diff --git a/DESCRIPTION b/DESCRIPTION index 0411788a..511b7806 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,30 +1,30 @@ Package: AMR -Version: 0.9.0.9012 +Version: 0.9.0.9013 Date: 2020-01-26 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), - family = "Berends", given = c("Matthijs", "S"), email = "m.s.berends@umcg.nl", comment = c(ORCID = "0000-0001-7620-1800")), + family = "Berends", given = c("Matthijs", "S."), email = "m.s.berends@umcg.nl", comment = c(ORCID = "0000-0001-7620-1800")), person(role = c("aut", "ctb"), - family = "Luz", given = c("Christian", "F"), email = "c.f.luz@umcg.nl", comment = c(ORCID = "0000-0001-5809-5995")), + family = "Luz", given = c("Christian", "F."), email = "c.f.luz@umcg.nl", comment = c(ORCID = "0000-0001-5809-5995")), person(role = c("aut", "ths"), - family = "Friedrich", given = c("Alexander", "W"), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")), + family = "Friedrich", given = c("Alexander", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")), person(role = c("aut", "ths"), - family = "Sinha", given = c("Bhanu", "N", "M"), email = "b.sinha@umcg.nl", comment = c(ORCID = "0000-0003-1634-0010")), + family = "Sinha", given = c("Bhanu", "N.", "M."), email = "b.sinha@umcg.nl", comment = c(ORCID = "0000-0003-1634-0010")), person(role = c("aut", "ths"), - family = "Albers", given = c("Casper", "J"), email = "c.j.albers@rug.nl", comment = c(ORCID = "0000-0002-9213-6743")), + family = "Albers", given = c("Casper", "J."), email = "c.j.albers@rug.nl", comment = c(ORCID = "0000-0002-9213-6743")), person(role = c("aut", "ths"), family = "Glasner", given = "Corinna", email = "c.glasner@umcg.nl", comment = c(ORCID = "0000-0003-1241-1328")), person(role = "ctb", - family = "Fonville", given = c("Judith", "M"), email = "j.fonville@pamm.nl"), + family = "Fonville", given = c("Judith", "M."), email = "j.fonville@pamm.nl"), person(role = "ctb", - family = "Hassing", given = c("Erwin", "E", "A"), email = "e.hassing@certe.nl"), + family = "Hassing", given = c("Erwin", "E.", "A."), email = "e.hassing@certe.nl"), person(role = "ctb", - family = "Hazenberg", given = c("Eric", "H", "L", "C", "M"), email = "e.hazenberg@jbz.nl"), + family = "Hazenberg", given = c("Eric", "H.", "L.", "C", "M"), email = "e.hazenberg@jbz.nl"), person(role = "ctb", family = "Lenglet", given = "Annick", email = "annick.lenglet@amsterdam.msf.org"), person(role = "ctb", - family = "Meijer", given = c("Bart", "C"), email = "b.meijerg@certe.nl"), + family = "Meijer", given = c("Bart", "C."), email = "b.meijerg@certe.nl"), person(role = "ctb", family = "Ny", given = "Sofia", email = "sofia.ny@folkhalsomyndigheten.se"), person(role = "ctb", diff --git a/NEWS.md b/NEWS.md index d6b2d3d7..47157bf1 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.9.0.9012 +# AMR 0.9.0.9013 ## Last updated: 26-Jan-2020 ### New diff --git a/R/data.R b/R/data.R index 8e4f491d..bbe3ee76 100755 --- a/R/data.R +++ b/R/data.R @@ -37,7 +37,7 @@ #' - `oral_units`\cr Units of `oral_ddd` #' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment #' - `iv_units`\cr Units of `iv_ddd` -#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the antimicrobial name of the drug. Use [ab_loic()] to retrieve them quickly, see [ab_property()]. +#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use [ab_loinc()] to retrieve them quickly, see [ab_property()]. #' #' ### For the [antivirals] data set: a [`data.frame`] with 102 observations and 9 variables: #' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC diff --git a/_pkgdown.yml b/_pkgdown.yml index 13e0b910..ba74e29a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -168,15 +168,15 @@ reference: - "`AMR-deprecated`" authors: - Matthijs S Berends: + Matthijs S. Berends: href: https://www.rug.nl/staff/m.s.berends/ - Christian F Luz: + Christian F. Luz: href: https://www.rug.nl/staff/c.f.luz/ - Alexander W Friedrich: + Alexander W. Friedrich: href: https://www.rug.nl/staff/a.w.friedrich/ - Bhanu N M Sinha: + Bhanu N. M. Sinha: href: https://www.rug.nl/staff/b.sinha/ - Casper J Albers: + Casper J. Albers: href: https://www.rug.nl/staff/c.j.albers/ Corinna Glasner: href: https://www.rug.nl/staff/c.glasner/ diff --git a/docs/404.html b/docs/404.html index 9af6f713..ccf739df 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@
