AMR.RmdNote: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 31 May 2019.
+Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 01 June 2019.
So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values M and F. From a researcher perspective: there are slightly more men. Nothing we didn’t already know.
The data is already quite clean, but we still need to transform some variables. The bacteria column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The mutate() function of the dplyr package makes this really easy:
data <- data %>%
@@ -449,14 +449,14 @@
# Pasteurella multocida (no new changes)
# Staphylococcus (no new changes)
# Streptococcus groups A, B, C, G (no new changes)
-# Streptococcus pneumoniae (1533 new changes)
+# Streptococcus pneumoniae (1519 new changes)
# Viridans group streptococci (no new changes)
#
# EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
-# Table 01: Intrinsic resistance in Enterobacteriaceae (1285 new changes)
+# Table 01: Intrinsic resistance in Enterobacteriaceae (1280 new changes)
# Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no new changes)
# Table 03: Intrinsic resistance in other Gram-negative bacteria (no new changes)
-# Table 04: Intrinsic resistance in Gram-positive bacteria (2841 new changes)
+# Table 04: Intrinsic resistance in Gram-positive bacteria (2810 new changes)
# Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no new changes)
# Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no new changes)
# Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no new changes)
@@ -464,24 +464,24 @@
# Table 13: Interpretive rules for quinolones (no new changes)
#
# Other rules
-# Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2277 new changes)
-# Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (127 new changes)
+# Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2266 new changes)
+# Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (95 new changes)
# Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no new changes)
# Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no new changes)
# Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no new changes)
# Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no new changes)
#
# --------------------------------------------------------------------------
-# EUCAST rules affected 6,664 out of 20,000 rows, making a total of 8,063 edits
+# EUCAST rules affected 6,560 out of 20,000 rows, making a total of 7,970 edits
# => added 0 test results
#
-# => changed 8,063 test results
-# - 121 test results changed from S to I
-# - 4,826 test results changed from S to R
-# - 1,112 test results changed from I to S
-# - 355 test results changed from I to R
-# - 1,622 test results changed from R to S
-# - 27 test results changed from R to I
+# => changed 7,970 test results
+# - 118 test results changed from S to I
+# - 4,807 test results changed from S to R
+# - 1,119 test results changed from I to S
+# - 318 test results changed from I to R
+# - 1,590 test results changed from R to S
+# - 18 test results changed from R to I
# --------------------------------------------------------------------------
#
# Use verbose = TRUE to get a data.frame with all specified edits instead.So only 28.4% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:
So only 28.5% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:
For future use, the above two syntaxes can be shortened with the filter_first_isolate() function:
| isolate | @@ -674,8 +674,8 @@|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | -2010-01-20 | -P7 | +2010-01-23 | +H6 | B_ESCHR_COL | S | S | @@ -686,8 +686,8 @@||||||
| 2 | -2010-02-28 | -P7 | +2010-03-03 | +H6 | B_ESCHR_COL | R | S | @@ -698,23 +698,23 @@||||||
| 3 | -2010-04-09 | -P7 | +2010-03-26 | +H6 | B_ESCHR_COL | -R | S | S | R | +S | FALSE | TRUE | |
| 4 | -2010-04-23 | -P7 | +2010-04-21 | +H6 | B_ESCHR_COL | R | -R | +S | S | S | FALSE | @@ -722,20 +722,8 @@||
| 5 | -2010-05-07 | -P7 | -B_ESCHR_COL | -R | -R | -S | -S | -FALSE | -FALSE | -||||
| 6 | -2010-05-15 | -P7 | +2010-07-15 | +H6 | B_ESCHR_COL | S | S | @@ -744,12 +732,24 @@FALSE | TRUE | ||||
| 6 | +2010-08-13 | +H6 | +B_ESCHR_COL | +S | +S | +S | +S | +FALSE | +FALSE | +||||
| 7 | -2010-07-16 | -P7 | +2010-09-29 | +H6 | B_ESCHR_COL | -R | +S | S | R | S | @@ -758,8 +758,8 @@|||
| 8 | -2010-07-31 | -P7 | +2010-10-10 | +H6 | B_ESCHR_COL | R | S | @@ -770,11 +770,11 @@||||||
| 9 | -2010-09-10 | -P7 | +2010-12-09 | +H6 | B_ESCHR_COL | -S | -S | +R | +R | S | S | FALSE | @@ -782,23 +782,23 @@|
| 10 | -2010-11-09 | -P7 | +2010-12-11 | +H6 | B_ESCHR_COL | -S | -S | R | S | +S | +S | FALSE | TRUE |
Instead of 1, now 9 isolates are flagged. In total, 75.8% of all isolates are marked ‘first weighted’ - 47.4% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.
