diff --git a/DESCRIPTION b/DESCRIPTION index 8c5618c5..4bad12d0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.1.1.9012 -Date: 2024-02-25 +Version: 2.1.1.9013 +Date: 2024-03-03 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index ea000492..9ad3c198 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9012 +# AMR 2.1.1.9013 *(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!)* @@ -165,7 +165,7 @@ The new function `add_custom_antimicrobials()` allows users to add custom antimi The `antibiotics` data set was greatly updated: - * The following 20 antibiotics have been added (also includes the [new J01RA ATC group](https://www.whocc.no/atc_ddd_index/?code=J01RA&showdescription=no)): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT) + * The following 20 antibiotics have been added (also includes the [new J01RA ATC group](https://atcddd.fhi.no/atc_ddd_index/?code=J01RA&showdescription=no)): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT) * Added some missing ATC codes * Updated DDDs and PubChem Compound IDs * Updated some antibiotic name spelling, now used by WHOCC (such as cephalexin -> cefalexin, and phenethicillin -> pheneticillin) @@ -178,7 +178,7 @@ Also, we added support for using antibiotic selectors in scoped `dplyr` verbs (w We now added extensive support for antiviral agents! For the first time, the `AMR` package has extensive support for antiviral drugs and to work with their names, codes and other data in any way. -* The `antivirals` data set has been extended with 18 new drugs (also from the [new J05AJ ATC group](https://www.whocc.no/atc_ddd_index/?code=J05AJ&showdescription=no)) and now also contains antiviral identifiers and LOINC codes +* The `antivirals` data set has been extended with 18 new drugs (also from the [new J05AJ ATC group](https://atcddd.fhi.no/atc_ddd_index/?code=J05AJ&showdescription=no)) and now also contains antiviral identifiers and LOINC codes * A new data type `av` (*antivirals*) has been added, which is functionally similar to `ab` for antibiotics * Functions `as.av()`, `av_name()`, `av_atc()`, `av_synonyms()`, `av_from_text()` have all been added as siblings to their `ab_*()` equivalents diff --git a/R/sysdata.rda b/R/sysdata.rda index 11211e27..d59f453f 100755 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/pkgdown/extra.css b/pkgdown/extra.css index a50028c3..8eae06b3 100644 --- a/pkgdown/extra.css +++ b/pkgdown/extra.css @@ -29,18 +29,30 @@ # ==================================================================== # */ -:root { - --bs-primary: #128F76 !important; - --bs-primary-color: #128F76 !important; - --bs-primary-rgb: 18, 143, 118 !important; - - --bs-secondary: #a7dbc3 !important; - --bs-secondary-color: #a7dbc3 !important; - --bs-secondary-rgb: 167, 219, 195 !important; - +:root, .navbar * { + --bs-primary: #a7dbc3 !important; + --bs-primary-color: #a7dbc3 !important; + --bs-primary-rgb: 167, 219, 195 !important; + --bs-secondary: #ffffff !important; + --bs-secondary-color: #ffffff !important; + --bs-secondary-rgb: 255, 255, 255 !important; + --bs-navbar-brand-color: var(--bs-body-color) !important; + --bs-navbar-brand-color-hover: var(--bs-body-color) !important; + --bs-nav-link-color: var(--bs-body-color) !important; --bs-bg-opacity: 1 !important; } +.nav-text.text-muted { + color: var(--bs-success) !important; +} +.template-home img.logo { + width: 200px; +} +@media (max-width: 575.98px) { + .template-home img.logo { + width: 140px; + } +} /* fix some footer issues with the logos */ @media (min-width: 576px) { footer .pkgdown-footer-right {