-associated neurocognitive disorder")disturbances of sensation of smell and taste
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "disorderss",
"disorders"
)
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "anxiety disorders disorderss",
"anxiety disorders"
)
)gbd_data <- data.table::fread(here::here("data/gbd/ihme_gbd_2019_global_disease_burden_rate_all_ages.csv"))
gbd_data$cause <- stringr::str_remove_all(gbd_data$cause, ",")
diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l2_all_disease_terms[gwas_study_info$l2_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
gbd_data$cause[!tolower(gbd_data$cause) %in% unique(diseases)] |> sort() [1] "Acute glomerulonephritis"
[2] "Acute glomerulonephritis"
[3] "Acute glomerulonephritis"
[4] "Bacterial skin diseases"
[5] "Bacterial skin diseases"
[6] "Bacterial skin diseases"
[7] "Bladder cancer"
[8] "Bladder cancer"
[9] "Bladder cancer"
[10] "Brain and central nervous system cancer"
[11] "Brain and central nervous system cancer"
[12] "Brain and central nervous system cancer"
[13] "Cardiomyopathy and myocarditis"
[14] "Cardiomyopathy and myocarditis"
[15] "Cardiomyopathy and myocarditis"
[16] "Congenital birth defects"
[17] "Congenital birth defects"
[18] "Congenital birth defects"
[19] "Diabetes mellitus type 1"
[20] "Diabetes mellitus type 1"
[21] "Diabetes mellitus type 1"
[22] "Diabetes mellitus type 2"
[23] "Diabetes mellitus type 2"
[24] "Diabetes mellitus type 2"
[25] "Drug use disorders"
[26] "Drug use disorders"
[27] "Drug use disorders"
[28] "Endocrine metabolic blood and immune disorders"
[29] "Endocrine metabolic blood and immune disorders"
[30] "Endocrine metabolic blood and immune disorders"
[31] "Fungal skin diseases"
[32] "Fungal skin diseases"
[33] "Fungal skin diseases"
[34] "Gallbladder and biliary tract cancer"
[35] "Gallbladder and biliary tract cancer"
[36] "Gallbladder and biliary tract cancer"
[37] "Hemoglobinopathies and hemolytic anemias"
[38] "Hemoglobinopathies and hemolytic anemias"
[39] "Hemoglobinopathies and hemolytic anemias"
[40] "Idiopathic developmental intellectual disability"
[41] "Idiopathic developmental intellectual disability"
[42] "Idiopathic epilepsy"
[43] "Idiopathic epilepsy"
[44] "Idiopathic epilepsy"
[45] "Inguinal femoral and abdominal hernia"
[46] "Inguinal femoral and abdominal hernia"
[47] "Inguinal femoral and abdominal hernia"
[48] "Interstitial lung disease and pulmonary sarcoidosis"
[49] "Interstitial lung disease and pulmonary sarcoidosis"
[50] "Interstitial lung disease and pulmonary sarcoidosis"
[51] "Lower extremity peripheral arterial disease"
[52] "Lower extremity peripheral arterial disease"
[53] "Lower extremity peripheral arterial disease"
[54] "Malignant neoplasm of bone and articular cartilage"
[55] "Malignant neoplasm of bone and articular cartilage"
[56] "Malignant neoplasm of bone and articular cartilage"
[57] "Malignant skin melanoma"
[58] "Malignant skin melanoma"
[59] "Malignant skin melanoma"
[60] "Nasopharynx cancer"
[61] "Nasopharynx cancer"
[62] "Nasopharynx cancer"
[63] "Neuroblastoma and other peripheral nervous cell tumors"
[64] "Neuroblastoma and other peripheral nervous cell tumors"
[65] "Neuroblastoma and other peripheral nervous cell tumors"
[66] "Non-rheumatic valvular heart disease"
[67] "Non-rheumatic valvular heart disease"
[68] "Non-rheumatic valvular heart disease"
[69] "Oral disorders"
[70] "Oral disorders"
[71] "Oral disorders"
[72] "Other cardiovascular and circulatory diseases"
[73] "Other cardiovascular and circulatory diseases"
[74] "Other chronic respiratory diseases"
[75] "Other digestive diseases"
[76] "Other malignant neoplasms"
[77] "Other malignant neoplasms"
[78] "Other malignant neoplasms"
[79] "Other mental disorders"
[80] "Other mental disorders"
[81] "Other mental disorders"
[82] "Other musculoskeletal disorders"
[83] "Other musculoskeletal disorders"
[84] "Other neoplasms"
[85] "Other neoplasms"
[86] "Other neoplasms"
[87] "Other neurological disorders"
[88] "Other neurological disorders"
[89] "Other neurological disorders"
[90] "Other sense organ diseases"
[91] "Other sense organ diseases"
[92] "Other sense organ diseases"
[93] "Other skin and subcutaneous diseases"
[94] "Other skin and subcutaneous diseases"
[95] "Other skin and subcutaneous diseases"
[96] "Paralytic ileus and intestinal obstruction"
[97] "Paralytic ileus and intestinal obstruction"
[98] "Paralytic ileus and intestinal obstruction"
[99] "Pulmonary Arterial Hypertension"
[100] "Pulmonary Arterial Hypertension"
[101] "Pulmonary Arterial Hypertension"
[102] "Scabies"
[103] "Scabies"
[104] "Scabies"
[105] "Soft tissue and other extraosseous sarcomas"
[106] "Soft tissue and other extraosseous sarcomas"
[107] "Soft tissue and other extraosseous sarcomas"
[108] "Sudden infant death syndrome"
[109] "Total burden related to Non-alcoholic fatty liver disease (NAFLD)"
[110] "Total burden related to Non-alcoholic fatty liver disease (NAFLD)"
[111] "Total burden related to Non-alcoholic fatty liver disease (NAFLD)"
[112] "Upper digestive system diseases"
[113] "Upper digestive system diseases"
[114] "Upper digestive system diseases"
[115] "Urinary diseases and male infertility"
[116] "Urinary diseases and male infertility"
[117] "Urinary diseases and male infertility"
[118] "Vascular intestinal disorders"
[119] "Vascular intestinal disorders"
[120] "Vascular intestinal disorders"
[121] "Viral skin diseases"
[122] "Viral skin diseases"
[123] "Viral skin diseases" gbd_data =
gbd_data |>
mutate(cause = tolower(cause))
gwas_disease_traits = data.frame(cause = diseases)
# gwas_study_info |>
# filter(DISEASE_STUDY == T) |>
# select(all_disease_terms, l1_all_disease_terms, cause = l2_all_disease_terms) |>
# distinct()
left_join(gwas_disease_traits,
gbd_data) |>
head()Joining with `by = join_by(cause)`Warning in left_join(gwas_disease_traits, gbd_data): Detected an unexpected many-to-many relationship between `x` and `y`.