@@ -240,7 +240,7 @@ Content not found. Please use links in the navbar. # Author: WHO (World Health Organization) # Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/ # -# => Found 4374 MDROs out of 5000 tested isolates (87.5%) +# => Found 4338 MDROs out of 5000 tested isolates (86.8%)Create a frequency table of the results:
Frequency table
@@ -356,40 +356,40 @@ Unique: 5Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
SPSS.Rmd
R is (nowadays) the preferred analysis software in academic papers.
At present, R is among the world most powerful statistical languages, and it is generally very popular in science (Bollmann et al., 2017). For all the above reasons, the number of references to R as an analysis method in academic papers is rising continuously and has even surpassed SPSS for academic use (Muenchen, 2014).
-I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself has been restyled completely by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2019, I don’t see any reason why SPSS would be of any better use than R.
+I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself has been restyled completely by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2020, I don’t see any reason why SPSS would be of any better use than R.
To demonstrate the first point:
@@ -403,7 +403,7 @@Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
WHONET.Rmd
Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
benchmarks.Rmd
In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.
To achieve this speed, the as.mo
function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of Methanosarcina semesiae (B_MTHNSR_SEMS
), a bug probably never found before in humans:
That takes 6.3 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like Methanosarcina semesiae) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.
+# 1616.00 10 +# 1631.00 10 +# 37.45 10 +# 39.12 10 +# 32.03 10 +That takes 6.5 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like Methanosarcina semesiae) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.
In the figure below, we compare Escherichia coli (which is very common) with Prevotella brevis (which is moderately common) and with Methanosarcina semesiae (which is uncommon):
The highest outliers are the first times. All next determinations were done in only thousands of seconds, because the as.mo()
function learns from its own output to speed up determinations for next times.
So transforming 500,000 values (!!) of 50 unique values only takes 0.63 seconds (627 ms). You only lose time on your unique input values.
+# mo_name(x) 570 630 657 650 674 777 100 +So transforming 500,000 values (!!) of 50 unique values only takes 0.65 seconds (649 ms). You only lose time on your unique input values.
So going from mo_name("Staphylococcus aureus")
to "Staphylococcus aureus"
takes 0.0009 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:
So going from mo_name("Staphylococcus aureus")
to "Staphylococcus aureus"
takes 0.0008 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:
run_it <- microbenchmark(A = mo_species("aureus"),
B = mo_genus("Staphylococcus"),
C = mo_name("Staphylococcus aureus"),
@@ -326,14 +341,14 @@
print(run_it, unit = "ms", signif = 3)
# Unit: milliseconds
# expr min lq mean median uq max neval
-# A 0.528 0.552 0.572 0.564 0.573 0.653 10
-# B 0.583 0.602 0.623 0.618 0.647 0.665 10
-# C 0.965 0.979 1.020 1.000 1.040 1.220 10
-# D 0.582 0.621 0.632 0.627 0.636 0.696 10
-# E 0.548 0.552 0.585 0.582 0.599 0.646 10
-# F 0.538 0.540 0.555 0.548 0.567 0.588 10
-# G 0.539 0.554 0.573 0.568 0.585 0.646 10
-# H 0.512 0.545 0.554 0.551 0.556 0.628 10
Of course, when running mo_phylum("Firmicutes")
the function has zero knowledge about the actual microorganism, namely S. aureus. But since the result would be "Firmicutes"
too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.
Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.
@@ -380,7 +395,7 @@Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
resistance_predict.Rmd
The function plot
is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:
Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
Matthijs S Berends. Author, maintainer.
+
Matthijs S. Berends. Author, maintainer.
Christian F Luz. Author, contributor.
+
Christian F. Luz. Author, contributor.
Alexander W Friedrich. Author, thesis advisor.
+
Alexander W. Friedrich. Author, thesis advisor.
Bhanu N M Sinha. Author, thesis advisor.
+
Bhanu N. M. Sinha. Author, thesis advisor.
Casper J Albers. Author, thesis advisor.
+
Casper J. Albers. Author, thesis advisor.
Judith M Fonville. Contributor. +
Judith M. Fonville. Contributor.
Erwin E A Hassing. Contributor. +
Erwin E. A. Hassing. Contributor.
Eric H L C M Hazenberg. Contributor. +
Eric H. L. C M Hazenberg. Contributor.
Bart C Meijer. Contributor. +
Bart C. Meijer. Contributor.
Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
as.mo(..., allow_uncertain = 3)
Contents
@@ -323,7 +323,7 @@ This package contains all ~550 antibiotic, antimycotic and antiviral dru
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html
index 42fa5bf3..28074657 100644
--- a/docs/reference/as.ab.html
+++ b/docs/reference/as.ab.html
@@ -85,7 +85,7 @@
@@ -336,7 +336,7 @@ This package contains all ~550 antibiotic, antimycotic and antiviral dru
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html
index c9de77ee..c3f5006c 100644
--- a/docs/reference/as.disk.html
+++ b/docs/reference/as.disk.html
@@ -85,7 +85,7 @@
@@ -305,7 +305,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html
index a513bc23..60a7b0f7 100644
--- a/docs/reference/as.mic.html
+++ b/docs/reference/as.mic.html
@@ -85,7 +85,7 @@
@@ -315,7 +315,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html
index 8abed42f..2b8facbc 100644
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@@ -85,7 +85,7 @@
@@ -471,7 +471,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html
index 4ba152c4..dbac8750 100644
--- a/docs/reference/as.rsi.html
+++ b/docs/reference/as.rsi.html
@@ -85,7 +85,7 @@
@@ -379,7 +379,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html
index 9a0539af..5fd036ac 100644
--- a/docs/reference/atc_online.html
+++ b/docs/reference/atc_online.html
@@ -86,7 +86,7 @@ This function requires an internet connection." />
@@ -347,7 +347,7 @@ The
lifecycle of this function is questioni
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/availability.html b/docs/reference/availability.html
index ef3b2ea1..ed0cdf07 100644
--- a/docs/reference/availability.html
+++ b/docs/reference/availability.html
@@ -85,7 +85,7 @@
@@ -303,7 +303,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html
index 0e647492..05e9d9ab 100644
--- a/docs/reference/bug_drug_combinations.html
+++ b/docs/reference/bug_drug_combinations.html
@@ -85,7 +85,7 @@
@@ -371,7 +371,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html
index e0aaebcf..9999ca89 100644
--- a/docs/reference/catalogue_of_life.html
+++ b/docs/reference/catalogue_of_life.html
@@ -85,7 +85,7 @@
@@ -317,7 +317,7 @@ Function
as.mo()
to use the data for intel
- Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html
index 5c7debe5..d0c9e833 100644
--- a/docs/reference/catalogue_of_life_version.html
+++ b/docs/reference/catalogue_of_life_version.html
@@ -85,7 +85,7 @@
@@ -284,7 +284,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
- Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/count.html b/docs/reference/count.html
index 7302ed74..435553d4 100644
--- a/docs/reference/count.html
+++ b/docs/reference/count.html
@@ -86,7 +86,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
@@ -446,7 +446,7 @@ A microorganism is categorised as Susceptible, Increased exposure when
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html
index bc2a6d53..ce95cb67 100644
--- a/docs/reference/eucast_rules.html
+++ b/docs/reference/eucast_rules.html
