Last updated: 08-Oct-2019
+Last updated: 11-Oct-2019
"testvalue" could never be
New
Function bug_drug_combinations() to quickly get a data.frame with the antimicrobial resistance of any bug-drug combination in a data set. The columns with microorganism codes is guessed automatically and its input is transformed with mo_shortname() at default:
Function bug_drug_combinations() to quickly get a data.frame with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with mo_shortname() at default:
x <- bug_drug_combinations(example_isolates)
-# NOTE: Using column `mo` as input for `col_mo`.
-x[1:5, ]
-#> ab mo S I R total
-#> 1 AMC CoNS 178 0 132 310
-#> 2 AMC E. coli 332 74 61 467
-#> 3 AMC K. pneumoniae 49 3 6 58
-#> 4 AMC P. aeruginosa 0 0 30 30
-#> 5 AMC P. mirabilis 28 7 1 36
+#> NOTE: Using column `mo` as input for `col_mo`.
+x[1:4, ]
+#> mo ab S I R total
+#> 1 A. baumannii AMC 0 0 3 3
+#> 2 A. baumannii AMK 0 0 0 0
+#> 3 A. baumannii AMP 0 0 3 3
+#> 4 A. baumannii AMX 0 0 3 3
+#> NOTE: Use 'format()' on this result to get a publicable/printable format.
# change the transformation with the FUN argument to anything you like:
x <- bug_drug_combinations(example_isolates, FUN = mo_gramstain)
-# NOTE: Using column `mo` as input for `col_mo`.
+#> NOTE: Using column `mo` as input for `col_mo`.
x[1:4, ]
-#> ab mo S I R total
-#> 1 AMC Gram-negative 469 89 174 732
-#> 2 AMC Gram-positive 873 2 272 1147
-#> 3 AMK Gram-negative 251 0 2 253
-#> 4 AMK Gram-positive 0 0 100 100You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R format() function:
Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for portion_* functions or count_* functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter only_all_tested (which defaults to FALSE) replaces the old also_single_tested and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the portion and count help pages), where the %SI is being determined:
Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for portion_* functions or count_* functions. This can be used to determine the empiric susceptibility of a combination therapy. A new parameter only_all_tested (which defaults to FALSE) replaces the old also_single_tested and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the portion and count help pages), where the %SI is being determined:
# --------------------------------------------------------------------
# only_all_tested = FALSE only_all_tested = TRUE
# ----------------------- -----------------------
@@ -377,6 +378,7 @@ Since this is a major change, usage of the old also_single_tested w
Other
- Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors
+- Cleaned the coding style of every single syntax line in this package with the help of the
lintr package
as.mo(..., allow_uncertain = 3)
Contents
# \donttest{ x <- bug_drug_combinations(example_isolates) x -format(x) +format(x, translate_ab = "name (atc)") # Use FUN to change to transformation of microorganism codes x <- bug_drug_combinations(example_isolates, diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index 49a6b735..d70d5d72 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -15,21 +15,25 @@ + + - + + - - + + + @@ -45,15 +49,15 @@ + - - + @@ -64,6 +68,7 @@ + @@ -80,7 +85,7 @@ @@ -189,7 +194,6 @@ --