Date: Thu, 21 Feb 2019 23:32:30 +0100
Subject: [PATCH] unit tests
---
NEWS.md | 10 +-
R/mo.R | 15 +-
R/zzz.R | 258 +++++++++--
docs/articles/AMR.html | 413 +++++++++---------
.../AMR_files/figure-html/plot 1-1.png | Bin 33765 -> 33759 bytes
.../AMR_files/figure-html/plot 3-1.png | Bin 21104 -> 21126 bytes
.../AMR_files/figure-html/plot 4-1.png | Bin 69613 -> 69626 bytes
.../AMR_files/figure-html/plot 5-1.png | Bin 51365 -> 51368 bytes
docs/articles/benchmarks.html | 91 ++--
.../figure-html/unnamed-chunk-5-1.png | Bin 32533 -> 31806 bytes
.../figure-html/unnamed-chunk-5-2.png | Bin 33108 -> 33488 bytes
docs/news/index.html | 13 +-
reproduction_of_microorganisms.R | 5 +-
tests/testthat/test-data.R | 6 +
tests/testthat/test-mo.R | 16 +
tests/testthat/test-mo_property.R | 3 +
16 files changed, 534 insertions(+), 296 deletions(-)
diff --git a/NEWS.md b/NEWS.md
index 6d347bb1..fca8315b 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -11,10 +11,14 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
#### New
* **BREAKING**: removed deprecated functions, parameters and references to 'bactid'. Use `as.mo()` to identify an MO code.
* Catalogue of Life as a new taxonomic source for data about microorganisms, which also contains all ITIS data we used previously. The `microorganisms` data set now contains:
- * All ~55,000 species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses
- * All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera *Aspergillus*, *Candida*, *Pneumocystis*, *Saccharomyces* and *Trichophyton*).
- * All ~15,000 previously accepted names of species that have been taxonomically renamed
+ * All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses
+ * All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales.
+
+ The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of *Aspergillus*, *Candida*, *Pneumocystis*, *Saccharomyces* and *Trichophyton*).
+ * All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed
* The responsible author(s) and year of scientific publication
+
+ This data is updated annually - check the included version with `catalogue_of_life_version()`.
* Due to this change, some `mo` codes changed (e.g. *Streptococcus* changed from `B_STRPTC` to `B_STRPT`). A translation table is used internally to support older microorganism IDs, so users will not notice this difference.
* Support for data from [WHONET](https://whonet.org/) and [EARS-Net](https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net) (European Antimicrobial Resistance Surveillance Network):
* Exported files from WHONET can be read and used in this package. For functions like `first_isolate()` and `eucast_rules()`, all parameters will be filled in automatically.
diff --git a/R/mo.R b/R/mo.R
index cd495022..ecf598ae 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -372,7 +372,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
x[i] <- microorganismsDT[mo == 'B_ENTRC', ..property][[1]][1L]
next
}
- if (toupper(x_trimmed[i]) %in% c('EHEC', 'EPEC', 'EIEC', 'STEC', 'ATEC')) {
+ if (toupper(x_trimmed[i]) %in% c("EHEC", "EPEC", "EIEC", "STEC", "ATEC")) {