+Instead of 1, now 9 isolates are flagged. In total, 75.9% of all isolates are marked ‘first weighted’ - 47.4% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.
As with filter_first_isolate(), there’s a shortcut for this new algorithm too:
So we end up with 15,152 isolates for analysis.
+So we end up with 15,183 isolates for analysis.
We can remove unneeded columns:
@@ -806,6 +806,7 @@| date | patient_id | hospital | @@ -822,8 +823,9 @@|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2015-03-08 | -Q4 | +1 | +2011-01-05 | +W4 | Hospital B | B_ESCHR_COL | S | @@ -837,23 +839,9 @@TRUE | |||||||
| 2015-12-18 | -J6 | -Hospital B | -B_ESCHR_COL | -S | -S | -S | -S | -M | -Gram negative | -Escherichia | -coli | -TRUE | -|||
| 2016-07-07 | -W7 | +2 | +2013-05-10 | +W2 | Hospital A | B_STPHY_AUR | R | @@ -866,13 +854,30 @@aureus | TRUE | ||||||
| 2011-12-08 | -G9 | -Hospital C | -B_STPHY_AUR | +||||||||||||
| 4 | +2017-12-18 | +P2 | +Hospital B | +B_ESCHR_COL | S | S | +R | +S | +F | +Gram negative | +Escherichia | +coli | +TRUE | +||
| 6 | +2013-05-25 | +L4 | +Hospital A | +B_STPHY_AUR | +R | +S | S | S | M | @@ -882,30 +887,32 @@TRUE | |||||
| 2012-09-08 | -Y8 | +7 | +2016-09-17 | +F3 | +Hospital D | +B_KLBSL_PNE | +R | +S | +S | +S | +M | +Gram negative | +Klebsiella | +pneumoniae | +TRUE | +
| 8 | +2010-06-30 | +L8 | Hospital B | B_ESCHR_COL | S | S | S | S | -F | -Gram negative | -Escherichia | -coli | -TRUE | -||
| 2017-05-04 | -X10 | -Hospital C | -B_ESCHR_COL | -R | -S | -S | -R | -F | +M | Gram negative | Escherichia | coli | @@ -928,9 +935,9 @@|||
| 1 | Escherichia coli | -7,455 | -49.2% | -7,455 | -49.2% | +7,416 | +48.8% | +7,416 | +48.8% | ||||||
| 2 | Staphylococcus aureus | -3,759 | -24.8% | -11,214 | -74.0% | +3,781 | +24.9% | +11,197 | +73.7% | ||||||
| 3 | Streptococcus pneumoniae | -2,398 | -15.8% | -13,612 | -89.8% | +2,391 | +15.7% | +13,588 | +89.5% | ||||||
| 4 | Klebsiella pneumoniae | -1,540 | -10.2% | -15,152 | +1,595 | +10.5% | +15,183 | 100.0% | |||||||
| Hospital A | -0.4577496 | +0.4789879 | |||||||||||||
| Hospital B | -0.4703985 | +0.4752328 | |||||||||||||
| Hospital C | -0.4736842 | +0.4525453 | |||||||||||||
| Hospital D | -0.4736322 | +0.4688136 |
EUCAST.RmdG_test.RmdMDR.RmdThe data set looks like this now:
head(my_TB_data)
# rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-# 1 R R S R R S
-# 2 I S R R I I
-# 3 S I R R R R
-# 4 S R S R R S
-# 5 S S I S S S
-# 6 R R S S R S
+# 1 S R S S R S
+# 2 S S I R R R
+# 3 S S R R I S
+# 4 S S R R S R
+# 5 S R R R R R
+# 6 R R S S S I
# kanamycin
-# 1 I
-# 2 S
-# 3 S
-# 4 S
+# 1 R
+# 2 R
+# 3 I
+# 4 R
# 5 S
-# 6 RWe can now add the interpretation of MDR-TB to our data set:
my_TB_data$mdr <- mdr_tb(my_TB_data)