ℹ Row 3 of `x` matches multiple rows in `y`.
ℹ Row 19 of `y` matches multiple rows in `x`.
ℹ If a many-to-many relationship is expected, set `relationship =
"many-to-many"` to silence this warning. cause measure
1 idiopathic cardiomyopathy <NA>
2 cleft lip <NA>
3 tracheal bronchus and lung cancer DALYs (Disability-Adjusted Life Years)
4 tracheal bronchus and lung cancer Prevalence
5 tracheal bronchus and lung cancer Incidence
6 tracheal bronchus and lung cancer DALYs (Disability-Adjusted Life Years)
location sex age metric year val upper lower
1 <NA> <NA> <NA> <NA> NA NA NA NA
2 <NA> <NA> <NA> <NA> NA NA NA NA
3 Global Both All ages Rate 2019 580.36100 627.79984 532.74652
4 Global Both All ages Rate 2019 40.27440 43.51721 37.12978
5 Global Both All ages Rate 2019 28.16826 30.49575 25.77712
6 Global Both All ages Rate 2019 580.36100 627.79984 532.74652gwas_study_info |> select(cause = l2_all_disease_terms) |>
distinct() |>
left_join(gbd_data) |>
head()Joining with `by = join_by(cause)` cause measure
<char> <char>
1: <NA>
2: idiopathic cardiomyopathy <NA>
3: cleft lip <NA>
4: tracheal bronchus and lung cancer DALYs (Disability-Adjusted Life Years)
5: tracheal bronchus and lung cancer Prevalence
6: tracheal bronchus and lung cancer Incidence
location sex age metric year val upper lower
<char> <char> <char> <char> <int> <num> <num> <num>
1: <NA> <NA> <NA> <NA> NA NA NA NA
2: <NA> <NA> <NA> <NA> NA NA NA NA
3: <NA> <NA> <NA> <NA> NA NA NA NA
4: Global Both All ages Rate 2019 580.36100 627.79984 532.74652
5: Global Both All ages Rate 2019 40.27440 43.51721 37.12978
6: Global Both All ages Rate 2019 28.16826 30.49575 25.77712diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l2_all_disease_terms[gwas_study_info$l2_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))[1] 1748# 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
10835 7089
type 2 diabetes mellitus depressive disorders
922 513
alzheimer's disease and other dementias ischemic heart disease
509 501
benign neoplasm schizophrenia
434 368
breast cancer asthma
355 348 gwas_study_info <- fwrite(gwas_study_info,
here::here("output/gwas_cat/gwas_study_info_trait_group_l2.csv"))
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] jsonlite_2.0.0 httr_1.4.7 stringr_1.5.1 ggplot2_3.5.2
[5] data.table_1.17.8 dplyr_1.1.4 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] gtable_0.3.6 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 scales_1.4.0 yaml_2.3.10
[13] fastmap_1.2.0 here_1.0.1 R6_2.6.1 generics_0.1.4
[17] curl_6.4.0 knitr_1.50 tibble_3.3.0 rprojroot_2.1.0
[21] RColorBrewer_1.1-3 bslib_0.9.0 pillar_1.11.0 rlang_1.1.6
[25] cachem_1.1.0 stringi_1.8.7 httpuv_1.6.16 xfun_0.52
[29] getPass_0.2-4 fs_1.6.6 sass_0.4.10 cli_3.6.5
[33] withr_3.0.2 magrittr_2.0.3 ps_1.9.1 grid_4.3.1
[37] digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1 lifecycle_1.0.4
[41] vctrs_0.6.5 evaluate_1.0.4 glue_1.8.0 farver_2.1.2
[45] whisker_0.4.1 rmarkdown_2.29 tools_4.3.1 pkgconfig_2.0.3
[49] htmltools_0.5.8.1