P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-26 18:46:13 +01:00
Code Releases Activity

mdro fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends 2019-05-11 23:30:10 +02:00
parent 68cc7ef0d0
commit fcc77164e9
11 changed files with 223 additions and 324 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
DESCRIPTION
View File

@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.6.1.9003 Version: 0.6.1.9003
Date: 2019-05-10 Date: 2019-05-11
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(

2
R/get_locale.R
View File

@ -26,7 +26,7 @@
#' #'
#' \code{system.file("translations.tsv", package = "AMR")} #' \code{system.file("translations.tsv", package = "AMR")}
#' #'
#' This file will be read by all functions where a translated output can be desired, like all \code{\link{mo_property}} functions (\code{\link{mo_fullname}}, \code{\link{mo_type}}, etc.). Please suggest your own translations \href{https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation suggestion}{by creating a new issue on our repository}. #' This file will be read by all functions where a translated output can be desired, like all \code{\link{mo_property}} functions (\code{\link{mo_fullname}}, \code{\link{mo_type}}, etc.). Please suggest your own translations \href{https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation\%20suggestion}{by creating a new issue on our repository}.
#' #'
#' The system language will be used at default, if supported, using \code{\link{get_locale}}. The system language can be overwritten with \code{\link{getOption}("AMR_locale")}. #' The system language will be used at default, if supported, using \code{\link{get_locale}}. The system language can be overwritten with \code{\link{getOption}("AMR_locale")}.
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!

15
R/mdro.R
View File

@ -321,15 +321,12 @@ mdro <- function(x,
& !ab_missing(CIP) & !ab_missing(CIP)
& !ab_missing(CAZ) & !ab_missing(CAZ)
& !ab_missing(TZP) ) { & !ab_missing(TZP) ) {
tbl_ <- tbl_ %>% mutate( tbl_$psae <- 0
psae = 0, tbl_[which(tbl_[, MEM] == "R" | tbl_[, IPM] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, MEM] == "R" | tbl_[, IPM] == "R"), "psae"]
psae = ifelse(MEM == "R" | IPM == "R", psae + 1, psae), tbl_[which(tbl_[, GEN] == "R" & tbl_[, TOB] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, GEN] == "R" & tbl_[, TOB] == "R"), "psae"]
psae = ifelse(GEN == "R" & TOB == "R", psae + 1, psae), tbl_[which(tbl_[, CIP] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, CIP] == "R"), "psae"]
psae = ifelse(CIP == "R", psae + 1, psae), tbl_[which(tbl_[, CAZ] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, CAZ] == "R"), "psae"]
psae = ifelse(CAZ == "R", psae + 1, psae), tbl_[which(tbl_[, TZP] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, TZP] == "R"), "psae"]
psae = ifelse(TZP == "R", psae + 1, psae),
psae = ifelse(is.na(psae), 0, psae)
)
} else { } else {
tbl_$psae <- 0 tbl_$psae <- 0
} }

6
R/whocc.R
View File

@ -33,8 +33,8 @@
#' @name WHOCC #' @name WHOCC
#' @rdname WHOCC #' @rdname WHOCC
#' @examples #' @examples
#' as.atc("meropenem") #' as.ab("meropenem")
#' atc_name("J01DH02") #' ab_name("J01DH02")
#' #'
#' atc_tradenames("flucloxacillin") #' ab_tradenames("flucloxacillin")
NULL NULL

BIN
data/antibiotics.rda
View File

Binary file not shown.

10
docs/reference/WHOCC.html
View File

@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
</span> </span>
</div> </div>
@ -145,7 +145,7 @@
</a> </a>
</li> </li>
<li> <li>
<a href="../reference/atc_property.html"> <a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span> <span class="fa fa-capsules"></span>
Get properties of an antibiotic Get properties of an antibiotic
@ -258,10 +258,10 @@ This package contains <strong>all ~500 antimicrobial drugs</strong> and their An
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span> <pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'><a href='as.atc.html'>as.atc</a></span>(<span class='st'>"meropenem"</span>) <span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"meropenem"</span>)
<span class='fu'><a href='atc_property.html'>atc_name</a></span>(<span class='st'>"J01DH02"</span>) <span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01DH02"</span>)
<span class='fu'><a href='atc_property.html'>atc_tradenames</a></span>(<span class='st'>"flucloxacillin"</span>) <span class='fu'><a href='ab_property.html'>ab_tradenames</a></span>(<span class='st'>"flucloxacillin"</span>)
<span class='co'># }</span></pre> <span class='co'># }</span></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

