big website update, licence txt update

man/septic_patients.Rd

@@ -21,46 +21,12 @@
 septic_patients
 }
 \description{
-An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This \code{data.frame} can be used to practice AMR analysis. For examples, press F1.
+An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This \code{data.frame} can be used to practice AMR analysis. For examples, please read \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{the tutorial on our website}.
 }
-\examples{
-# ----------- #
-# PREPARATION #
-# ----------- #
+\section{Read more on our website!}{
 
-# Save this example data set to an object, so we can edit it:
-my_data <- septic_patients
-
-# load the dplyr package to make data science A LOT easier
-library(dplyr)
-
-# Add first isolates to our data set:
-my_data <- my_data \%>\%
-  mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "mo"))
-
-# -------- #
-# ANALYSIS #
-# -------- #
-
-# 1. Get the amoxicillin resistance percentages (p)
-#     and numbers (n) of E. coli, divided by hospital:
-
-my_data \%>\%
-  filter(mo == guess_mo("E. coli"),
-         first_isolates == TRUE) \%>\%
-  group_by(hospital_id) \%>\%
-  summarise(n = n_rsi(amox),
-            p = portion_IR(amox))
-
-
-# 2. Get the amoxicillin/clavulanic acid resistance
-#    percentages of E. coli, trend over the years:
-
-my_data \%>\%
-  filter(mo == guess_mo("E. coli"),
-         first_isolates == TRUE) \%>\%
-  group_by(year = format(date, "\%Y")) \%>\%
-  summarise(n = n_rsi(amcl),
-            p = portion_IR(amcl, minimum = 20))
+\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
+On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R.
 }
+
 \keyword{datasets}