Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(admiraldev)
## ----message=FALSE------------------------------------------------------------
library(admiral)
library(pharmaversesdtm)
library(dplyr, warn.conflicts = FALSE)
library(stringr)
library(tibble)
data("lb")
adsl <- admiral_adsl
lb <- convert_blanks_to_na(lb)
## ----echo=FALSE---------------------------------------------------------------
lb <- filter(lb, USUBJID %in% c("01-701-1115", "01-705-1186", "01-705-1349", "01-708-1286", "01-707-1037", "01-716-1024"))
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv4 %>%
filter(!is.na(TERM)) %>%
dataset_vignette(
display_vars = exprs(TERM)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv5 %>%
filter(!is.na(TERM)) %>%
dataset_vignette(
display_vars = exprs(TERM)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_daids %>%
filter(!is.na(TERM)) %>%
distinct(TERM) %>%
dataset_vignette(
display_vars = exprs(TERM)
)
## ---- eval=TRUE---------------------------------------------------------------
# Look-up tables ----
# Assign PARAMCD, PARAM, and PARAMN
param_lookup <- tibble::tribble(
~LBTESTCD, ~PARAMCD, ~PARAM, ~PARAMN,
"ALB", "ALB", "Albumin (g/L)", 1,
"ALP", "ALKPH", "Alkaline Phosphatase (U/L)", 2,
"ALT", "ALT", "Alanine Aminotransferase (U/L)", 3,
"ANISO", "ANISO", "Anisocytes", 4,
"AST", "AST", "Aspartate Aminotransferase (U/L)", 5,
"BASO", "BASO", "Basophils (10^9/L)", 6,
"BASOLE", "BASOLE", "Basophils/Leukocytes (FRACTION)", 7,
"BILI", "BILI", "Bilirubin (umol/L)", 8,
"BUN", "BUN", "Blood Urea Nitrogen (mmol/L)", 9,
"CA", "CA", "Calcium (mmol/L)", 10,
"CHOL", "CHOLES", "Cholesterol (mmol/L)", 11,
"CK", "CK", "Creatinine Kinase (U/L)", 12,
"CL", "CL", "Chloride (mmol/L)", 13,
"COLOR", "COLOR", "Color", 14,
"CREAT", "CREAT", "Creatinine (umol/L)", 15,
"EOS", "EOS", "Eosinophils (10^9/L)", 16,
"EOSLE", "EOSLE", "Eosinophils/Leukocytes (FRACTION)", 17,
"GGT", "GGT", "Gamma Glutamyl Transferase (U/L)", 18,
"GLUC", "GLUC", "Glucose (mmol/L)", 19,
"HBA1C", "HBA1C", "Hemoglobin A1C (1)", 20,
"HCT", "HCT", "Hematocrit (1)", 21,
"HGB", "HGB", "Hemoglobin (mmol/L)", 22,
"K", "POTAS", "Potassium (mmol/L)", 23,
"KETONES", "KETON", "Ketones", 24,
"LYM", "LYMPH", "Lymphocytes (10^9/L)", 25,
"LYMLE", "LYMPHLE", "Lymphocytes/Leukocytes (FRACTION)", 26,
"MACROCY", "MACROC", "Macrocytes", 27,
"MCH", "MCH", "Ery. Mean Corpuscular Hemoglobin (fmol(Fe))", 28,
"MCHC", "MCHC", "Ery. Mean Corpuscular HGB Concentration (mmol/L)", 29,
"MCV", "MCV", "Ery. Mean Corpuscular Volume (f/L)", 30,
"MICROCY", "MICROC", "Microcytes", 31,
"MONO", "MONO", "Monocytes (10^9/L)", 32,
"MONOLE", "MONOLE", "Monocytes/Leukocytes (FRACTION)", 33,
"PH", "PH", "pH", 34,
"PHOS", "PHOS", "Phosphate (mmol/L)", 35,
"PLAT", "PLAT", "Platelet (10^9/L)", 36,
"POIKILO", "POIKIL", "Poikilocytes", 37,
"POLYCHR", "POLYCH", "Polychromasia", 38,
"PROT", "PROT", "Protein (g/L)", 39,
"RBC", "RBC", "Erythrocytes (TI/L)", 40,
"SODIUM", "SODIUM", "Sodium (mmol/L)", 41,
"SPGRAV", "SPGRAV", "Specific Gravity", 42,
"TSH", "TSH", "Thyrotropin (mU/L)", 43,
"URATE", "URATE", "Urate (umol/L)", 44,
"UROBIL", "UROBIL", "Urobilinogen", 45,
"VITB12", "VITB12", "Vitamin B12 (pmol/L)", 46,
"WBC", "WBC", "Leukocytes (10^9/L)", 47
)
adlb <- lb %>%
## Add PARAMCD PARAM and PARAMN - from LOOK-UP table
derive_vars_merged_lookup(
dataset_add = param_lookup,
new_vars = exprs(PARAMCD, PARAM, PARAMN),
by_vars = exprs(LBTESTCD)
) %>%
## Calculate PARCAT1 AVAL AVALC ANRLO ANRHI
## Dummy the values for BASE
mutate(
PARCAT1 = LBCAT,
AVAL = LBSTRESN,
AVALC = LBSTRESC,
ANRLO = LBSTNRLO,
ANRHI = LBSTNRHI,
BASE = AVAL - 10
)