2
docs/reference/translate.html
View File

@ -247,7 +247,7 @@
<p>Strings will be translated to foreign languages if they are defined in a local translation file. This file comes with this package and can be found when running:</p> <p>Strings will be translated to foreign languages if they are defined in a local translation file. This file comes with this package and can be found when running:</p>
<p><code><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file("translations.tsv", package = "AMR")</a></code></p> <p><code><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file("translations.tsv", package = "AMR")</a></code></p>
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property</a></code> functions (<code><a href='mo_property.html'>mo_fullname</a></code>, <code><a href='mo_property.html'>mo_type</a></code>, etc.). Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation suggestion'>by creating a new issue on our repository</a>.</p> <p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property</a></code> functions (<code><a href='mo_property.html'>mo_fullname</a></code>, <code><a href='mo_property.html'>mo_type</a></code>, etc.). Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion'>by creating a new issue on our repository</a>.</p>
<p>The system language will be used at default, if supported, using <code>get_locale</code>. The system language can be overwritten with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>.</p> <p>The system language will be used at default, if supported, using <code>get_locale</code>. The system language can be overwritten with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2> <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

499
inst/translations.tsv
View File

@ -154,303 +154,204 @@ pt vegetative vegetativo FALSE FALSE
pt ([([ ]*?)group \\1grupo FALSE FALSE pt ([([ ]*?)group \\1grupo FALSE FALSE
pt ([([ ]*?)Group \\1Grupo FALSE FALSE pt ([([ ]*?)Group \\1Grupo FALSE FALSE
nl 4-aminosalicylic acid aminosalicylzuur nl 4-aminosalicylic acid 4-aminosalicylzuur
nl adefovir dipivoxil adefovir nl Adefovir dipivoxil Adefovir
nl aldesulfone sodium aldesulfon nl Aldesulfone sodium Aldesulfon
nl amikacin amikacine nl Amikacin Amikacine
nl amoxicillin amoxicilline nl Amoxicillin Amoxicilline
nl amoxicillin and beta-lactamase inhibitor amoxicilline met enzymremmer nl Amoxicillin/beta-lactamase inhibitor Amoxicilline/enzymremmer
nl amphotericin B amfotericine B nl Amphotericin B Amfotericine B
nl ampicillin ampicilline nl Ampicillin Ampicilline
nl ampicillin and beta-lactamase inhibitor ampicilline met enzymremmer nl Ampicillin/beta-lactamase inhibitor Ampicilline/enzymremmer
nl ampicillin, combinations ampicilline, combinatiepreparaten nl Anidulafungin Anidulafungine
nl anidulafungin anidulafungine nl Azidocillin Azidocilline
nl anthrax antigen anthrax-antigeen nl Azithromycin Azitromycine
nl anti-d (rh) immunoglobulin rhesus(d)immunoglobuline nl Azlocillin Azlocilline
nl azidocillin azidocilline nl Bacampicillin Bacampicilline
nl azithromycin azitromycine nl Bacitracin Bacitracine
nl azlocillin azlocilline nl Benzathine benzylpenicillin Benzylpenicillinebenzathine
nl bacampicillin bacampicilline nl Benzathine phenoxymethylpenicillin Fenoxymethylpenicillinebenzathine
nl bacitracin bacitracine nl Benzylpenicillin Benzylpenicilline
nl benzathine benzylpenicillin benzylpenicillinebenzathine nl Calcium aminosalicylate Aminosalicylzuur
nl benzathine phenoxymethylpenicillin fenoxymethylpenicillinebenzathine nl Capreomycin Capreomycine
nl benzylpenicillin benzylpenicilline nl Carbenicillin Carbenicilline
nl botulinum antitoxin serum tegen botulisme nl Carindacillin Carindacilline
nl brucella antigen brucella-antigeen nl Caspofungin Caspofungine
nl calcium aminosalicylate aminosalicylzuur nl Cefacetrile Cefacetril
