Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.height = 4,
fig.width = 7
)
## ----pkgs, message = FALSE, warning=FALSE-------------------------------------
library(epocakir)
library(dplyr)
library(units)
## ----clinical_data------------------------------------------------------------
# Example workflow: clinical_obvs <- read.csv("cohort.csv")
glimpse(clinical_obvs)
tidy_obvs <- clinical_obvs %>%
combine_date_time_cols() %>%
mutate(
Age = dob2age(`Date of Birth`),
Height = as_metric(height = set_units(as.numeric(Height), "cm"))
) %>%
binary2factor(Male, Surgery)
glimpse(tidy_obvs)
## ----aki----------------------------------------------------------------------
# Example workflow: aki_pt_data <- read.csv("aki.csv")
head(aki_pt_data)
aki_staging(aki_pt_data,
SCr = "SCr_", bCr = "bCr_", UO = "UO_",
dttm = "dttm_", pt_id = "pt_id_"
)
aki_pt_data %>%
mutate(aki = aki_staging(
SCr = SCr_, bCr = bCr_, UO = UO_,
dttm = dttm_, pt_id = pt_id_
)) %>%
select(pt_id_, SCr_:dttm_, aki)
aki_pt_data %>%
mutate(aki = aki_SCr(
SCr = SCr_, dttm = dttm_, pt_id = pt_id_
)) %>%
select(pt_id_, SCr_:dttm_, aki)
## ----eGFR---------------------------------------------------------------------
# Example workflow: aki_pt_data <- read.csv("aki.csv")
head(eGFR_pt_data)
eGFR(eGFR_pt_data,
SCr = "SCr_", SCysC = "SCysC_",
Age = "Age_", height = "height_", BUN = "BUN_",
male = "male_", black = "black_", pediatric = "pediatric_"
)
eGFR_pt_data %>%
dplyr::mutate(eGFR = eGFR(
SCr = SCr_, SCysC = SCysC_,
Age = Age_, height = height_, BUN = BUN_,
male = male_, black = black_, pediatric = pediatric_
)) %>%
select(SCr_:pediatric_, eGFR)
eGFR_pt_data %>%
dplyr::mutate(eGFR = eGFR_adult_SCr(
SCr = SCr_, Age = Age_, male = male_, black = black_
)) %>%
select(SCr_:pediatric_, eGFR)
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