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92 lines
2.5 KiB
R
Executable File
92 lines
2.5 KiB
R
Executable File
## ----setup, include = FALSE, results = 'markup'--------------------------
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knitr::opts_chunk$set(
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collapse = TRUE,
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comment = "#"
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)
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library(dplyr)
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library(AMR)
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## ---- echo = TRUE, results = 'hide'--------------------------------------
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# # just using base R
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freq(septic_patients$sex)
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# # using base R to select the variable and pass it on with a pipe
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septic_patients$sex %>% freq()
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# # do it all with pipes, using the `select` function of the dplyr package
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septic_patients %>%
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select(sex) %>%
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freq()
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## ---- echo = TRUE--------------------------------------------------------
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freq(septic_patients$sex)
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## ---- echo = TRUE, results = 'hide'--------------------------------------
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my_patients <- septic_patients %>%
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left_join_microorganisms()
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## ---- echo = TRUE--------------------------------------------------------
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colnames(microorganisms)
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## ---- echo = TRUE--------------------------------------------------------
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dim(septic_patients)
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dim(my_patients)
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## ---- echo = TRUE--------------------------------------------------------
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my_patients %>%
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select(genus, species) %>%
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freq()
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## ---- echo = TRUE--------------------------------------------------------
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# # get age distribution of unique patients
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septic_patients %>%
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distinct(patient_id, .keep_all = TRUE) %>%
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select(age) %>%
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freq(nmax = 5)
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## ---- echo = TRUE--------------------------------------------------------
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septic_patients %>%
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select(hospital_id) %>%
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freq()
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## ---- echo = TRUE--------------------------------------------------------
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septic_patients %>%
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select(hospital_id) %>%
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freq(sort.count = TRUE)
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## ---- echo = TRUE--------------------------------------------------------
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septic_patients %>%
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select(amox) %>%
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freq()
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## ---- echo = TRUE--------------------------------------------------------
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septic_patients %>%
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select(date) %>%
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freq(nmax = 5)
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## ---- echo = TRUE--------------------------------------------------------
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septic_patients %>%
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select(amox) %>%
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freq(na.rm = FALSE)
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## ---- echo = TRUE--------------------------------------------------------
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septic_patients %>%
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select(hospital_id) %>%
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freq(markdown = TRUE)
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## ---- echo = TRUE--------------------------------------------------------
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my_df <- septic_patients %>%
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select(hospital_id) %>%
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freq(as.data.frame = TRUE)
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my_df
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class(my_df)
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## ---- echo = FALSE-------------------------------------------------------
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# this will print "2018" in 2018, and "2018-yyyy" after 2018.
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yrs <- c(2018:format(Sys.Date(), "%Y"))
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yrs <- c(min(yrs), max(yrs))
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yrs <- paste(unique(yrs), collapse = "-")
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