From 423d1d3c41f77a51c4c14e25532b8b672d9a7647 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Sun, 26 Jan 2020 20:38:54 +0100 Subject: [PATCH] (v0.9.0.9013) Support for LOINC codes --- DESCRIPTION | 20 +- NEWS.md | 2 +- R/data.R | 2 +- _pkgdown.yml | 10 +- docs/404.html | 4 +- docs/LICENSE-text.html | 4 +- docs/articles/AMR.html | 445 +++++++++--------- .../AMR_files/figure-html/plot 1-1.png | Bin 65526 -> 65906 bytes .../AMR_files/figure-html/plot 3-1.png | Bin 52106 -> 52127 bytes .../AMR_files/figure-html/plot 4-1.png | Bin 104531 -> 104569 bytes .../AMR_files/figure-html/plot 5-1.png | Bin 85061 -> 85062 bytes docs/articles/EUCAST.html | 6 +- docs/articles/MDR.html | 60 +-- docs/articles/SPSS.html | 8 +- docs/articles/WHONET.html | 6 +- docs/articles/benchmarks.html | 117 +++-- .../figure-html/unnamed-chunk-5-1.png | Bin 94787 -> 95552 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 75937 -> 75966 bytes .../figure-html/unnamed-chunk-9-1.png | Bin 76195 -> 76175 bytes docs/articles/index.html | 4 +- docs/articles/resistance_predict.html | 9 +- .../figure-html/unnamed-chunk-4-1.png | Bin 97113 -> 98470 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 96164 -> 96559 bytes .../figure-html/unnamed-chunk-5-2.png | Bin 92911 -> 94033 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 96509 -> 97173 bytes .../figure-html/unnamed-chunk-7-1.png | Bin 88976 -> 89975 bytes docs/authors.html | 22 +- docs/index.html | 14 +- docs/news/index.html | 10 +- docs/reference/AMR-deprecated.html | 4 +- docs/reference/AMR.html | 4 +- docs/reference/WHOCC.html | 4 +- docs/reference/WHONET.html | 4 +- docs/reference/ab_property.html | 4 +- docs/reference/age.html | 4 +- docs/reference/age_groups.html | 4 +- docs/reference/antibiotics.html | 6 +- docs/reference/as.ab.html | 4 +- docs/reference/as.disk.html | 4 +- docs/reference/as.mic.html | 4 +- docs/reference/as.mo.html | 4 +- docs/reference/as.rsi.html | 4 +- docs/reference/atc_online.html | 4 +- docs/reference/availability.html | 4 +- docs/reference/bug_drug_combinations.html | 4 +- docs/reference/catalogue_of_life.html | 4 +- docs/reference/catalogue_of_life_version.html | 4 +- docs/reference/count.html | 4 +- docs/reference/eucast_rules.html | 4 +- docs/reference/example_isolates.html | 4 +- docs/reference/extended-functions.html | 4 +- docs/reference/filter_ab_class.html | 4 +- docs/reference/first_isolate.html | 4 +- docs/reference/g.test.html | 4 +- docs/reference/ggplot_rsi.html | 4 +- docs/reference/guess_ab_col.html | 4 +- docs/reference/index.html | 4 +- docs/reference/join.html | 4 +- docs/reference/key_antibiotics.html | 4 +- docs/reference/kurtosis.html | 4 +- docs/reference/lifecycle.html | 4 +- docs/reference/like.html | 4 +- docs/reference/mdro.html | 4 +- docs/reference/microorganisms.codes.html | 4 +- docs/reference/microorganisms.html | 4 +- docs/reference/microorganisms.old.html | 4 +- docs/reference/mo_property.html | 4 +- docs/reference/mo_source.html | 4 +- docs/reference/p_symbol.html | 4 +- docs/reference/proportion.html | 4 +- docs/reference/read.4D.html | 4 +- docs/reference/reexports.html | 4 +- docs/reference/resistance_predict.html | 4 +- docs/reference/rsi_translation.html | 4 +- docs/reference/skewness.html | 4 +- docs/reference/translate.html | 4 +- man/antibiotics.Rd | 2 +- 77 files changed, 479 insertions(+), 456 deletions(-) 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 @@ AMR (for R) - 0.9.0.9012 + 0.9.0.9013 @@ -240,7 +240,7 @@ Content not found. Please use links in the navbar.