# NOTE: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.
@@ -285,39 +285,39 @@ Unique: 5
1
Mono-resistance
-3,232
-64.6%
-3,232
-64.6%
+3,300
+66.0%
+3,300
+66.0%
2
Negative
-693
-13.9%
-3,925
-78.5%
+649
+13.0%
+3,949
+79.0%
3
Multidrug resistance
-603
-12.1%
-4,528
-90.6%
+586
+11.7%
+4,535
+90.7%
4
Poly-resistance
-276
-5.5%
-4,804
+270
+5.4%
+4,805
96.1%
5
Extensive drug resistance
-196
+195
3.9%
5,000
100.0%
diff --git a/docs/articles/SPSS.html b/docs/articles/SPSS.html
index 3933169b..50553237 100644
--- a/docs/articles/SPSS.html
+++ b/docs/articles/SPSS.html
@@ -40,7 +40,7 @@
@@ -199,7 +199,7 @@
How to import data from SPSS / SAS / Stata
Matthijs S. Berends
- 31 May 2019
+ 01 June 2019
SPSS.Rmd
diff --git a/docs/articles/WHONET.html b/docs/articles/WHONET.html
index 9e00f2e4..906ba876 100644
--- a/docs/articles/WHONET.html
+++ b/docs/articles/WHONET.html
@@ -40,7 +40,7 @@
@@ -199,7 +199,7 @@
How to work with WHONET data
Matthijs S. Berends
- 31 May 2019
+ 01 June 2019
WHONET.Rmd
diff --git a/docs/articles/ab_property.html b/docs/articles/ab_property.html
index 4202bd9b..a5be0779 100644
--- a/docs/articles/ab_property.html
+++ b/docs/articles/ab_property.html
@@ -40,7 +40,7 @@
@@ -199,7 +199,7 @@
How to get properties of an antibiotic
Matthijs S. Berends
- 31 May 2019
+ 01 June 2019
ab_property.Rmd
diff --git a/docs/articles/benchmarks.html b/docs/articles/benchmarks.html
index 1242d63c..748aa88a 100644
--- a/docs/articles/benchmarks.html
+++ b/docs/articles/benchmarks.html
@@ -40,7 +40,7 @@
@@ -199,7 +199,7 @@
Benchmarks
Matthijs S. Berends
- 31 May 2019
+ 01 June 2019
benchmarks.Rmd
@@ -224,14 +224,14 @@
times = 10)
print(S.aureus, unit = "ms", signif = 2)
# Unit: milliseconds
-# expr min lq mean median uq max neval
-# as.mo("sau") 17 18 24 18 18 78.0 10
-# as.mo("stau") 48 48 52 48 48 92.0 10
-# as.mo("staaur") 18 18 27 18 18 62.0 10
-# as.mo("STAAUR") 18 18 18 18 18 18.0 10
-# as.mo("S. aureus") 28 29 46 29 73 73.0 10
-# as.mo("S. aureus") 28 29 42 29 29 110.0 10
-# as.mo("Staphylococcus aureus") 8 8 8 8 8 8.1 10
+# expr min lq mean median uq max neval
+# as.mo("sau") 17.0 18 37 18 62.0 80.0 10
+# as.mo("stau") 48.0 48 52 48 48.0 92.0 10
+# as.mo("staaur") 18.0 18 31 18 62.0 66.0 10
+# as.mo("STAAUR") 17.0 18 18 18 18.0 18.0 10
+# as.mo("S. aureus") 28.0 28 37 28 29.0 110.0 10
+# as.mo("S. aureus") 28.0 29 33 29 29.0 72.0 10
+# as.mo("Staphylococcus aureus") 7.9 8 8 8 8.1 8.1 10
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 Thermus islandicus (B_THERMS_ISL), a bug probably never found before in humans:
T.islandicus <- microbenchmark(as.mo("theisl"),
@@ -243,12 +243,12 @@
print(T.islandicus, unit = "ms", signif = 2)
# Unit: milliseconds
# expr min lq mean median uq max neval
-# as.mo("theisl") 470 470 500 520 520 520 10
-# as.mo("THEISL") 470 470 500 500 520 520 10
-# as.mo("T. islandicus") 74 74 79 75 76 120 10
-# as.mo("T. islandicus") 74 74 90 74 120 140 10
-# as.mo("Thermus islandicus") 73 73 83 74 76 120 10
-That takes 8.1 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 Thermus islandicus) are almost fast - these are the most probable input from most data sets.