nl capreomycin capreomycine nl Cefalexin Cefalexine
nl carbenicillin carbenicilline nl Cefalotin Cefalotine
nl carindacillin carindacilline nl Cefamandole Cefamandol
nl caspofungin caspofungine nl Cefapirin Cefapirine
nl cefacetrile cefacetril nl Cefazedone Cefazedon
nl cefalexin cefalexine nl Cefazolin Cefazoline
nl cefalotin cefalotine nl Cefepime Cefepim
nl cefamandole cefamandol nl Cefixime Cefixim
nl cefapirin cefapirine nl Cefmenoxime Cefmenoxim
nl cefazedone cefazedon nl Cefmetazole Cefmetazol
nl cefazolin cefazoline nl Cefodizime Cefodizim
nl cefepime cefepim nl Cefonicid Cefonicide
nl cefixime cefixim nl Cefoperazone Cefoperazon
nl cefmenoxime cefmenoxim nl Cefoperazone/beta-lactamase inhibitor Cefoperazon combinatiepreparaten
nl cefmetazole cefmetazol nl Cefotaxime Cefotaxim
nl cefodizime cefodizim nl Cefoxitin Cefoxitine
nl cefonicid cefonicide nl Cefpirome Cefpirom
nl cefoperazone cefoperazon nl Cefpodoxime Cefpodoxim
nl cefoperazone and beta-lactamase inhibitor cefoperazon combinatiepreparaten nl Cefsulodin Cefsulodine
nl cefotaxime cefotaxim nl Ceftazidime Ceftazidim
nl cefoxitin cefoxitine nl Ceftezole Ceftezol
nl cefpirome cefpirom nl Ceftizoxime Ceftizoxim
nl cefpodoxime cefpodoxim nl Ceftriaxone Ceftriaxon
nl cefsulodin cefsulodine nl Cefuroxime Cefuroxim
nl ceftazidime ceftazidim nl Cefuroxime/metronidazole Cefuroxim/andere antibacteriele middelen
nl ceftezole ceftezol nl Chloramphenicol Chlooramfenicol
nl ceftizoxime ceftizoxim nl Chlortetracycline Chloortetracycline
nl ceftriaxone ceftriaxon nl Cinoxacin Cinoxacine
nl ceftriaxone, combinations ceftriaxon, combinatiepreparaten nl Ciprofloxacin Ciprofloxacine
nl cefuroxime cefuroxim nl Clarithromycin Claritromycine
nl cefuroxime and metronidazole cefuroxim met andere antibacteriele middelen nl Clavulanic acid Clavulaanzuur
nl chloramphenicol chlooramfenicol
nl chlortetracycline chloortetracycline
nl cholera, combinations with typhoid vaccine, inactivated, whole cell choleravaccin met tyfusvaccin, geinactiveerd, hele cel
nl cholera, inactivated, whole cell cholera, geinactiveerd, hele cel
nl cholera, live attenuated cholera, levend verzwakt
nl cinoxacin cinoxacine
nl ciprofloxacin ciprofloxacine
nl clarithromycin claritromycine
nl clavulanic acid clavulaanzuur nl clavulanic acid clavulaanzuur
nl clindamycin clindamycine nl Clindamycin Clindamycine
nl clometocillin clometocilline nl Clometocillin Clometocilline
nl clotrimazole clotrimazol nl Clotrimazole Clotrimazol
nl cloxacillin cloxacilline nl Cloxacillin Cloxacilline
nl colistin colistine nl Colistin Colistine
nl combinations combinatiepreparaten nl Dapsone Dapson
nl combinations combinatiepreparaten nl Daptomycin Daptomycine
nl combinations combinatiepreparaten nl Dibekacin Dibekacine
nl combinations combinatiepreparaten nl Dicloxacillin Dicloxacilline
nl combinations combinatiepreparaten nl Dirithromycin Diritromycine
nl combinations combinatiepreparaten nl Econazole Econazol
nl combinations combinatiepreparaten nl Enoxacin Enoxacine
nl combinations of penicillins combinatiepreparaten nl Epicillin Epicilline
nl combinations of tetracyclines tetracycline combinatiepreparaten nl Erythromycin Erytromycine
nl cytomegalovirus immunoglobulin cytomegalie-immunoglobuline nl Ethambutol/isoniazid Ethambutol/isoniazide
nl dapsone dapson nl Fleroxacin Fleroxacine
nl daptomycin daptomycine nl Flucloxacillin Flucloxacilline
nl dibekacin dibekacine nl Fluconazole Fluconazol
nl dicloxacillin dicloxacilline nl Flucytosine Fluorocytosine
nl diphtheria antitoxin serum tegen difterie nl Flurithromycin Fluritromycine
nl diphtheria immunoglobulin difterie-immunoglobuline nl Fosfomycin Fosfomycine
nl diphtheria toxoid difterietoxoide nl Fusidic acid Fusidinezuur
nl diphtheria-hemophilus influenzae b-pertussis-poliomyelitis-tetanus difterie-haemophilus-kinkhoest-poliomyelitis-tetanus nl Gatifloxacin Gatifloxacine