x[i] <- microorganismsDT[mo == 'B_ESCHR_COL', ..property][[1]][1L]
next
}
@@ -614,8 +614,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
if (NROW(found) > 0) {
col_id_new <- found[1, col_id_new]
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
- # mo_ref("Chlamydia psittaci) = "Page, 1968" (with warning)
- # mo_ref("Chlamydophila psittaci) = "Everett et al., 1999"
+ # mo_ref("Chlamydia psittaci") = "Page, 1968" (with warning)
+ # mo_ref("Chlamydophila psittaci") = "Everett et al., 1999"
if (property == "ref") {
x[i] <- found[1, ref]
} else {
@@ -632,7 +632,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# check for uncertain results ----
if (allow_uncertain == TRUE) {
- uncertain_fn <- function(a.x_backup, b.x_trimmed, c.x_withspaces_start_end, d.x_withspaces_start_only, e.x) {
+ uncertain_fn <- function(a.x_backup, b.x_trimmed, c.x_withspaces_start_end, d.x_withspaces_start_only) {
# (1) look for genus only, part of name ----
if (nchar(b.x_trimmed) > 4 & !b.x_trimmed %like% " ") {
@@ -650,8 +650,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# (2) look again for old taxonomic names, now for G. species ----
found <- microorganisms.oldDT[fullname %like% c.x_withspaces_start_end
- | fullname %like% d.x_withspaces_start_only
- | fullname %like% e.x,]
+ | fullname %like% d.x_withspaces_start_only]
if (NROW(found) > 0 & nchar(b.x_trimmed) >= 6) {
if (property == "ref") {
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
@@ -715,7 +714,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
}
}
- # (6) not yet implemented taxonomic changes in ITIS ----
+ # (6) not yet implemented taxonomic changes in Catalogue of Life ----
found <- suppressMessages(suppressWarnings(exec_as.mo(TEMPORARY_TAXONOMY(b.x_trimmed), clear_options = FALSE, allow_uncertain = FALSE)))
if (!is.na(found)) {
found_result <- found
@@ -732,7 +731,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
return(NA_character_)
}
- x[i] <- uncertain_fn(x_backup[i], x_trimmed[i], x_withspaces_start_end[i], x_withspaces_start_only[i], x[i])
+ x[i] <- uncertain_fn(x_backup[i], x_trimmed[i], x_withspaces_start_end[i], x_withspaces_start_only[i])
if (!is.na(x[i])) {
next
}
diff --git a/R/zzz.R b/R/zzz.R
index 349055cb..17bdba90 100755
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -19,60 +19,246 @@
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
-#' @importFrom dplyr mutate case_when
#' @importFrom data.table as.data.table setkey
.onLoad <- function(libname, pkgname) {
# get new functions not available in older versions of R
backports::import(pkgname)
# register data
- if (!all(c("microorganismsDT",
- "microorganisms.prevDT",
- "microorganisms.unprevDT",
- "microorganisms.oldDT") %in% ls(envir = asNamespace("AMR")))) {
-
- # packageStartupMessage("Loading taxonomic database...", appendLF = FALSE)
-
- microorganismsDT <- AMR::microorganisms %>%
- mutate(prevalence = case_when(
- # most important Gram negatives # Streptococci and Staphylococci
- class == "Gammaproteobacteria"
- | order %in% c("Lactobacillales", "Bacillales")
- ~ 1,
- phylum %in% c("Proteobacteria",
- "Firmicutes",
- "Actinobacteria",
- "Bacteroidetes")