+# as.mo("theisl") 470 470 480 470 480 510 10
+# as.mo("THEISL") 470 470 500 520 520 530 10
+# as.mo("T. islandicus") 74 74 93 75 120 130 10
+# as.mo("T. islandicus") 74 74 94 78 120 120 10
+# as.mo("Thermus islandicus") 73 73 83 73 75 130 10
+That takes 8 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 Thermus islandicus) are almost fast - these 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 Thermus islandicus (which is very uncommon):
par(mar = c(5, 16, 4, 2)) # set more space for left margin text (16)
@@ -294,8 +294,8 @@
print(run_it, unit = "ms", signif = 3)
# Unit: milliseconds
# expr min lq mean median uq max neval
-# mo_fullname(x) 725 767 825 792 903 944 10
-So transforming 500,000 values (!!) of 50 unique values only takes 0.79 seconds (791 ms). You only lose time on your unique input values.
+# mo_fullname(x) 636 664 728 716 763 880 10
+So transforming 500,000 values (!!) of 50 unique values only takes 0.72 seconds (715 ms). You only lose time on your unique input values.
@@ -307,10 +307,10 @@
times = 10)
print(run_it, unit = "ms", signif = 3)
# Unit: milliseconds
-# expr min lq mean median uq max neval
-# A 13.20 13.30 17.90 13.40 13.40 58.30 10
-# B 25.60 25.80 26.00 26.00 26.20 26.50 10
-# C 1.62 1.81 1.78 1.81 1.82 1.86 10
+# expr min lq mean median uq max neval
+# A 13.3 13.30 18.10 13.50 14.20 57.90 10
+# B 25.7 25.80 26.50 26.20 27.50 27.50 10
+# C 1.6 1.82 1.86 1.84 2.02 2.07 10
So going from mo_fullname("Staphylococcus aureus") to "Staphylococcus aureus" takes 0.0018 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"),
@@ -324,14 +324,14 @@
print(run_it, unit = "ms", signif = 3)
# Unit: milliseconds
# expr min lq mean median uq max neval
-# A 0.517 0.550 0.608 0.588 0.637 0.839 10
-# B 0.540 0.548 0.666 0.679 0.744 0.829 10
-# C 1.690 1.790 1.880 1.860 1.990 2.050 10
-# D 0.588 0.632 0.704 0.694 0.731 0.944 10
-# E 0.487 0.504 0.629 0.614 0.703 0.920 10
-# F 0.477 0.540 0.587 0.579 0.640 0.754 10
-# G 0.505 0.550 0.628 0.605 0.755 0.768 10
-# H 0.189 0.266 0.294 0.297 0.362 0.379 10
+# A 0.483 0.579 0.616 0.615 0.654 0.729 10
+# B 0.578 0.657 0.680 0.671 0.680 0.834 10
+# C 1.550 1.640 1.840 1.920 1.980 2.100 10
+# D 0.562 0.746 0.796 0.782 0.847 1.010 10
+# E 0.502 0.578 0.641 0.601 0.755 0.786 10
+# F 0.482 0.553 0.613 0.614 0.684 0.751 10
+# G 0.540 0.560 0.586 0.571 0.604 0.672 10
+# H 0.216 0.272 0.301 0.296 0.352 0.380 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.
@@ -358,13 +358,13 @@
print(run_it, unit = "ms", signif = 4)
# Unit: milliseconds
# expr min lq mean median uq max neval
-# en 18.45 18.51 18.69 18.72 18.78 19.01 10
-# de 23.32 23.41 23.67 23.45 24.00 24.41 10
-# nl 36.79 36.88 41.71 37.39 37.57 81.66 10
-# es 23.32 23.39 23.75 23.65 23.93 24.82 10
-# it 23.31 23.33 33.07 23.38 29.77 69.13 10
-# fr 23.33 23.38 27.93 23.43 23.55 67.91 10
-# pt 23.35 23.38 28.12 23.47 23.82 67.82 10
+# en 18.43 18.46 23.22 18.61 18.81 64.60 10
+# de 20.89 20.99 25.96 21.39 22.23 66.53 10
+# nl 34.35 34.46 34.62 34.55 34.68 35.22 10
+# es 20.88 20.92 21.31 21.06 21.58 22.21 10
+# it 20.59 20.85 20.94 20.93 21.14 21.22 10
+# fr 20.85 21.09 21.15 21.13 21.23 21.58 10
+# pt 20.95 21.22 25.92 21.44 21.61 66.66 10
Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.