nl diphtheria-hemophilus influenzae b-pertussis-poliomyelitis-tetanus-hepatitis B difterie-haemophilus-kinkhoest-polio-tetanus-hepatitis B nl Gemifloxacin Gemifloxacine
nl diphtheria-hemophilus influenzae b-pertussis-tetanus-hepatitis B difterie-haemophilus-kinkhoest-tetanus-hepatitis B nl Gentamicin Gentamicine
nl diphtheria-hepatitis b-pertussis-tetanus difterie-hepatitis b-kinkhoest-tetanus nl Grepafloxacin Grepafloxacine
nl diphtheria-hepatitis b-tetanus difterie-hepatitis b-tetanus nl Hachimycin Hachimycine
nl diphtheria-pertussis-poliomyelitis-tetanus difterie-kinkhoest-poliomyelitis-tetanus nl Hetacillin Hetacilline
nl diphtheria-pertussis-poliomyelitis-tetanus-hepatitis B difterie-kinkhoest-poliomyelitis-tetanus-hepatitis B nl Imipenem/cilastatin Imipenem/enzymremmer
nl diphtheria-poliomyelitis-tetanus difterie-poliomyelitis-tetanus nl Inosine pranobex Inosiplex
nl diphtheria-rubella-tetanus difterie-rubella-tetanus nl Isepamicin Isepamicine
nl dirithromycin diritromycine nl Isoconazole Isoconazol
nl econazole econazol nl Isoniazid Isoniazide
nl encephalitis, japanese, inactivated, whole virus japanse-encefalitis, geinactiveerd, intact virus nl Itraconazole Itraconazol
nl encephalitis, tick borne immunoglobulin teken-encephalitis-immunoglobuline nl Josamycin Josamycine
nl encephalitis, tick borne, inactivated, whole virus tekenencefalitis, geinactiveerd, intact virus nl Kanamycin Kanamycine
nl enoxacin enoxacine nl Ketoconazole Ketoconazol
nl epicillin epicilline nl Levofloxacin Levofloxacine
nl erythromycin erytromycine nl Lincomycin Lincomycine
nl ethambutol and isoniazid ethambutol met isoniazide nl Lomefloxacin Lomefloxacine
nl fleroxacin fleroxacine nl Lysozyme Lysozym
nl flucloxacillin flucloxacilline nl Mandelic acid Amandelzuur
nl fluconazole fluconazol nl Metampicillin Metampicilline
nl flucytosine fluorocytosine nl Meticillin Meticilline
nl flurithromycin fluritromycine nl Metisazone Metisazon
nl fosfomycin fosfomycine nl Metronidazole Metronidazol
nl fusidic acid fusidinezuur nl Mezlocillin Mezlocilline
nl gas-gangrene sera serum tegen gasgangreen nl Micafungin Micafungine
nl gatifloxacin gatifloxacine nl Miconazole Miconazol
nl gemifloxacin gemifloxacine nl Midecamycin Midecamycine
nl gentamicin gentamicine nl Miocamycin Miocamycine
nl grepafloxacin grepafloxacine nl Moxifloxacin Moxifloxacine
nl hachimycin hachimycine nl Mupirocin Mupirocine
nl hemophilus influenzae B and hepatitis B haemophilus influenzae b-hepatitis B nl Nalidixic acid Nalidixinezuur
nl hemophilus influenzae B and poliomyelitis haemophilus influenzae b-poliomyelitis nl Neomycin Neomycine
nl hemophilus influenzae B, combinations with pertussis and toxoids haemophilus influenzae B met kinkhoest en toxoiden nl Netilmicin Netilmicine
nl hemophilus influenzae B, combinations with toxoids haemophilus influenzae B met toxoiden nl Nitrofurantoin Nitrofurantoine
nl hemophilus influenzae B, purified antigen conjugated haemophilus influenzae B, gezuiverd geconjugeerd antigeen nl Norfloxacin Norfloxacine
nl hepatitis A immunoglobulin hepatitis a-immunoglobuline nl Novobiocin Novobiocine
nl hepatitis A, inactivated, whole virus hepatitis A, geinactiveerd, intact virus nl Nystatin Nystatine
nl hepatitis B immunoglobulin hepatitis b-immunoglobuline nl Ofloxacin Ofloxacine
nl hepatitis B, purified antigen hepatitis B, gezuiverd antigeen nl Oleandomycin Oleandomycine
nl hetacillin hetacilline nl Ornidazole Ornidazol
nl imipenem and cilastatin imipenem met enzymremmer nl Oxacillin Oxacilline
nl immunoglobulins, normal human, for extravascular adm, immunoglobuline, normaal, extravasculair nl Oxolinic acid Oxolinezuur
nl immunoglobulins, normal human, for intravascular adm, immunoglobuline, normaal, intravasculair nl Oxytetracycline Oxytetracycline