## ---- eval=TRUE---------------------------------------------------------------
# Assign ATOXDSCL and ATOXDSCH to hold lab grading terms
# ATOXDSCL and ATOXDSCH hold terms defined by NCI-CTCAEv4.
grade_lookup <- tibble::tribble(
~PARAMCD, ~ATOXDSCL, ~ATOXDSCH,
"ALB", "Hypoalbuminemia", NA_character_,
"ALKPH", NA_character_, "Alkaline phosphatase increased",
"ALT", NA_character_, "Alanine aminotransferase increased",
"AST", NA_character_, "Aspartate aminotransferase increased",
"BILI", NA_character_, "Blood bilirubin increased",
"CA", "Hypocalcemia", "Hypercalcemia",
"CHOLES", NA_character_, "Cholesterol high",
"CK", NA_character_, "CPK increased",
"CREAT", NA_character_, "Creatinine increased",
"GGT", NA_character_, "GGT increased",
"GLUC", "Hypoglycemia", "Hyperglycemia",
"HGB", "Anemia", "Hemoglobin increased",
"POTAS", "Hypokalemia", "Hyperkalemia",
"LYMPH", "CD4 lymphocytes decreased", NA_character_,
"PHOS", "Hypophosphatemia", NA_character_,
"PLAT", "Platelet count decreased", NA_character_,
"SODIUM", "Hyponatremia", "Hypernatremia",
"WBC", "White blood cell decreased", "Leukocytosis",
)
adlb <- adlb %>%
derive_vars_merged(
dataset_add = grade_lookup,
by_vars = exprs(PARAMCD),
)
## ---- eval=TRUE---------------------------------------------------------------
adlb <- adlb %>%
derive_var_atoxgr_dir(
new_var = ATOXGRL,
tox_description_var = ATOXDSCL,
meta_criteria = atoxgr_criteria_ctcv4,
criteria_direction = "L",
get_unit_expr = extract_unit(PARAM)
) %>%
derive_var_atoxgr_dir(
new_var = ATOXGRH,
tox_description_var = ATOXDSCH,
meta_criteria = atoxgr_criteria_ctcv4,
criteria_direction = "H",
get_unit_expr = extract_unit(PARAM)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv4 %>%
filter(!is.na(SI_UNIT_CHECK)) %>%
dataset_vignette(
display_vars = exprs(TERM, SI_UNIT_CHECK),
)
## ---- eval=TRUE---------------------------------------------------------------
adlb <- adlb %>%
derive_var_atoxgr()
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
adlb %>%
filter((ATOXGRL == "1") | (ATOXGRH == "1")) %>%
dataset_vignette(
display_vars = exprs(ATOXDSCL, ATOXDSCH, ATOXGRL, ATOXGRH, ATOXGR)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv4 %>%
filter(str_detect(TERM, "calcemia")) %>%
dataset_vignette(
display_vars = exprs(TERM, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv4 %>%
filter(str_detect(TERM, "glycemia")) %>%
dataset_vignette(
display_vars = exprs(TERM, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv4 %>%
filter(str_detect(TERM, "INR")) %>%
dataset_vignette(
display_vars = exprs(TERM, Grade_1)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv4 %>%
filter(str_detect(TERM, "INR")) %>%
dataset_vignette(
display_vars = exprs(TERM, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv4 %>%
filter(str_detect(TERM, "Hyperuricemia")) %>%
dataset_vignette(
display_vars = exprs(TERM, Grade_1, Grade_3, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv4 %>%
filter(str_detect(TERM, "Hypokalemia")) %>%
dataset_vignette(
display_vars = exprs(TERM, Grade_1, Grade_2, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv5 %>%
filter(str_detect(TERM, "calcemia")) %>%
dataset_vignette(
display_vars = exprs(TERM, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv5 %>%
filter(str_detect(TERM, "INR")) %>%
dataset_vignette(
display_vars = exprs(TERM, Grade_1)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv5 %>%
filter(str_detect(TERM, "INR")) %>%
dataset_vignette(
display_vars = exprs(TERM, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv5 %>%
filter(str_detect(TERM, "Lipase") | str_detect(TERM, "amylase")) %>%
dataset_vignette(
display_vars = exprs(TERM, Grade_2, Grade_3, Grade_4)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv5 %>%
filter(str_detect(TERM, "INR") | str_detect(TERM, "amylase")) %>%
dataset_vignette(
display_vars = exprs(TERM, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv5 %>%
filter(str_detect(TERM, "Hyperuricemia")) %>%
dataset_vignette(
display_vars = exprs(TERM, Grade_1, Grade_3, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_ctcv5 %>%
filter(str_detect(TERM, "Hypokalemia") | str_detect(TERM, "Hyponatremia")) %>%
dataset_vignette(
display_vars = exprs(TERM, Grade_1, Grade_2, Grade_3, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_daids %>%
filter(str_detect(TERM, "Cholesterol")) %>%
dataset_vignette(
display_vars = exprs(TERM, FILTER)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_daids %>%
filter(str_detect(COMMENT, "No criteria given")) %>%
dataset_vignette(
display_vars = exprs(TERM, FILTER, GRADE_CRITERIA_CODE)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_daids %>%
filter(TERM %in% c("INR, High", "PT, High", "PTT, High")) %>%
dataset_vignette(
display_vars = exprs(TERM, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_daids %>%
filter(str_detect(COMMENT, "HIV infected")) %>%
dataset_vignette(
display_vars = exprs(TERM, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_daids %>%
filter(str_detect(COMMENT, "lifethreatening")) %>%
dataset_vignette(
display_vars = exprs(TERM, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_daids %>%
filter(str_detect(TERM, "Lactate")) %>%
dataset_vignette(
display_vars = exprs(TERM, Grade_1, Grade_1)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_daids %>%
filter(str_detect(TERM, "Lactate")) %>%
dataset_vignette(
display_vars = exprs(TERM, COMMENT)
)
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
atoxgr_criteria_daids %>%
filter(str_detect(COMMENT, "conver")) %>%
dataset_vignette(
display_vars = exprs(TERM, FILTER, COMMENT)
)
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