diff --git a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-5-1.png
index 7b546a3d..d55efca6 100644
Binary files a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-5-1.png and b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-5-1.png differ
diff --git a/docs/articles/freq.html b/docs/articles/freq.html
index a7055f34..f0ed5d82 100644
--- a/docs/articles/freq.html
+++ b/docs/articles/freq.html
@@ -40,7 +40,7 @@
@@ -199,7 +199,7 @@
How to create frequency tables
Matthijs S. Berends
- 31 May 2019
+ 01 June 2019
freq.Rmd
@@ -275,16 +275,17 @@ Longest: 1
colnames(microorganisms)
# [1] "mo" "col_id" "fullname" "kingdom" "phylum"
# [6] "class" "order" "family" "genus" "species"
-# [11] "subspecies" "rank" "ref" "species_id" "source"
-If we compare the dimensions between the old and new dataset, we can see that these 14 variables were added:
+# [11] "subspecies" "rank" "ref" "species_id" "source"
+# [16] "prevalence"
+If we compare the dimensions between the old and new dataset, we can see that these 15 variables were added:
+# [1] 2000 64
So now the genus and species variables are available. A frequency table of these combined variables can be created like this:
-Frequency table of genus and species from a data.frame (2,000 x 63)
+Frequency table of genus and species from a data.frame (2,000 x 64)
Columns: 2
Length: 2,000 (of which NA: 0 = 0.00%)
Unique: 95
diff --git a/docs/articles/index.html b/docs/articles/index.html
index fa4a8446..e9fdf32e 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -78,7 +78,7 @@
diff --git a/docs/articles/mo_property.html b/docs/articles/mo_property.html
index 48aa0834..33f8a93d 100644
--- a/docs/articles/mo_property.html
+++ b/docs/articles/mo_property.html
@@ -40,7 +40,7 @@
@@ -199,7 +199,7 @@
How to get properties of a microorganism
Matthijs S. Berends
- 31 May 2019
+ 01 June 2019
mo_property.Rmd
diff --git a/docs/articles/resistance_predict.html b/docs/articles/resistance_predict.html
index 6b303754..6c8bb0a9 100644
--- a/docs/articles/resistance_predict.html
+++ b/docs/articles/resistance_predict.html
@@ -40,7 +40,7 @@
@@ -199,7 +199,7 @@
How to predict antimicrobial resistance
Matthijs S. Berends
- 31 May 2019
+ 01 June 2019
resistance_predict.Rmd
diff --git a/docs/authors.html b/docs/authors.html
index f393c393..84f55c48 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -78,7 +78,7 @@
diff --git a/docs/extra.css b/docs/extra.css
index 5c65410b..7175fb98 100644
--- a/docs/extra.css
+++ b/docs/extra.css
@@ -17,7 +17,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
-# Visit our website for more info: https://msberends.gitab.io/AMR. #
+# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
*/
@@ -138,7 +138,9 @@ help {
/* hide version label */
.version.label {
+ /*
display: none;
+ */
}
/* Date of vignettes */
diff --git a/docs/index.html b/docs/index.html
index 78d5f8f0..610bb6c9 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -42,7 +42,7 @@
diff --git a/docs/news/index.html b/docs/news/index.html
index 44a96c66..ee2f3c8d 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -78,7 +78,7 @@
@@ -239,9 +239,9 @@
-
+
-AMR 0.6.1.90xx Unreleased
+AMR 0.6.1.9052 Unreleased
Note: latest development version
@@ -272,7 +272,9 @@
All references to antibiotics in our package now use EARS-Net codes, like AMX for amoxicillin
Functions atc_certe, ab_umcg and atc_trivial_nl have been removed
All atc_* functions are superceded by ab_* functions
-All output will be translated by using an included translation file which can be viewed here Please create an issue in one of our repositories if you want additions in this file.
+
+All output will be translated by using an included translation file which can be viewed here.
+Please create an issue in one of our repositories if you want additions in this file.
