mo
glimpse(our_data_1st) diff --git a/articles/EUCAST.html b/articles/EUCAST.html index 88240a53..e2f149ca 100644 --- a/articles/EUCAST.html +++ b/articles/EUCAST.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9048 + 2.1.1.9049 diff --git a/articles/MDR.html b/articles/MDR.html index b86d8177..d714bfde 100644 --- a/articles/MDR.html +++ b/articles/MDR.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9048 + 2.1.1.9049 diff --git a/articles/PCA.html b/articles/PCA.html index 36c4e2f7..5ff221c2 100644 --- a/articles/PCA.html +++ b/articles/PCA.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9048 + 2.1.1.9049 diff --git a/articles/WHONET.html b/articles/WHONET.html index 1bbe7ec6..ed3b112b 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9048 + 2.1.1.9049 @@ -372,7 +372,7 @@ Longest: 40 Frequency table Class: factor > ordered > sir (numeric) Length: 500 -Levels: 5: S < SDD < I < R < N +Levels: 5: S < SDD < I < R < NI Available: 481 (96.2%, NA: 19 = 3.8%) Unique: 3 Drug: Amoxicillin/clavulanic acid (AMC, J01CR02) diff --git a/articles/datasets.html b/articles/datasets.html index bc284c93..bd80796e 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9048 + 2.1.1.9049 @@ -194,7 +194,7 @@ Data sets for download / own use - 13 June 2024 + 14 June 2024 Source: vignettes/datasets.Rmd datasets.Rmd @@ -526,14 +526,14 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: antibiotics: Antibiotic (+Antifungal) Drugs -A data set with 484 rows and 14 columns, containing the following +A data set with 485 rows and 14 columns, containing the following column names:ab, cid, name, group, atc, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, and loinc. This data set is in R available as antibiotics, after you load the AMR package. -It was last updated on 13 June 2024 18:55:17 UTC. Find more info +It was last updated on 14 June 2024 20:39:01 UTC. Find more info about the structure of this data set here. Direct download links: @@ -905,47 +905,47 @@ inhibitors clinical_breakpoints: Interpretation from MIC values & disk diameters to SIR -A data set with 29 883 rows and 13 columns, containing the following +A data set with 34 085 rows and 13 columns, containing the following column names:guideline, type, host, method, site, mo, rank_index, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, and uti. This data set is in R available as clinical_breakpoints, after you load the AMR package. -It was last updated on 24 February 2024 14:16:52 UTC. Find more info +It was last updated on 14 June 2024 20:39:01 UTC. Find more info about the structure of this data set here. Direct download links: Download as original -R Data Structure (RDS) file (61 kB) +R Data Structure (RDS) file (71 kB) Download as tab-separated -text file (2.5 MB) +text file (2.9 MB) Download as Microsoft -Excel workbook (1.4 MB) +Excel workbook (1.6 MB) Download as Apache -Feather file (1.3 MB) +Feather file (4.9 MB) Download as Apache -Parquet file (91 kB) +Parquet file (0 kB) Download as SAS -transport (XPT) file (8.2 MB) +transport (XPT) file (9.3 MB) Download as IBM -SPSS Statistics data file (4.9 MB) +SPSS Statistics data file (5.6 MB) Download as Stata -DTA file (8.1 MB) +DTA file (9.2 MB) Source This data set contains interpretation rules for MIC values and disk -diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST -(2011-2023). +diffusion diameters. Included guidelines are CLSI (2011-2024) and EUCAST +(2011-2024). Clinical breakpoints in this package were validated through and imported from WHONET, a free desktop Windows application developed and supported by the WHO Collaborating @@ -1007,7 +1007,7 @@ use.
Frequency table
Class: factor > ordered > sir (numeric) Length: 500 -Levels: 5: S < SDD < I < R < N +Levels: 5: S < SDD < I < R < NI Available: 481 (96.2%, NA: 19 = 3.8%) Unique: 3
Drug: Amoxicillin/clavulanic acid (AMC, J01CR02) diff --git a/articles/datasets.html b/articles/datasets.html index bc284c93..bd80796e 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 2.1.1.9048 + 2.1.1.9049 @@ -194,7 +194,7 @@ Data sets for download / own use - 13 June 2024 + 14 June 2024 Source: vignettes/datasets.Rmd datasets.Rmd @@ -526,14 +526,14 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: antibiotics: Antibiotic (+Antifungal) Drugs -A data set with 484 rows and 14 columns, containing the following +A data set with 485 rows and 14 columns, containing the following column names:ab, cid, name, group, atc, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, and loinc. This data set is in R available as antibiotics, after you load the AMR package. -It was last updated on 13 June 2024 18:55:17 UTC. Find more info +It was last updated on 14 June 2024 20:39:01 UTC. Find more info about the structure of this data set here. Direct download links: @@ -905,47 +905,47 @@ inhibitors clinical_breakpoints: Interpretation from MIC values & disk diameters to SIR -A data set with 29 883 rows and 13 columns, containing the following +A data set with 34 085 rows and 13 columns, containing the following column names:guideline, type, host, method, site, mo, rank_index, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, and uti. This data set is in R available as clinical_breakpoints, after you load the AMR package. -It was last updated on 24 February 2024 14:16:52 UTC. Find more info +It was last updated on 14 June 2024 20:39:01 UTC. Find more info about the structure of this data set here. Direct download links: Download as original -R Data Structure (RDS) file (61 kB) +R Data Structure (RDS) file (71 kB) Download as tab-separated -text file (2.5 MB) +text file (2.9 MB) Download as Microsoft -Excel workbook (1.4 MB) +Excel workbook (1.6 MB) Download as Apache -Feather file (1.3 MB) +Feather file (4.9 MB) Download as Apache -Parquet file (91 kB) +Parquet file (0 kB) Download as SAS -transport (XPT) file (8.2 MB) +transport (XPT) file (9.3 MB) Download as IBM -SPSS Statistics data file (4.9 MB) +SPSS Statistics data file (5.6 MB) Download as Stata -DTA file (8.1 MB) +DTA file (9.2 MB) Source This data set contains interpretation rules for MIC values and disk -diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST -(2011-2023). +diffusion diameters. Included guidelines are CLSI (2011-2024) and EUCAST +(2011-2024). Clinical breakpoints in this package were validated through and imported from WHONET, a free desktop Windows application developed and supported by the WHO Collaborating @@ -1007,7 +1007,7 @@ use.