- | genus %in% c("Candida",
- "Aspergillus",
- "Trichophyton",
- "Giardia",
- "Dientamoeba",
- "Entamoeba")
- ~ 2,
- TRUE ~ 3
- )) %>%
- as.data.table()
- setkey(microorganismsDT, kingdom, prevalence, fullname)
+ if (!all(c("microorganismsDT", "microorganisms.oldDT") %in% ls(envir = asNamespace("AMR")))) {
microorganisms.oldDT <- as.data.table(AMR::microorganisms.old)
setkey(microorganisms.oldDT, col_id, fullname)
assign(x = "microorganismsDT",
- value = microorganismsDT,
+ value = make_DT(),
envir = asNamespace("AMR"))
assign(x = "microorganisms.oldDT",
value = microorganisms.oldDT,
envir = asNamespace("AMR"))
- # conversion of old MO codes from v0.5.0 (ITIS) to later versions (Catalogue of Life)
- mo_codes_v0.5.0 <- c(B_ACHRMB = "B_ACHRM", B_ANNMA = "B_ACTNS", B_ACLLS = "B_ALCYC", B_AHNGM = "B_ARCHN", B_ARMTM = "B_ARMTMN", B_ARTHRS = "B_ARTHR", B_APHLS = "B_AZRHZP", B_BRCHA = "B_BRCHY", B_BCTRM = "B_BRVBCT", B_CLRBCT = "B_CLRBC", B_CTRDM = "B_CLSTR", B_CPRMM = "B_CYLND", B_DLCLN = "B_DPLCL", B_DMCLM = "B_DSLFT", B_DSLFVB = "B_DSLFV", B_FCTRM = "B_FSBCT", B_GNRLA = "B_GRDNR", B_HNRBM = "B_HLNRB", B_HPHGA = "B_HNPHGA", B_HCCCS = "B_HYDRC", B_MCRCLS = "B_MCRCL", B_MTHYLS = "B_MLSMA", B_MARCLS = "B_MRCLS", B_MGCLS = "B_MSTGC", B_MCLLA = "B_MTHYLC", B_MYCPLS = "B_MYCPL", B_NBCTR = "B_NTRBC", B_OCLLS = "B_OCNBC", B_PTHRX = "B_PLNKT", B_PCCCS = "B_PRCHL", B_PSPHN = "B_PRPHY", B_PDMNS = "B_PSDMN", B_SCCHRP = "B_SCCHR", B_SRBCTR = "B_SHRBCTR", B_STRPTC = "B_STRPT", B_SHMNS = "B_SYNTR", B_TRBCTR = "B_THRMN", P_ALBMN = "C_ABMNA", F_ACHLY = "C_ACHLY", P_ACINT = "C_ACINT", P_ARTCL = "C_ACLNA", P_ACRVL = "C_ACRVL", P_ADRCT = "C_ADRCT", P_AMPHS = "C_AHSRS", F_ALBUG = "C_ALBUG", P_ALCNT = "C_ALCNT", P_ALFRD = "C_ALFRD", P_ALLGR = "C_ALLGR", P_AMPHL = "C_ALPTS", F_ALTHR = "C_ALTHR", P_AMLLA = "C_AMLLA", P_ANMLN = "C_AMLNA", P_AMMBC = "C_AMMBC", P_AMMDS = "C_AMMDS", P_AMMLG = "C_AMMLG", P_AMMMR = "C_AMMMR", P_AMMMS = "C_AMMMS", P_AMMON = "C_AMMON", P_AMMSC = "C_AMMSC", P_AMMSP = "C_AMMSP", P_AMMST = "C_AMMST", P_AMMTM = "C_AMMTM", F_AMYCS = "C_AMYCS", P_ANARM = "C_ANARM", P_ANGLD = "C_ANGLD", P_ANGLG = "C_ANGLG", P_ANNLC = "C_ANNLC", F_ANSLP = "C_ANSLP", F_APDCH = "C_APDCH", F_APHND = "C_APHND", F_APLNC = "C_APLNC", F_AQLND = "C_AQLND", P_ARCHS = "C_ARCHAS", P_ASTRN = "C_ARNNN", P_ARNPR = "C_ARNPR", F_ARSPR = "C_ARSPR", P_ARTST = "C_ARTSTR", P_AMPHC = "C_ARYNA", P_ASCHM = "C_ASCHM", P_ASPDS = "C_ASPDS", P_ASTCL = "C_ASTCL", P_ASTRG = "C_ASTRGR", P_ASTRM = "C_ASTRMM", P_ASTRR = "C_ASTRR", P_ASTRT = "C_ASTRTR", F_ATKNS = "C_ATKNS", F_AYLLA = "C_AYLLA", P_BAGGN = "C_BAGGN", P_BCCLL = "C_BCCLL", P_BDLLD = "C_BDLLD", P_BGNRN = "C_BGNRN", P_BLCLN = "C_BLCLN", P_BLMND = "C_BLMND", P_BLMNL = "C_BLMNL", P_BLPHR = "C_BLPHR", P_BLVNT = "C_BLVNT", P_BOLVN = "C_BOLVN", P_BORLS = "C_BORLS", P_BRNNM = "C_BRNNM", P_BRSLN = "C_BRSLN", P_BRSRD = "C_BRSRD", F_BRVLG = "C_BRVLG", F_BNLLA = "C_BRVLGN", P_BSCCM = "C_BSCCM", F_BSDPH = "C_BSDPH", P_BTHYS = "C_BTHYS", P_BTLLN = "C_BTLLN", P_BULMN = "C_BULMN", P_CCLDM = "C_CCLDM", P_CDNLL = "C_CDNLL", P_CLPSS = "C_CDNLLP", P_CHLDN = "C_CHLDNL", P_CHLST = "C_CHLST", P_CHNLM = "C_CHNLM", P_CHRYS = "C_CHRYSL", P_CHTSP = "C_CHTSP", P_CBCDS = "C_CIBCDS", P_CLCRN = "C_CLCRN", P_CLMNA = "C_CLMNA", P_CLPDM = "C_CLPDM", P_CLPHR = "C_CLPHRY", P_CLVLN = "C_CLVLN", P_CMPNL = "C_CMPNL", P_CNCRS = "C_CNCRS", P_CNTCH = "C_CNTCH", F_CNTRM = "C_CNTRMY", P_COLPD = "C_COLPD", P_COLPS = "C_COLPS", P_CPRDS = "C_CPRDS", P_CRNSP = "C_CPRMA", P_CRBNL = "C_CRBNL", P_CRBRB = "C_CRBRB", P_CRBRG = "C_CRBRG", P_CRBRS = "C_CRBRS", P_CRCHS = "C_CRCHS", P_CRCLC = "C_CRCLC", P_CRNLC = "C_CRNLC", P_CRNTH = "C_CRNTH", P_CRPNT = "C_CRPNT", P_CRSTG = "C_CRSTG", P_CRTHN = "C_CRTHN", P_CRTRN = "C_CRTRN", P_CYMBL = "C_CRTTA", P_CRYPT = "C_CRYPT", P_CSHMN = "C_CSHMNL", P_CSSDL = "C_CSSDL", P_CLNDS = "C_CSSDLN", P_CHRNA = "C_CTHRN", P_CTPSS = "C_CTPSS", P_CUNLN = "C_CUNLN", P_CYLND = "C_CVLNA", P_CYCLC = "C_CYCLCB", P_CDNTA = "C_CYCLD", P_CYCLG = "C_CYCLG", P_CYCLM = "C_CYCLM", P_CYRTL = "C_CYRTL", P_CYSTM = "C_CYSTM", P_DCHLM = "C_DCHLM", P_DCRBS = "C_DCRBS", P_DCTYC = "C_DCTYC", P_DIDNM = "C_DIDNM", P_DLPTS = "C_DLPTS", P_DNTLN = "C_DNTLN", P_DNTST = "C_DNTST", P_DORTH = "C_DORTH", P_DCTYP = "C_DPHMS", F_DPLCY = "C_DPLCY", P_DNDRT = "C_DRTNA", P_DSCMM = "C_DSCMM", P_DSCRB = "C_DSCRB", P_DSCRN = "C_DSCRN", P_DSCSP = "C_DSCSP", P_DSNBR = "C_DSNBR", P_DYCBC = "C_DYCBC", F_DCTYC = "C_DYCHS", F_ECTRG = "C_ECTRG", B_EDWRD = "C_EDWRD", P_EGGRL = "C_EGGRL", P_EHLYS = "C_EHLYS", P_EHRNB = "C_EHRNB", P_ELPHD = "C_ELPHD", P_ENCHL = "C_ELYDM", P_EPHDM = "C_EPHDM", P_EPLTS = "C_EPLTS", P_EPLXL = "C_EPLXL", P_EPNDL = "C_EPNDL", P_EPNDS = "C_EPNDS", P_ENLLA = "C_EPSTM", P_EPSTY = "C_EPSTY", F_ERYCH = "C_ERYCH", F_ESMDM = "C_ESMDM", P_ESSYR = "C_ESSYR", P_FSCHR = "C_FHRNA", P_FLRLS = "C_FLRLS", P_FLNTN = "C_FNTNA", P_FRNDC = "C_FRNDC", P_FRNTN = "C_FRNTN", P_FRSNK = "C_FRSNK", P_FNLLA = "C_FSCHRN", P_FSSRN = "C_FSSRN", P_FVCSS = "C_FVCSS", P_GDRYN = "C_GDRYN", F_GELGN = "C_GELGN", P_GERDA = "C_GERDA", P_GLACM = "C_GLACM", P_GLBBL = "C_GLBBL", P_GLBGR = "C_GLBGR", P_GLBLN = "C_GLBLN", P_GRTLA = "C_GLBRT", P_GLBTX = "C_GLBTX", P_GLLNA = "C_GLLNA", P_GLMSP = "C_GLMSP", P_GLNDL = "C_GLNDL", F_GNMCH = "C_GNMCH", P_GOSLL = "C_GOSLL", P_GRNDS = "C_GRNDS", P_GRNTA = "C_GRNTA", P_GLBRT = "C_GTLLA", P_GTTLN = "C_GTTLN", P_GVLNP = "C_GVLNP", P_GYPSN = "C_GYPSN", P_GYRDN = "C_GYRDN", P_HALTR = "C_HALTR", P_HANZW = "C_HANZW", P_HAURN = "C_HAURN", P_HELNN = "C_HELNN", P_HLPHR = "C_HHRYA", P_HLNTA = "C_HLNTA", F_HLPHT = "C_HLPHT", P_HLSTC = "C_HLSTC", P_HMSPH = "C_HMSPH", P_HMTRM = "C_HMTRM", P_HPKNS = "C_HPKNS", P_HPLPH = "C_HPLPH", P_HPPCR = "C_HPPCR", P_HNLLA = "C_HPPCRP", P_HRMSN = "C_HRMSN", P_HRNLL = "C_HRNLL", F_HRPCH = "C_HRPCH", P_HSTGR = "C_HSTGR", P_HSTTL = "C_HSTTL", P_HTRST = "C_HTGNA", P_HTRLL = "C_HTRLL", P_HTRPH = "C_HTRPH", F_HYPHC = "C_HYPHC", P_HYPRM = "C_HYPRM", P_INTRN = "C_INTRN", P_IRIDI = "C_IRIDI", P_ISLND = "C_ISLND", P_JCLLL = "C_JCLLL", P_KHLLL = "C_KHLLL", P_KRNPS = "C_KRNPS", P_KRRRL = "C_KRRRL", P_LABOE = "C_LABOE", P_LAGEN = "C_LAGEN", P_LBSLL = "C_LBSLL", F_LTHLA = "C_LBYRN", P_LCRYM = "C_LCRYM", P_LEMBS = "C_LEMBS", F_LGNDM = "C_LGNDM", P_LGNMM = "C_LGNMM", P_LGNPH = "C_LGNPHR", F_LGNSM = "C_LGNSM", P_LGYNP = "C_LGYNP", P_LITTB = "C_LITTB", P_LITUL = "C_LITUL", P_LMBDN = "C_LMBDN", P_LMRCK = "C_LMRCK", F_LBYRN = "C_LMYXA", P_LNGLN = "C_LNGLN", P_LNTCL = "C_LNTCL", P_LOXDS = "C_LOXDS", F_LPTLG = "C_LPTLG", F_LNLLA = "C_LPTLGN", F_LPTMT = "C_LPTMT", P_LRYNG = "C_LRYNG", P_LTCRN = "C_LTCRN", P_LTHPL = "C_LTHPL", P_LTNTS = "C_LTNTS", F_LTRST = "C_LTRST", P_LXPHY = "C_LXPHY", P_MCRTH = "C_MCRTH", P_MELNS = "C_MELNS", P_MSDNM = "C_MESDNM", P_METPS = "C_METPS", P_MIMSN = "C_MIMSN", P_MINCN = "C_MINCN", P_MLLNL = "C_MLLNL", P_MLMMN = "C_MLMMN", F_MNDNL = "C_MNDNL", P_MNLYS = "C_MNLYS", P_MNPSS = "C_MNPSS", P_MRGNL = "C_MRGNL", P_MRGNP = "C_MRGNP", P_MRSPL = "C_MRSPL", P_MRTNT = "C_MRTNT", P_MSSLN = "C_MSSLN", P_MSSSS = "C_MSSSS", P_MTCNT = "C_MTCNT", P_MYCHS = "C_MYCHS", P_MYSCH = "C_MYSCH", F_MYZCY = "C_MYZCY", P_NASSL = "C_NASSL", P_NBCLN = "C_NBCLN", P_NBCLR = "C_NBCLR", P_NCNRB = "C_NCNRB", P_NDBCL = "C_NDBCL", P_NRLLA = "C_NDBCLR", P_NMMLC = "C_NMMLC", F_NMTPH = "C_NMTPH", P_NNNLL = "C_NNNLL", P_NODSR = "C_NODSR", P_NONIN = "C_NONIN", P_NOURI = "C_NOURI", P_OCLNA = "C_OCLNA", P_OGLNA = "C_OGLNA", P_OPHTH = "C_OLMDM", F_OLPDP = "C_OLPDP", P_ONYCH = "C_OMPSS", P_OOLIN = "C_OOLIN", P_OPRCL = "C_OPRCL", P_ORBLN = "C_ORBLN", F_ORCAD = "C_ORCAD", P_ORDRS = "C_ORDRS", P_OPHRY = "C_ORYDM", P_OSNGL = "C_OSNGL", P_OXYTR = "C_OXYTR", P_PARRN = "C_PARRN", P_PATRS = "C_PATRS", P_PAVNN = "C_PAVNN", P_PTYCH = "C_PCYLS", P_PDPHR = "C_PDPHR", P_PELSN = "C_PELSN", F_PHGMY = "C_PHGMY", F_PSDSP = "C_PHRTA", P_PHRYG = "C_PHRYG", P_PHYSL = "C_PHYSL", F_PHYTP = "C_PHYTP", P_PLACS = "C_PLACS", P_PLCPS = "C_PLCPS", P_PLCPSL = "C_PLCPSL", P_PLCTN = "C_PLCTN", P_PLGPH = "C_PLGPH", B_PLGTH = "C_PLGTH", P_PLMRN = "C_PLMRN", P_PLNCT = "C_PLNCT", P_PLNDSC = "C_PLNDSC", P_PLNGY = "C_PLNGY", P_PLNRBL = "C_PLNLLA", P_PLNLN = "C_PLNLN", P_PLNLR = "C_PLNLR", P_PLNRB = "C_PLNRB", P_PLNSP = "C_PLNSPR", P_PLRNM = "C_PLRNM", P_PLRST = "C_PLRST", P_PLRTR = "C_PLRTR", F_PLSMD = "C_PLSMD", P_PLTYC = "C_PLTYC", P_PSDBL = "C_PLVNA", P_PLYMR = "C_PLYMR", P_PLTYN = "C_PNMTM", P_PNRPL = "C_PNRPL", F_PNTSM = "C_PNTSM", P_PRCNT = "C_PRCNT", P_PRFSS = "C_PRFSS", P_PRMCM = "C_PRMCUM", F_PRNSP = "C_PRNSP", P_PRPND = "C_PRPND", P_PRPYX = "C_PRPYX", P_PRRDN = "C_PRRDN", P_PSDDF = "C_PSDDF", P_PSDMC = "C_PSDMC", P_PSDND = "C_PSDND", P_PSDNN = "C_PSDNN", P_PSDPL = "C_PSDPLY", P_PSMMS = "C_PSMMS", P_PTLLN = "C_PTLLN", P_PTLLND = "C_PTLLND", F_PTRSN = "C_PTRSN", P_PULLN = "C_PULLN", P_PUTLN = "C_PUTLN", P_PRTTR = "C_PYMNA", P_PYRGL = "C_PYRGL", P_PYRGO = "C_PYRGO", P_PYRLN = "C_PYRLN", F_PYTHM = "C_PYTHIM", F_PYTHL = "C_PYTHL", P_PYXCL = "C_PYXCL", P_QNQLC = "C_QNQLC", P_RAMLN = "C_RAMLN", P_RBRTN = "C_RBRTN", P_RCRVD = "C_RCRVD", P_RCTBL = "C_RCTBL", P_RCTCB = "C_RCTCB", P_RCTGL = "C_RCTGL", P_RCTVG = "C_RCTVG", P_RDGDR = "C_RDGDR", P_REMNC = "C_REMNC", P_REPHX = "C_REPHX", P_RHBDM = "C_RHBDMM", F_RHBDS = "C_RHBDSP", P_RHPDD = "C_RHPDD", F_RHPDM = "C_RHPDM", F_RHZDMY = "C_RHZDM", P_RHZMM = "C_RHZMM", P_RIVRN = "C_RIVRN", P_ROSLN = "C_ROSLN", P_ROTAL = "C_ROTAL", P_RPHDP = "C_RPHDP", P_RPRTN = "C_RPRTN", P_RSSLL = "C_RSSLL", P_RTLMM = "C_RTLMM", P_RTYLA = "C_RTYLA", P_RUGID = "C_RUGID", F_RZLLP = "C_RZLLP", P_SAGRN = "C_SAGRN", P_SCCMM = "C_SCCMM", P_SCCRH = "C_SCCRH", P_SCHLM = "C_SCHLM", F_SCLRS = "C_SCLRS", P_SCTLR = "C_SCTLR", P_SEBRK = "C_SEBRK", P_SGMLN = "C_SGMLN", P_SGMLP = "C_SGMLP", P_SGMMR = "C_SGMMR", P_SGMVR = "C_SGMVR", F_SMMRS = "C_SMMRS", P_SNNDS = "C_SNNDS", P_SORTS = "C_SORTS", P_SPHGN = "C_SPHGN", P_SPHNN = "C_SPHNN", P_SNLLA = "C_SPHNNL", P_SPHTR = "C_SPHTR", P_SPHTX = "C_SPHTX", P_SPHVG = "C_SPHVG", P_SPRDT = "C_SPRDT", P_SPRLC = "C_SPRLC", F_SPRLG = "C_SPRLG", P_SPRLL = "C_SPRLL", F_SPRMY = "C_SPRMY", P_SPRPL = "C_SPRPL", P_SPRSG = "C_SPRSG", P_SPRST = "C_SPRST", P_SPHNP = "C_SPRTA", P_SPRZN = "C_SPRZN", P_SPHRG = "C_SPSNA", P_STHDM = "C_SPTHD", P_SRCNR = "C_SRCNR", F_SRLPD = "C_SRLPD", F_SPNGS = "C_SSPRA", F_STEIN = "C_STEIN", P_SPTHD = "C_STHDDS", P_STHRP = "C_STHRP", P_STNFR = "C_STNFR", P_STNSM = "C_STNSM", P_STNTR = "C_STNTR", P_STRBL = "C_STRBL", P_STRMB = "C_STRMB", P_STTSN = "C_STTSN", P_STYLN = "C_SYCHA", F_SCHZC = "C_SYTRM", P_TBNLL = "C_TBNLL", P_TRCHL = "C_TCHLS", P_TCHNT = "C_TCHNT", P_THRCL = "C_THRCL", P_THRMM = "C_THRMM", P_TIARN = "C_TIARN", P_TKPHR = "C_TKPHR", P_TLNMA = "C_TLNMA", P_TLYPM = "C_TLYPM", P_TMNDS = "C_TMNDS", P_TMNTA = "C_TMNTA", P_TNTNN = "C_TNNDM", P_TTNNS = "C_TNTNN", P_TNPSS = "C_TNTNNP", P_TONTN = "C_TONTN", P_TOSAI = "C_TOSAI", P_TPHTR = "C_TPHTR", P_TRCHH = "C_TRCHH", P_TRPHS = "C_TRCHLR", P_TMMNA = "C_TRCHM", P_TRCHS = "C_TRCHSP", P_TRFRN = "C_TRFRN", P_TRLCL = "C_TRLCL", P_TRTXL = "C_TRTXL", P_TRTXS = "C_TRTXS", P_TTRHY = "C_TTRHY", F_TTRMY = "C_TTRMY", P_TXTLR = "C_TXTLR", F_THRST = "C_TYTRM", P_URLPT = "C_ULPTS", P_UNGLT = "C_UNGLT", P_URCNT = "C_URCNT", P_URONM = "C_URONM", P_UROSM = "C_UROSM", P_URTRC = "C_URTRC", P_URSTY = "C_UTYLA", P_UVGRN = "C_UVGRN", P_VLVLN = "C_VALVLN", P_VGNLN = "C_VGNLN", P_VGNLNP = "C_VGNLNP", P_VLNRA = "C_VLVLN", P_VGNCL = "C_VNCLA", P_VRGLN = "C_VRGLN", P_VRGLNP = "C_VRGLNP", P_VRTCL = "C_VRTCL", P_WBBNL = "C_WBBNL", P_WEBBN = "C_WEBBN", P_WSNRL = "C_WSNRL", P_ZTHMN = "C_ZHMNM", B_ZOOGL = "C_ZOOGL", F_DDSCS = "F_DPDSC", F_SCCHR = "F_SMYCS", P_AMTRN = "P_ACNTH", F_AMBDM = "P_AMBDM", F_ARCYR = "P_ARCYR", F_BADHM = "P_BADHM", F_BDHMP = "P_BDHMP", F_BRBYL = "P_BRBYL", F_BRFLD = "P_BRFLD", F_CLMYX = "P_CLMYX", F_CLSTD = "P_CLSTD", F_CMTRC = "P_CMTRC", F_CRBRR = "P_CRBRR", F_CRTMY = "P_CRTMY", F_CRTRM = "P_CRTRM", F_DCTYD = "P_DCTYD", F_DDYMM = "P_DDYMM", F_DIACH = "P_DIACH", F_DIANM = "P_DIANM", F_DIDRM = "P_DIDRM", F_ELMYX = "P_ELMYX", F_ESTLM = "P_ESTLM", F_FULIG = "P_FULIG", F_HMTRC = "P_HMTRC", F_LCRPS = "P_LCRPS", F_LICEA = "P_LICEA", F_LMPRD = "P_LMPRD", F_LPTDR = "P_LPTDR", F_LSTRL = "P_LSTRL", F_LYCGL = "P_LYCGL", F_MCBRD = "P_MCBRD", F_MNKTL = "P_MNKTL", F_MTTRC = "P_MTTRC", F_MUCLG = "P_MUCLG", F_PHYSR = "P_PHYSR", F_PRCHN = "P_PRCHN", F_PRMBD = "P_PRMBD", F_PRTPH = "P_PRTPH", F_PSRNA = "P_PSRNA", F_PYSRM = "P_PYSRM", F_RTCLR = "P_RTCLR", F_STMNT = "P_STMNT", F_SYMPH = "P_SYMPH", F_TRBRK = "P_TRBRK", F_TRICH = "P_TRICH", F_TUBFR = "P_TUBFR")
-
assign(x = "mo_codes_v0.5.0",
- value = mo_codes_v0.5.0,