nl influenza, inactivated, split virus or surface antigen influenza, gezuiverd antigeen nl Pazufloxacin Pazufloxacine
nl influenza, inactivated, whole virus influenza, geinactiveerd, intact virus nl Pefloxacin Pefloxacine
nl inosine pranobex inosiplex nl Penamecillin Penamecilline
nl isepamicin isepamicine nl Penicillin Penicilline
nl isoconazole isoconazol nl Pheneticillin Feneticilline
nl isoniazid isoniazide nl Phenoxymethylpenicillin Fenoxymethylpenicilline
nl isoniazid, combinations isoniazide, combinatiepreparaten nl Pipemidic acid Pipemidinezuur
nl itraconazole itraconazol nl Piperacillin Piperacilline
nl josamycin josamycine nl Piperacillin/beta-lactamase inhibitor Piperacilline/enzymremmer
nl kanamycin kanamycine nl Piromidic acid Piromidinezuur
nl ketoconazole ketoconazol nl Pivampicillin Pivampicilline
nl levofloxacin levofloxacine nl Polymyxin B Polymyxine B
nl lincomycin lincomycine nl Posaconazole Posaconazol
nl lomefloxacin lomefloxacine nl Pristinamycin Pristinamycine
nl lysozyme lysozym nl Procaine benzylpenicillin Benzylpenicillineprocaine
nl mandelic acid amandelzuur nl Propicillin Propicilline
nl measles immunoglobulin mazelenimmunoglobuline nl Prulifloxacin Prulifloxacine
nl measles, combinations with mumps and rubella, live attenuated mazelen met bof en rubella, levend verzwakt nl Quinupristin/dalfopristin Quinupristine/dalfopristine
nl measles, combinations with mumps, live attenuated mazelen met bof, levend verzwakt nl Ribostamycin Ribostamycine
nl measles, combinations with mumps, rubella and varicella, live attenuated mazelen met bof, rubella en varicella, levend verzwakt nl Rifabutin Rifabutine
nl measles, combinations with rubella, live attenuated mazelen met rubella, levend verzwakt nl Rifampicin Rifampicine
nl measles, live attenuated mazelen, levend verzwakt nl Rifampicin, pyrazinamide, ethambutol/isoniazid Rifampicine/pyrazinamide, ethambutol en isoniazide
nl meningococcus A, purified polysaccharides antigen meningokok A, gezuiverd polysaccharidenantigeen nl Rifampicin, pyrazinamide/isoniazid Rifampicine/pyrazinamide en isoniazide
nl meningococcus A,c, bivalent purified polysaccharides antigen meningokok, 2 typen, gezuiverd polysaccharidenantigeen nl Rifampicin/isoniazid Rifampicine/isoniazide
nl meningococcus A,c,y,w-135, tetravalent purified polysaccharides antigen meningokok, 4 typen, gezuiverd polysaccharidenantigeen nl Rifamycin Rifamycine
nl meningococcus B, outer membrane vesicle vaccine meningokok B, buitenmembraanvaccin nl Rifaximin Rifaximine
nl meningococcus C, purified polysaccharides antigen conjugated meningokok C, gezuiverd saccharidenantigeen geconjugeerd nl Rokitamycin Rokitamycine
nl metampicillin metampicilline nl Rosoxacin Rosoxacine
nl meticillin meticilline nl Roxithromycin Roxitromycine
nl metisazone metisazon nl Rufloxacin Rufloxacine
nl metronidazole metronidazol nl Sisomicin Sisomicine
nl mezlocillin mezlocilline nl Sodium aminosalicylate Aminosalicylzuur,4- (na-zout)
nl micafungin micafungine nl Sparfloxacin Sparfloxacine
nl miconazole miconazol nl Spectinomycin Spectinomycine
nl midecamycin midecamycine nl Spiramycin Spiramycine
nl miocamycin miocamycine nl Spiramycin/metronidazole Spiramycine/andere antibacteriele middelen
nl moxifloxacin moxifloxacine nl Staphylococcus immunoglobulin Stafylokokkenimmunoglobuline
nl mumps immunoglobulin bofimmunoglobuline nl Streptoduocin Streptoduocine
nl mumps, live attenuated bof, levend verzwakt nl Streptomycin Streptomycine
nl mupirocin mupirocine nl Streptomycin/isoniazid Streptomycine/isoniazide
nl nalidixic acid nalidixinezuur nl Sulbenicillin Sulbenicilline
nl neomycin neomycine nl Sulfadiazine/tetroxoprim Sulfadiazine/tetroxoprim
nl netilmicin netilmicine nl Sulfadiazine/trimethoprim Sulfadiazine/trimethoprim
