addins and small improvements to microorganisms dataset

vignettes/freq.R

@@ -0,0 +1,89 @@
+## ----setup, include = FALSE, results = 'markup'--------------------------
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#"
+)
+library(dplyr)
+library(AMR)
+
+## ---- echo = TRUE, results = 'hide'--------------------------------------
+# just using base R
+freq(septic_patients$sex)
+
+# using base R to select the variable and pass it on with a pipe from the dplyr package
+septic_patients$sex %>% freq()
+
+# do it all with pipes, using the `select` function from the dplyr package
+septic_patients %>%
+  select(sex) %>%
+  freq()
+
+# or the preferred way: using a pipe to pass the variable on to the freq function
+septic_patients %>% freq(sex) # this also shows 'age' in the title
+
+
+## ---- echo = TRUE--------------------------------------------------------
+freq(septic_patients$sex)
+
+## ---- echo = TRUE, results = 'hide'--------------------------------------
+my_patients <- septic_patients %>% left_join_microorganisms()
+
+## ---- echo = TRUE--------------------------------------------------------
+colnames(microorganisms)
+
+## ---- echo = TRUE--------------------------------------------------------
+dim(septic_patients)
+dim(my_patients)
+
+## ---- echo = TRUE--------------------------------------------------------
+my_patients %>% freq(genus, species)
+
+## ---- echo = TRUE--------------------------------------------------------
+# # get age distribution of unique patients
+septic_patients %>% 
+  distinct(patient_id, .keep_all = TRUE) %>% 
+  freq(age, nmax = 5)
+
+## ---- echo = TRUE--------------------------------------------------------
+septic_patients %>%
+  freq(hospital_id)
+
+## ---- echo = TRUE--------------------------------------------------------
+septic_patients %>%
+  freq(hospital_id, sort.count = TRUE)
+
+## ---- echo = TRUE--------------------------------------------------------
+septic_patients %>%
+  select(amox) %>% 
+  freq()
+
+## ---- echo = TRUE--------------------------------------------------------
+septic_patients %>%
+  select(date) %>% 
+  freq(nmax = 5)
+
+## ---- echo = TRUE--------------------------------------------------------
+my_df <- septic_patients %>% freq(age)
+class(my_df)
+
+## ---- echo = TRUE--------------------------------------------------------
+dim(my_df)
+
+## ---- echo = TRUE--------------------------------------------------------
+septic_patients %>%
+  freq(amox, na.rm = FALSE)
+
+## ---- echo = TRUE--------------------------------------------------------
+septic_patients %>%
+  freq(hospital_id, row.names = FALSE)
+
+## ---- echo = TRUE--------------------------------------------------------
+septic_patients %>%
+  freq(hospital_id, markdown = TRUE)
+
+## ---- echo = FALSE-------------------------------------------------------
+# this will print "2018" in 2018, and "2018-yyyy" after 2018.
+yrs <- c(2018:format(Sys.Date(), "%Y"))
+yrs <- c(min(yrs), max(yrs))
+yrs <- paste(unique(yrs), collapse = "-")
+