+ value = make_trans_tbl(),
envir = asNamespace("AMR"))
-
- # packageStartupMessage("OK.", appendLF = TRUE)
}
}
+
+#' @importFrom dplyr mutate case_when
+#' @importFrom data.table as.data.table setkey
+make_DT <- function() {
+ microorganismsDT <- AMR::microorganisms %>%
+ mutate(prevalence = case_when(
+ class == "Gammaproteobacteria"
+ | order %in% c("Lactobacillales", "Bacillales")
+ ~ 1,
+ phylum %in% c("Proteobacteria",
+ "Firmicutes",
+ "Actinobacteria",
+ "Bacteroidetes")
+ | genus %in% c("Candida",
+ "Aspergillus",
+ "Trichophyton",
+ "Giardia",
+ "Dientamoeba",
+ "Entamoeba")
+ ~ 2,
+ TRUE ~ 3
+ )) %>%
+ as.data.table()
+ setkey(microorganismsDT,
+ kingdom,
+ prevalence,
+ fullname)
+ microorganismsDT
+}
+
+make_trans_tbl <- function() {
+# conversion of old MO codes from v0.5.0 (ITIS) to later versions (Catalogue of Life)
+ c(B_ACHRMB = "B_ACHRM", B_ANNMA = "B_ACTNS", B_ACLLS = "B_ALCYC",
+ B_AHNGM = "B_ARCHN", B_ARMTM = "B_ARMTMN", B_ARTHRS = "B_ARTHR",
+ B_APHLS = "B_AZRHZP", B_BRCHA = "B_BRCHY", B_BCTRM = "B_BRVBCT",
+ B_CLRBCT = "B_CLRBC", B_CTRDM = "B_CLSTR", B_CPRMM = "B_CYLND",
+ B_DLCLN = "B_DPLCL", B_DMCLM = "B_DSLFT", B_DSLFVB = "B_DSLFV",
+ B_FCTRM = "B_FSBCT", B_GNRLA = "B_GRDNR", B_HNRBM = "B_HLNRB",
+ B_HPHGA = "B_HNPHGA", B_HCCCS = "B_HYDRC", B_MCRCLS = "B_MCRCL",
+ B_MTHYLS = "B_MLSMA", B_MARCLS = "B_MRCLS", B_MGCLS = "B_MSTGC",
+ B_MCLLA = "B_MTHYLC", B_MYCPLS = "B_MYCPL", B_NBCTR = "B_NTRBC",
+ B_OCLLS = "B_OCNBC", B_PTHRX = "B_PLNKT", B_PCCCS = "B_PRCHL",
+ B_PSPHN = "B_PRPHY", B_PDMNS = "B_PSDMN", B_SCCHRP = "B_SCCHR",
+ B_SRBCTR = "B_SHRBCTR", B_STRPTC = "B_STRPT", B_SHMNS = "B_SYNTR",
+ B_TRBCTR = "B_THRMN", P_ALBMN = "C_ABMNA", F_ACHLY = "C_ACHLY",
+ P_ACINT = "C_ACINT", P_ARTCL = "C_ACLNA", P_ACRVL = "C_ACRVL",
+ P_ADRCT = "C_ADRCT", P_AMPHS = "C_AHSRS", F_ALBUG = "C_ALBUG",
+ P_ALCNT = "C_ALCNT", P_ALFRD = "C_ALFRD", P_ALLGR = "C_ALLGR",
+ P_AMPHL = "C_ALPTS", F_ALTHR = "C_ALTHR", P_AMLLA = "C_AMLLA",
+ P_ANMLN = "C_AMLNA", P_AMMBC = "C_AMMBC", P_AMMDS = "C_AMMDS",
+ P_AMMLG = "C_AMMLG", P_AMMMR = "C_AMMMR", P_AMMMS = "C_AMMMS",
+ P_AMMON = "C_AMMON", P_AMMSC = "C_AMMSC", P_AMMSP = "C_AMMSP",
+ P_AMMST = "C_AMMST", P_AMMTM = "C_AMMTM", F_AMYCS = "C_AMYCS",
+ P_ANARM = "C_ANARM", P_ANGLD = "C_ANGLD", P_ANGLG = "C_ANGLG",
+ P_ANNLC = "C_ANNLC", F_ANSLP = "C_ANSLP", F_APDCH = "C_APDCH",
+ F_APHND = "C_APHND", F_APLNC = "C_APLNC", F_AQLND = "C_AQLND",
+ P_ARCHS = "C_ARCHAS", P_ASTRN = "C_ARNNN", P_ARNPR = "C_ARNPR",
+ F_ARSPR = "C_ARSPR", P_ARTST = "C_ARTSTR", P_AMPHC = "C_ARYNA",
+ P_ASCHM = "C_ASCHM", P_ASPDS = "C_ASPDS", P_ASTCL = "C_ASTCL",
+ P_ASTRG = "C_ASTRGR", P_ASTRM = "C_ASTRMM", P_ASTRR = "C_ASTRR",
+ P_ASTRT = "C_ASTRTR", F_ATKNS = "C_ATKNS", F_AYLLA = "C_AYLLA",
+ P_BAGGN = "C_BAGGN", P_BCCLL = "C_BCCLL", P_BDLLD = "C_BDLLD",
+ P_BGNRN = "C_BGNRN", P_BLCLN = "C_BLCLN", P_BLMND = "C_BLMND",
+ P_BLMNL = "C_BLMNL", P_BLPHR = "C_BLPHR", P_BLVNT = "C_BLVNT",
+ P_BOLVN = "C_BOLVN", P_BORLS = "C_BORLS", P_BRNNM = "C_BRNNM",
+ P_BRSLN = "C_BRSLN", P_BRSRD = "C_BRSRD", F_BRVLG = "C_BRVLG",
+ F_BNLLA = "C_BRVLGN", P_BSCCM = "C_BSCCM", F_BSDPH = "C_BSDPH",