vignettes/datasets.Rmd
datasets.Rmd
antibiotics
A data set with 484 rows and 14 columns, containing the following +
A data set with 485 rows and 14 columns, containing the following column names:ab, cid, name, group, atc, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, and loinc.
This data set is in R available as antibiotics, after you load the AMR package.
AMR
It was last updated on 13 June 2024 18:55:17 UTC. Find more info +
It was last updated on 14 June 2024 20:39:01 UTC. Find more info about the structure of this data set here.
Direct download links:
clinical_breakpoints
A data set with 29 883 rows and 13 columns, containing the following +
A data set with 34 085 rows and 13 columns, containing the following column names:guideline, type, host, method, site, mo, rank_index, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, and uti.
This data set is in R available as clinical_breakpoints, after you load the AMR package.
It was last updated on 24 February 2024 14:16:52 UTC. Find more info +
This data set contains interpretation rules for MIC values and disk -diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST -(2011-2023).
Clinical breakpoints in this package were validated through and imported from WHONET, a free desktop Windows application developed and supported by the WHO Collaborating @@ -1007,7 +1007,7 @@ use.
microorganisms.codes
A data set with 4 958 rows and 2 columns, containing the following +
A data set with 4 972 rows and 2 columns, containing the following column names:code and mo.
This data set is in R available as microorganisms.codes, after you load the AMR package.
It was last updated on 13 June 2024 05:37:53 UTC. Find more info +
Manually, using:
install.packages("remotes") # if you haven't already -remotes::install_github("msberends/AMR")
Automatically, using the rOpenSci R-universe platform, by adding our R-universe address to your list of repositories (‘repos’):
(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support!)
This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the University of Prince Edward Island, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
rsi
sir
as.sir()
breakpoint_type = "animal"
host
ab_url()
as.double()
NA
summary()
scale_*_mic()
scale_x_mic()
scale_y_mic()
scale_colour_mic()
scale_fill_mic()
rescale_mic()
mo_group_members()
mo_group_members("Strep group C")
ab
uti
as.sir(..., ab = "column1", mo = "column2", uti = "column3")
nitrofurans()
rifamycins()
CLI1
lincosamides()
only_treatable = TRUE
AMO
antifungals()
keep_operators
as.mic()
"all"
"none"
"edges"
as.ab()
as.mo()
aminoglycosides()
only_treatable = FALSE
AMR_custom_ab A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in add_custom_antimicrobials().
AMR_custom_ab
add_custom_antimicrobials()
AMR_custom_mo A file location to an RDS file, to use custom microorganisms with this package. This is explained in add_custom_microorganisms().
AMR_custom_mo
add_custom_microorganisms()
AMR_eucastrules A character to set the default types of rules for eucast_rules() function, must be one or more of: "breakpoints", "expert", "other", "custom", "all", and defaults to c("breakpoints", "expert").
AMR_eucastrules
eucast_rules()
"breakpoints"
"expert"
"other"
"custom"
c("breakpoints", "expert")
AMR_guideline A character to set the default guideline for interpreting MIC values and disk diffusion diameters with as.sir(). Can be only the guideline name (e.g., "CLSI") or the name with a year (e.g. "CLSI 2019"). The default to the latest implemented EUCAST guideline, currently "EUCAST 2023". Supported guideline are currently EUCAST (2011-2023) and CLSI (2011-2023).
AMR_guideline
"CLSI"
"CLSI 2019"
"EUCAST 2023"
AMR_guideline A character to set the default guideline for interpreting MIC values and disk diffusion diameters with as.sir(). Can be only the guideline name (e.g., "CLSI") or the name with a year (e.g. "CLSI 2019"). The default to the latest implemented EUCAST guideline, currently "EUCAST 2024". Supported guideline are currently EUCAST (2011-2024) and CLSI (2011-2024).
"EUCAST 2024"
AMR_ignore_pattern A regular expression to ignore (i.e., make NA) any match given in as.mo() and all mo_* functions.
AMR_ignore_pattern
mo_*
AMR_include_PKPD A logical to use in as.sir(), to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is TRUE.
AMR_include_PKPD
TRUE
AMR_include_screening A logical to use in as.sir(), to indicate that clinical breakpoints for screening are allowed - the default is FALSE.
AMR_include_screening
FALSE
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