nl nitrofurantoin nitrofurantoine nl Sulfadimidine/trimethoprim Sulfadimidine/trimethoprim
nl norfloxacin norfloxacine nl Sulfafurazole Sulfafurazol
nl novobiocin novobiocine nl Sulfaisodimidine Sulfisomidine
nl nystatin nystatine nl Sulfalene Sulfaleen
nl ofloxacin ofloxacine nl Sulfamazone Sulfamazon
nl oleandomycin oleandomycine nl Sulfamerazine/trimethoprim Sulfamerazine/trimethoprim
nl ornidazole ornidazol nl Sulfamethizole Sulfamethizol
nl other meningococcal monovalent purified polysaccharides antigen meningokok, 1 type, gezuiverd polysaccaridenantigeen nl Sulfamethoxazole Sulfamethoxazol
nl other meningococcal polyvalent purified polysaccharides antigen meningokok, meer typen, gezuiverd polysaccharidenantigeen nl Sulfamethoxazole/trimethoprim Sulfamethoxazol/trimethoprim
nl oxacillin oxacilline nl Sulfametoxydiazine Sulfamethoxydiazine
nl oxolinic acid oxolinezuur nl Sulfametrole/trimethoprim Sulfametrol/trimethoprim
nl oxytetracycline, combinations oxytetracycline, combinatiepreparaten nl Sulfamoxole Sulfamoxol
nl pazufloxacin pazufloxacine nl Sulfamoxole/trimethoprim Sulfamoxol/trimethoprim
nl pefloxacin pefloxacine nl Sulfaperin Sulfaperine
nl penamecillin penamecilline nl Sulfaphenazole Sulfafenazol
nl penicillins, combinations with other antibacterials penicillines met andere antibacteriele middelen nl Sulfathiazole Sulfathiazol
nl pertussis immunoglobulin kinkhoestimmunoglobuline nl Sulfathiourea Sulfathioureum
nl pertussis, inactivated, whole cell pertussis, geinactiveerd, hele cel nl Sultamicillin Sultamicilline
nl pertussis, inactivated, whole cell, combinations with toxoids pertussis, geinactiveerd hele cel, met toxoiden nl Talampicillin Talampicilline
nl pertussis, purified antigen pertussis, gezuiverd antigeen nl Teicoplanin Teicoplanine
nl pertussis, purified antigen, combinations with toxoids pertussis, gezuiverd antigeen, met toxoiden nl Telithromycin Telitromycine
nl pheneticillin feneticilline nl Temafloxacin Temafloxacine
nl phenoxymethylpenicillin fenoxymethylpenicilline nl Temocillin Temocilline
nl pipemidic acid pipemidinezuur nl Tenofovir disoproxil Tenofovir
nl piperacillin piperacilline nl Terizidone Terizidon
nl piperacillin and beta-lactamase inhibitor piperacilline met enzymremmer nl Thiamphenicol Thiamfenicol
nl piromidic acid piromidinezuur nl Thiamphenicol Thiamfenicol combinatiepreparaten
nl pivampicillin pivampicilline nl Thioacetazone/isoniazid Thioacetazon/isoniazide
nl plague, inactivated, whole cell yersinia pestis, geinactiveerd, hele cel nl Ticarcillin Ticarcilline
nl pneumococcus, purified polysaccharides antigen pneumokok, gezuiverd polysaccharidenantigeen nl Ticarcillin/beta-lactamase inhibitor Ticarcilline/enzymremmer
nl pneumococcus, purified polysaccharides antigen conjugated pneumokok, gezuiverd geconjugeerd polysaccharidenantigeen nl Tinidazole Tinidazol
nl poliomyelitis oral, monovalent, live attenuated poliomyelitis, oraal, 1 type, levend verzwakt nl Tobramycin Tobramycine
nl poliomyelitis oral, trivalent, live attenuated poliomyelitis, oraal, 3 typen, levend verzwakt nl Troleandomycin Troleandomycine
nl poliomyelitis, trivalent, inactivated, whole virus poliomyelitis, 3 typen, geinactiveerd, intact virus nl Trovafloxacin Trovafloxacine
nl polymyxin B polymyxine B nl Vancomycin Vancomycine
nl posaconazole posaconazol nl Voriconazole Voriconazol
nl pristinamycin pristinamycine
nl procaine benzylpenicillin benzylpenicillineprocaine
nl propicillin propicilline
nl prulifloxacin prulifloxacine
nl quinupristin/dalfopristin quinupristine/dalfopristine
nl rabies immunoglobulin rabiesimmunoglobuline
nl rabies serum serum tegen rabies
nl rabies, inactivated, whole virus rabies, geinactiveerd, intact virus
nl ribostamycin ribostamycine
nl rifabutin rifabutine
nl rifampicin rifampicine