@@ -86,7 +86,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
@@ -468,7 +468,7 @@ The
lifecycle of this function is maturing<
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/example_isolates.html b/docs/reference/example_isolates.html
index d46311a3..926316e8 100644
--- a/docs/reference/example_isolates.html
+++ b/docs/reference/example_isolates.html
@@ -85,7 +85,7 @@
@@ -274,7 +274,7 @@
- Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/extended-functions.html b/docs/reference/extended-functions.html
index 12664884..8ee70add 100644
--- a/docs/reference/extended-functions.html
+++ b/docs/reference/extended-functions.html
@@ -85,7 +85,7 @@
@@ -269,7 +269,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html
index 0bb26635..da27ee30 100644
--- a/docs/reference/filter_ab_class.html
+++ b/docs/reference/filter_ab_class.html
@@ -85,7 +85,7 @@
@@ -344,7 +344,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html
index 847c85e6..4e552154 100644
--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@@ -85,7 +85,7 @@
@@ -469,7 +469,7 @@ To conduct an analysis of antimicrobial resistance, you should only include the
- Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html
index cf7f3c19..53c89b8d 100644
--- a/docs/reference/g.test.html
+++ b/docs/reference/g.test.html
@@ -85,7 +85,7 @@
@@ -402,7 +402,7 @@ The
lifecycle of this function is questioni
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html
index a74f000a..f2b3c916 100644
--- a/docs/reference/ggplot_rsi.html
+++ b/docs/reference/ggplot_rsi.html
@@ -85,7 +85,7 @@
@@ -528,7 +528,7 @@ The
lifecycle of this function is maturing<
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html
index 09e683de..928e1192 100644
--- a/docs/reference/guess_ab_col.html
+++ b/docs/reference/guess_ab_col.html
@@ -85,7 +85,7 @@
@@ -320,7 +320,7 @@ The
lifecycle of this function is maturing<
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 53ce2ce9..dea05a80 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -84,7 +84,7 @@
@@ -591,7 +591,7 @@
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/join.html b/docs/reference/join.html
index 46efe370..68268603 100644
--- a/docs/reference/join.html
+++ b/docs/reference/join.html
@@ -85,7 +85,7 @@
@@ -319,7 +319,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html
index ff9e6057..961ff01f 100644
--- a/docs/reference/key_antibiotics.html
+++ b/docs/reference/key_antibiotics.html
@@ -85,7 +85,7 @@
@@ -433,7 +433,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html
index 69ba3a99..d0aba710 100644
--- a/docs/reference/kurtosis.html
+++ b/docs/reference/kurtosis.html
@@ -85,7 +85,7 @@
@@ -292,7 +292,7 @@ The
lifecycle of this function is questioni
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html
index a22e1a42..97a34877 100644
--- a/docs/reference/lifecycle.html
+++ b/docs/reference/lifecycle.html
@@ -87,7 +87,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
@@ -306,7 +306,7 @@ The lifecycle of this function is questioning. We are no longer
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/like.html b/docs/reference/like.html
index 23d68e0f..c0c7c353 100644
--- a/docs/reference/like.html
+++ b/docs/reference/like.html
@@ -85,7 +85,7 @@
@@ -325,7 +325,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html
index 3fd6f62f..36e1ebae 100644
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@@ -85,7 +85,7 @@
@@ -475,7 +475,7 @@ A microorganism is categorised as Susceptible, Increased exposure when
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html
index 5fd3ef69..e5b5d4f1 100644
--- a/docs/reference/microorganisms.codes.html
+++ b/docs/reference/microorganisms.codes.html
@@ -85,7 +85,7 @@
@@ -278,7 +278,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
- Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html
index 46715dda..fc297a1b 100644
--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.html
@@ -85,7 +85,7 @@
@@ -310,7 +310,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
- Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html
index 5f8d5b2b..322c7ddd 100644
--- a/docs/reference/microorganisms.old.html
+++ b/docs/reference/microorganisms.old.html
@@ -85,7 +85,7 @@
@@ -285,7 +285,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
- Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html
index ddd2008e..efd3d5ff 100644
--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.html
@@ -85,7 +85,7 @@
@@ -457,7 +457,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
- Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html
index 420914d0..3d795975 100644
--- a/docs/reference/mo_source.html
+++ b/docs/reference/mo_source.html
@@ -86,7 +86,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
@@ -335,7 +335,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/p_symbol.html b/docs/reference/p_symbol.html
index 96f1dc34..b43ce09d 100644
--- a/docs/reference/p_symbol.html
+++ b/docs/reference/p_symbol.html
@@ -85,7 +85,7 @@
@@ -283,7 +283,7 @@ The
lifecycle of this function is questioni
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html
index 8849206b..d7810061 100644
--- a/docs/reference/proportion.html
+++ b/docs/reference/proportion.html
@@ -86,7 +86,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
@@ -490,7 +490,7 @@ A microorganism is categorised as Susceptible, Increased exposure when
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/read.4D.html b/docs/reference/read.4D.html
index 20dd3106..0428a6bd 100644
--- a/docs/reference/read.4D.html
+++ b/docs/reference/read.4D.html
@@ -85,7 +85,7 @@
@@ -421,7 +421,7 @@ The
lifecycle of this function is dormant
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index d8a57d81..cc4d51c4 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -90,7 +90,7 @@ below to see their documentation.
@@ -262,7 +262,7 @@ below to see their documentation.
- Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html
index c357b381..8caeeada 100644
--- a/docs/reference/resistance_predict.html
+++ b/docs/reference/resistance_predict.html
@@ -85,7 +85,7 @@
@@ -458,7 +458,7 @@ A microorganism is categorised as Susceptible, Increased exposure when
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html
index acec260d..46b100d4 100644
--- a/docs/reference/rsi_translation.html
+++ b/docs/reference/rsi_translation.html
@@ -85,7 +85,7 @@
@@ -273,7 +273,7 @@
- Developed by Matthijs S. Berends, Christian F. Luz, Alex W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html
index cc51ae32..01cff0a7 100644
--- a/docs/reference/skewness.html
+++ b/docs/reference/skewness.html
@@ -86,7 +86,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
@@ -294,7 +294,7 @@ The
lifecycle of this function is questioni
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/docs/reference/translate.html b/docs/reference/translate.html
index 163b1fea..3d053834 100644
--- a/docs/reference/translate.html
+++ b/docs/reference/translate.html
@@ -85,7 +85,7 @@
@@ -304,7 +304,7 @@ The
lifecycle of this function is stable
- Developed by Matthijs S Berends, Christian F Luz, Alexander W Friedrich, Bhanu N M Sinha, Casper J Albers, Corinna Glasner.
+ Developed by Matthijs S. Berends, Christian F. Luz, Alexander W. Friedrich, Bhanu N. M. Sinha, Casper J. Albers, Corinna Glasner.
diff --git a/man/antibiotics.Rd b/man/antibiotics.Rd
index 2d0623d9..2848ba90 100644
--- a/man/antibiotics.Rd
+++ b/man/antibiotics.Rd
@@ -20,7 +20,7 @@
\item \code{oral_units}\cr Units of \code{oral_ddd}
\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral treatment
\item \code{iv_units}\cr Units of \code{iv_ddd}
-\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the antimicrobial name of the drug. Use \code{\link[=ab_loic]{ab_loic()}} to retrieve them quickly, see \code{\link[=ab_property]{ab_property()}}.
+\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use \code{\link[=ab_loinc]{ab_loinc()}} to retrieve them quickly, see \code{\link[=ab_property]{ab_property()}}.
}
}