Improvements to plotting AMR results with ggplot_rsi():
@@ -305,7 +307,9 @@
-Removed all hardcoded EUCAST rules and replaced them with a new reference file which can be viewed here Please create an issue in one of our repositories if you want changes in this file.
+
+Removed all hardcoded EUCAST rules and replaced them with a new reference file which can be viewed here.
+Please create an issue in one of our repositories if you want changes in this file.
Added ceftazidim intrinsic resistance to Streptococci
Changed default settings for age_groups(), to let groups of fives and tens end with 100+ instead of 120+
@@ -318,7 +322,7 @@
Small algorithm fix for as.mo()
Removed viruses from data set microorganisms.codes and cleaned it up
-Fix for mo_shortname() where species would not be determined correctly
+Fix for mo_shortname() where species would not be determined correctly
as.mo(..., allow_uncertain = 3)
Contents
diff --git a/docs/reference/AMR.html b/docs/reference/AMR.html
index b015e709..2fe74de7 100644
--- a/docs/reference/AMR.html
+++ b/docs/reference/AMR.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html
index fb3ea3fb..0606fc6c 100644
--- a/docs/reference/WHOCC.html
+++ b/docs/reference/WHOCC.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html
index e6ecfb22..c70875fb 100644
--- a/docs/reference/WHONET.html
+++ b/docs/reference/WHONET.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html
index a14e414b..7945ea74 100644
--- a/docs/reference/ab_property.html
+++ b/docs/reference/ab_property.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/age.html b/docs/reference/age.html
index 8abf0658..acaf26c9 100644
--- a/docs/reference/age.html
+++ b/docs/reference/age.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html
index a7795c7d..a91a5f15 100644
--- a/docs/reference/age_groups.html
+++ b/docs/reference/age_groups.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html
index 232ef610..1c885ac7 100644
--- a/docs/reference/antibiotics.html
+++ b/docs/reference/antibiotics.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html
index 828c73a6..b0c57ea7 100644
--- a/docs/reference/as.ab.html
+++ b/docs/reference/as.ab.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/as.atc.html b/docs/reference/as.atc.html
index 9a9cbeb1..1940447c 100644
--- a/docs/reference/as.atc.html
+++ b/docs/reference/as.atc.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html
index e21d6ff7..ce337bc5 100644
--- a/docs/reference/as.disk.html
+++ b/docs/reference/as.disk.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html
index 449947d2..d2cd6827 100644
--- a/docs/reference/as.mic.html
+++ b/docs/reference/as.mic.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html
index 5fbd9bc4..1acd8373 100644
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html
index 976e414a..2dc8ec28 100644
--- a/docs/reference/as.rsi.html
+++ b/docs/reference/as.rsi.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html
index 9fec3870..4b90f630 100644
--- a/docs/reference/atc_online.html
+++ b/docs/reference/atc_online.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/availability.html b/docs/reference/availability.html
index 1319356b..8aad3ccc 100644
--- a/docs/reference/availability.html
+++ b/docs/reference/availability.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html
index 04e19062..0e2a4d7d 100644
--- a/docs/reference/catalogue_of_life.html
+++ b/docs/reference/catalogue_of_life.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html
index 714d13e7..b5114222 100644
--- a/docs/reference/catalogue_of_life_version.html
+++ b/docs/reference/catalogue_of_life_version.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/count.html b/docs/reference/count.html
index 8f7a81b9..4126ec36 100644
--- a/docs/reference/count.html
+++ b/docs/reference/count.html
@@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html
index b94e6b51..43315abb 100644
--- a/docs/reference/eucast_rules.html
+++ b/docs/reference/eucast_rules.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html
index 06da0ff1..49f478f1 100644
--- a/docs/reference/filter_ab_class.html
+++ b/docs/reference/filter_ab_class.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html
index 6ea8c805..61d3bfdf 100644
--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/freq.html b/docs/reference/freq.html
index 59cb060a..c31a6c1d 100644
--- a/docs/reference/freq.html
+++ b/docs/reference/freq.html
@@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html
index 1e3105f3..dce590dd 100644
--- a/docs/reference/g.test.html
+++ b/docs/reference/g.test.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html
index a320dbdb..ecdfc7b9 100644