nl rifampicin and isoniazid rifampicine met isoniazide
nl rifampicin, pyrazinamide and isoniazid rifampicine met pyrazinamide en isoniazide
nl rifampicin, pyrazinamide, ethambutol and isoniazid rifampicine met pyrazinamide, ethambutol en isoniazide
nl rifamycin rifamycine
nl rifaximin rifaximine
nl rokitamycin rokitamycine
nl rosoxacin rosoxacine
nl rota virus, live attenuated rotavirus, levend verzwakt
nl roxithromycin roxitromycine
nl rubella immunoglobulin rubella-immunoglobuline
nl rubella, combinations with mumps, live attenuated rubella met bof, levend verzwakt
nl rubella, live attenuated rubella, levend verzwakt
nl rufloxacin rufloxacine
nl sisomicin sisomicine
nl snake venom antiserum serum tegen slangebeet
nl sodium aminosalicylate aminosalicylzuur,4- (na-zout)
nl sparfloxacin sparfloxacine
nl spectinomycin spectinomycine
nl spiramycin spiramycine
nl spiramycin and metronidazole spiramycine met andere antibacteriele middelen
nl staphylococcus immunoglobulin stafylokokkenimmunoglobuline
nl streptoduocin streptoduocine
nl streptomycin streptomycine
nl streptomycin and isoniazid streptomycine met isoniazide
nl sulbenicillin sulbenicilline
nl sulfadiazine and tetroxoprim sulfadiazine met tetroxoprim
nl sulfadiazine and trimethoprim sulfadiazine met trimethoprim
nl sulfadimidine and trimethoprim sulfadimidine met trimethoprim
nl sulfafurazole sulfafurazol
nl sulfaisodimidine sulfisomidine
nl sulfalene sulfaleen
nl sulfamazone sulfamazon
nl sulfamerazine and trimethoprim sulfamerazine met trimethoprim
nl sulfamethizole sulfamethizol
nl sulfamethoxazole sulfamethoxazol
nl sulfamethoxazole and trimethoprim sulfamethoxazol met trimethoprim
nl sulfametoxydiazine sulfamethoxydiazine
nl sulfametrole and trimethoprim sulfametrol met trimethoprim
nl sulfamoxole sulfamoxol
nl sulfamoxole and trimethoprim sulfamoxol met trimethoprim
nl sulfaperin sulfaperine
nl sulfaphenazole sulfafenazol
nl sulfathiazole sulfathiazol
nl sulfathiourea sulfathioureum
nl sulfonamides, combinations with other antibacterials (excl, trimethoprim) sulfonamiden met andere antibacteriele middelen (exc trim)
nl sultamicillin sultamicilline
nl talampicillin talampicilline
nl teicoplanin teicoplanine
nl telithromycin telitromycine
nl temafloxacin temafloxacine
nl temocillin temocilline
nl tenofovir disoproxil tenofovir
nl terizidone terizidon
nl tetanus antitoxin serum tegen tetanus
nl tetanus immunoglobulin tetanusimmunoglobuline
nl tetanus toxoid tetanustoxoide
nl tetanus toxoid, combinations with diphtheria toxoid tetanustoxoide met difterietoxoide
nl tetanus toxoid, combinations with tetanus immunoglobulin tetanustoxoide met tetanusimmunoglobuline
nl thiamphenicol thiamfenicol
nl thiamphenicol, combinations thiamfenicol combinatiepreparaten
nl thioacetazone and isoniazid thioacetazon met isoniazide
nl ticarcillin ticarcilline
nl ticarcillin and beta-lactamase inhibitor ticarcilline met enzymremmer
nl tinidazole tinidazol
nl tobramycin tobramycine
nl troleandomycin troleandomycine
nl trovafloxacin trovafloxacine
nl tuberculosis, live attenuated bacillus calmette guerin, levend verzwakt
nl typhoid, combinations with paratyphi types buiktyfus met paratyfus-typen
nl typhoid, inactivated, whole cell buiktyfus, geinactiveerd, hele cel
nl typhoid, oral, live attenuated buiktyfus, oraal, levend verzwakt
nl typhoid, purified polysaccharide antigen buiktyfus, gezuiverd polysaccharidenantigeen
nl typhoid-hepatitis A buiktyfus-hepatitis A
nl typhus exanthematicus, inactivated, whole cell vlektyfus, geinactiveerd, hele cel
nl vaccinia immunoglobulin vaccinia-immunoglobuline
nl vancomycin vancomycine
nl varicella, live attenuated varicella, levend verzwakt
nl varicella/zoster immunoglobulin varicella-zoster-immunoglobuline
nl voriconazole voriconazol
nl yellow fever, live attenuated gele koorts, levend verzwakt

