microorganismsDT microorganisms.prevDT microorganisms.unprevDT microorganisms.oldDT
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diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html
index 141ff016..b8d69189 100644
--- a/docs/reference/microorganisms.html
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@@ -80,7 +80,7 @@
@@ -269,7 +269,7 @@ On our website https://msberends.gitla
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+ Translation table for microorganism codes
+ +microorganisms.codes.Rd
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+ A data set containing commonly used codes for microorganisms. Define your own with set_mo_source.
microorganisms.codes
+
+ Format
+ +A data.frame with 3,303 observations and 2 variables:
-
+
certeCommonly used code of a microorganism
+ moCode of microorganism in
microorganisms
+
Read more on our website!
+ + +
+On our website https://msberends.gitlab.io/AMR you can find a omprehensive tutorial about how to conduct AMR analysis and find the complete documentation of all functions, which reads a lot easier than in R.
See also
+ + + + +See also
- + diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html new file mode 100644 index 00000000..2a624675 --- /dev/null +++ b/docs/reference/mo_source.html @@ -0,0 +1,334 @@ + + + + + + + + +
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diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index c91fb660..5fde7870 100644
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+ Use predefined reference data set
+ +mo_source.Rd
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+ These functions can be used to predefine your own reference to be used in as.mo and consequently all mo_* functions like mo_genus and mo_gramstain.
set_mo_source(path) + +get_mo_source()+ +
Arguments
+| path | +location of your reference file, see Details |
+
|---|
Details
+ +The reference file can be a text file seperated with commas (CSV) or pipes, an Excel file (old 'xls' format or new 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the readxl package installed.
set_mo_source will check the file for validity: it must be a data.frame, must have a column named "mo" which contains values from microorganisms$mo and must have a reference column with your own defined values. If all tests pass, set_mo_source will read the file into R and export it to "~/.mo_source.rds". This compressed data file will then be used at default for MO determination (function as.mo and consequently all mo_* functions like mo_genus and mo_gramstain). The location of the original file will be saved as option with options(mo_source = path). Its timestamp will be saved with options(mo_source_datetime = ...).
get_mo_source will return the data set by reading "~/.mo_source.rds" with readRDS. If the original file has changed (the file defined with path), it will call set_mo_source to update the data file automatically.
Reading an Excel file (.xlsx) with only one row has a size of 8-9 kB. The compressed file will have a size of 0.1 kB and can be read by get_mo_source in only a couple of microseconds (a millionth of a second).
Read more on our website!
+ + +
+On our website https://msberends.gitlab.io/AMR you can find a omprehensive tutorial about how to conduct AMR analysis and find the complete documentation of all functions, which reads a lot easier than in R.
Examples
+# NOT RUN {
+# imagine this Excel file (mo codes looked up in `microorganisms` data set):
+# A B
+# 1 our code mo
+# 2 lab_mo_ecoli B_ESCHR_COL
+# 3 lab_mo_kpneumoniae B_KLBSL_PNE
+
+# 1. We save it as 'home/me/ourcodes.xlsx'
+
+# 2. We use it for input:
+set_mo_source("C:\path\ourcodes.xlsx")
+#> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
+
+# 3. And use it in our functions:
+as.mo("lab_mo_ecoli")
+#> B_ESCHR_COL
+
+mo_genus("lab_mo_kpneumoniae")
+#> "Klebsiella"
+
+# 4. It will look for changes itself:
+# (add new row to the Excel file and save it)
+
+mo_genus("lab_mo_kpneumoniae")
+#> Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
+#> "Klebsiella"
+# }
+
+ AMR (for R). Developed at the University of Groningen.Authors:") + + '
AMR (for R). Developed at the University of Groningen.Authors:') + ''); - //$('footer').prepend(""); + $('footer').addClass("university"); // Edit title of manual $('.template-reference-index h1').text('Manual'); diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R index 86e76c19..f02f8af8 100644 --- a/tests/testthat/test-mo.R +++ b/tests/testthat/test-mo.R @@ -194,7 +194,7 @@ test_that("as.mo works", { expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLA") # - Didymosphaeria spartinae (unprevalent) expect_warning(suppressMessages(as.mo("D spartin", allow_uncertain = TRUE))) - # - was renames to Leptosphaeria obiones + # - was renamed to Leptosphaeria obiones expect_equal(suppressWarnings(suppressMessages(as.character(as.mo("D spartin", allow_uncertain = TRUE)))), "F_LPTSP_OBI") @@ -205,15 +205,15 @@ test_that("as.mo works", { # predefined reference_df expect_equal(as.character(as.mo("TestingOwnID", - reference_df = data.frame(a = "TestingOwnID", b = "B_ESCHR_COL"))), + reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COL"))), "B_ESCHR_COL") expect_equal(as.character(as.mo(c("TestingOwnID", "E. coli"), - reference_df = data.frame(a = "TestingOwnID", b = "B_ESCHR_COL"))), + reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COL"))), c("B_ESCHR_COL", "B_ESCHR_COL")) expect_warning(as.mo("TestingOwnID", reference_df = NULL)) - expect_error(as.mo("E. coli", reference_df = data.frame(a = "TestingOwnID"))) + expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID"))) - # combination of existing mo and certe + # combination of existing mo and other code expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))), c("B_ESCHR_COL", "B_ESCHR_COL"))