--- a/docs/reference/ggplot_rsi.html
+++ b/docs/reference/ggplot_rsi.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html
index ecb432d4..1fd8a5b8 100644
--- a/docs/reference/guess_ab_col.html
+++ b/docs/reference/guess_ab_col.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/index.html b/docs/reference/index.html
index ff44e1ec..0d47c72c 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -78,7 +78,7 @@
diff --git a/docs/reference/join.html b/docs/reference/join.html
index aef9f25a..7524d37b 100644
--- a/docs/reference/join.html
+++ b/docs/reference/join.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html
index 7ed6e9bc..1e841a84 100644
--- a/docs/reference/key_antibiotics.html
+++ b/docs/reference/key_antibiotics.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html
index 913a3536..66846c89 100644
--- a/docs/reference/kurtosis.html
+++ b/docs/reference/kurtosis.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/like.html b/docs/reference/like.html
index 7cb6b125..3f32ac6e 100644
--- a/docs/reference/like.html
+++ b/docs/reference/like.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html
index e8e68474..6985ada4 100644
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html
index 35362ad6..4c9e52e0 100644
--- a/docs/reference/microorganisms.codes.html
+++ b/docs/reference/microorganisms.codes.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html
index 189cc177..07608340 100644
--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html
index bac80be8..968b7308 100644
--- a/docs/reference/microorganisms.old.html
+++ b/docs/reference/microorganisms.old.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html
index 9f510772..282f9e85 100644
--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html
index 56c4c077..ff1a81df 100644
--- a/docs/reference/mo_source.html
+++ b/docs/reference/mo_source.html
@@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
diff --git a/docs/reference/p.symbol.html b/docs/reference/p.symbol.html
index a1131a91..17817249 100644
--- a/docs/reference/p.symbol.html
+++ b/docs/reference/p.symbol.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/portion.html b/docs/reference/portion.html
index d8f51166..22e80d9d 100644
--- a/docs/reference/portion.html
+++ b/docs/reference/portion.html
@@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
diff --git a/docs/reference/read.4D.html b/docs/reference/read.4D.html
index 7cd9d989..d997f484 100644
--- a/docs/reference/read.4D.html
+++ b/docs/reference/read.4D.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html
index 3ddec5a5..5f9ad473 100644
--- a/docs/reference/resistance_predict.html
+++ b/docs/reference/resistance_predict.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html
index 770638b3..61729859 100644
--- a/docs/reference/rsi_translation.html
+++ b/docs/reference/rsi_translation.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/septic_patients.html b/docs/reference/septic_patients.html
index e1fe762e..787b0c55 100644
--- a/docs/reference/septic_patients.html
+++ b/docs/reference/septic_patients.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html
index d49f811e..836c67b4 100644
--- a/docs/reference/skewness.html
+++ b/docs/reference/skewness.html
@@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
diff --git a/docs/reference/translate.html b/docs/reference/translate.html
index 3453a276..efe692d6 100644
--- a/docs/reference/translate.html
+++ b/docs/reference/translate.html
@@ -80,7 +80,7 @@
diff --git a/git_premaster.sh b/git_premaster.sh
index 8d82a8e5..9e421fa6 100755
--- a/git_premaster.sh
+++ b/git_premaster.sh
@@ -27,9 +27,14 @@ current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'`
# combine tag (e.g. 0.1.0) and commit number (like 40) increased by 9000 to indicate beta version
new_version="$current_tag.$((current_commit + 9000))" # results in 0.1.0.9040
sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
+# update 1st line of NEWS.md
+sed -i -- "1s/${current_tag}.*/${new_version}/" NEWS.md
echo "First 3 lines of DESCRIPTION:"
head -3 DESCRIPTION
echo
+echo "First line of NEWS.md:"
+head -1 NEWS.md
+echo
echo "•••••••••••••••••••••••••••••••••"
echo "• Reloading/documenting package •"
echo "•••••••••••••••••••••••••••••••••"
diff --git a/pkgdown/extra.css b/pkgdown/extra.css
index 5c65410b..7175fb98 100644
--- a/pkgdown/extra.css
+++ b/pkgdown/extra.css
@@ -17,7 +17,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
-# Visit our website for more info: https://msberends.gitab.io/AMR. #
+# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
*/
@@ -138,7 +138,9 @@ help {
/* hide version label */
.version.label {
+ /*
display: none;
+ */
}
/* Date of vignettes */