Can't render this file because it has a wrong number of fields in line 157.

6
man/WHOCC.Rd
View File

@ -22,8 +22,8 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
} }
\examples{ \examples{
as.atc("meropenem") as.ab("meropenem")
atc_name("J01DH02") ab_name("J01DH02")
atc_tradenames("flucloxacillin") ab_tradenames("flucloxacillin")
} }

2
man/translate.Rd
View File

@ -15,7 +15,7 @@ Strings will be translated to foreign languages if they are defined in a local t
\code{system.file("translations.tsv", package = "AMR")} \code{system.file("translations.tsv", package = "AMR")}
This file will be read by all functions where a translated output can be desired, like all \code{\link{mo_property}} functions (\code{\link{mo_fullname}}, \code{\link{mo_type}}, etc.). Please suggest your own translations \href{https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation suggestion}{by creating a new issue on our repository}. This file will be read by all functions where a translated output can be desired, like all \code{\link{mo_property}} functions (\code{\link{mo_fullname}}, \code{\link{mo_type}}, etc.). Please suggest your own translations \href{https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation\%20suggestion}{by creating a new issue on our repository}.
The system language will be used at default, if supported, using \code{\link{get_locale}}. The system language can be overwritten with \code{\link{getOption}("AMR_locale")}. The system language will be used at default, if supported, using \code{\link{get_locale}}. The system language can be overwritten with \code{\link{getOption}("AMR_locale")}.
} }

3
reproduction_of_antibiotics.R
View File

@ -285,7 +285,7 @@ antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]] <- list(c("MOX
antibiotics <- filter(antibiotics, ab != "MOX") antibiotics <- filter(antibiotics, ab != "MOX")
# ESBL E-test codes: # ESBL E-test codes:
antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl")) antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl"))
antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz")) antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz", "cefta"))
antibiotics[which(antibiotics$ab == "CPC"), "abbreviations"][[1]] <- list(c("xpml")) antibiotics[which(antibiotics$ab == "CPC"), "abbreviations"][[1]] <- list(c("xpml"))
antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]], "xpm")) antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]], "xpm"))
antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c("xctl")) antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c("xctl"))
@ -295,3 +295,4 @@ class(antibiotics$ab) <- "ab"
class(antibiotics$atc) <- "atc" class(antibiotics$atc) <- "atc"
usethis::use_data(antibiotics, overwrite = TRUE) usethis::use_data(antibiotics, overwrite = TRUE)
rm(antibiotics)