+ P_BTHYS = "C_BTHYS", P_BTLLN = "C_BTLLN", P_BULMN = "C_BULMN",
+ P_CCLDM = "C_CCLDM", P_CDNLL = "C_CDNLL", P_CLPSS = "C_CDNLLP",
+ P_CHLDN = "C_CHLDNL", P_CHLST = "C_CHLST", P_CHNLM = "C_CHNLM",
+ P_CHRYS = "C_CHRYSL", P_CHTSP = "C_CHTSP", P_CBCDS = "C_CIBCDS",
+ P_CLCRN = "C_CLCRN", P_CLMNA = "C_CLMNA", P_CLPDM = "C_CLPDM",
+ P_CLPHR = "C_CLPHRY", P_CLVLN = "C_CLVLN", P_CMPNL = "C_CMPNL",
+ P_CNCRS = "C_CNCRS", P_CNTCH = "C_CNTCH", F_CNTRM = "C_CNTRMY",
+ P_COLPD = "C_COLPD", P_COLPS = "C_COLPS", P_CPRDS = "C_CPRDS",
+ P_CRNSP = "C_CPRMA", P_CRBNL = "C_CRBNL", P_CRBRB = "C_CRBRB",
+ P_CRBRG = "C_CRBRG", P_CRBRS = "C_CRBRS", P_CRCHS = "C_CRCHS",
+ P_CRCLC = "C_CRCLC", P_CRNLC = "C_CRNLC", P_CRNTH = "C_CRNTH",
+ P_CRPNT = "C_CRPNT", P_CRSTG = "C_CRSTG", P_CRTHN = "C_CRTHN",
+ P_CRTRN = "C_CRTRN", P_CYMBL = "C_CRTTA", P_CRYPT = "C_CRYPT",
+ P_CSHMN = "C_CSHMNL", P_CSSDL = "C_CSSDL", P_CLNDS = "C_CSSDLN",
+ P_CHRNA = "C_CTHRN", P_CTPSS = "C_CTPSS", P_CUNLN = "C_CUNLN",
+ P_CYLND = "C_CVLNA", P_CYCLC = "C_CYCLCB", P_CDNTA = "C_CYCLD",
+ P_CYCLG = "C_CYCLG", P_CYCLM = "C_CYCLM", P_CYRTL = "C_CYRTL",
+ P_CYSTM = "C_CYSTM", P_DCHLM = "C_DCHLM", P_DCRBS = "C_DCRBS",
+ P_DCTYC = "C_DCTYC", P_DIDNM = "C_DIDNM", P_DLPTS = "C_DLPTS",
+ P_DNTLN = "C_DNTLN", P_DNTST = "C_DNTST", P_DORTH = "C_DORTH",
+ P_DCTYP = "C_DPHMS", F_DPLCY = "C_DPLCY", P_DNDRT = "C_DRTNA",
+ P_DSCMM = "C_DSCMM", P_DSCRB = "C_DSCRB", P_DSCRN = "C_DSCRN",
+ P_DSCSP = "C_DSCSP", P_DSNBR = "C_DSNBR", P_DYCBC = "C_DYCBC",
+ F_DCTYC = "C_DYCHS", F_ECTRG = "C_ECTRG", B_EDWRD = "C_EDWRD",
+ P_EGGRL = "C_EGGRL", P_EHLYS = "C_EHLYS", P_EHRNB = "C_EHRNB",
+ P_ELPHD = "C_ELPHD", P_ENCHL = "C_ELYDM", P_EPHDM = "C_EPHDM",
+ P_EPLTS = "C_EPLTS", P_EPLXL = "C_EPLXL", P_EPNDL = "C_EPNDL",
+ P_EPNDS = "C_EPNDS", P_ENLLA = "C_EPSTM", P_EPSTY = "C_EPSTY",
+ F_ERYCH = "C_ERYCH", F_ESMDM = "C_ESMDM", P_ESSYR = "C_ESSYR",
+ P_FSCHR = "C_FHRNA", P_FLRLS = "C_FLRLS", P_FLNTN = "C_FNTNA",
+ P_FRNDC = "C_FRNDC", P_FRNTN = "C_FRNTN", P_FRSNK = "C_FRSNK",
+ P_FNLLA = "C_FSCHRN", P_FSSRN = "C_FSSRN", P_FVCSS = "C_FVCSS",
+ P_GDRYN = "C_GDRYN", F_GELGN = "C_GELGN", P_GERDA = "C_GERDA",
+ P_GLACM = "C_GLACM", P_GLBBL = "C_GLBBL", P_GLBGR = "C_GLBGR",
+ P_GLBLN = "C_GLBLN", P_GRTLA = "C_GLBRT", P_GLBTX = "C_GLBTX",
+ P_GLLNA = "C_GLLNA", P_GLMSP = "C_GLMSP", P_GLNDL = "C_GLNDL",
+ F_GNMCH = "C_GNMCH", P_GOSLL = "C_GOSLL", P_GRNDS = "C_GRNDS",
+ P_GRNTA = "C_GRNTA", P_GLBRT = "C_GTLLA", P_GTTLN = "C_GTTLN",
+ P_GVLNP = "C_GVLNP", P_GYPSN = "C_GYPSN", P_GYRDN = "C_GYRDN",
+ P_HALTR = "C_HALTR", P_HANZW = "C_HANZW", P_HAURN = "C_HAURN",
+ P_HELNN = "C_HELNN", P_HLPHR = "C_HHRYA", P_HLNTA = "C_HLNTA",
+ F_HLPHT = "C_HLPHT", P_HLSTC = "C_HLSTC", P_HMSPH = "C_HMSPH",
+ P_HMTRM = "C_HMTRM", P_HPKNS = "C_HPKNS", P_HPLPH = "C_HPLPH",
+ P_HPPCR = "C_HPPCR", P_HNLLA = "C_HPPCRP", P_HRMSN = "C_HRMSN",
+ P_HRNLL = "C_HRNLL", F_HRPCH = "C_HRPCH", P_HSTGR = "C_HSTGR",
+ P_HSTTL = "C_HSTTL", P_HTRST = "C_HTGNA", P_HTRLL = "C_HTRLL",
+ P_HTRPH = "C_HTRPH", F_HYPHC = "C_HYPHC", P_HYPRM = "C_HYPRM",
+ P_INTRN = "C_INTRN", P_IRIDI = "C_IRIDI", P_ISLND = "C_ISLND",
+ P_JCLLL = "C_JCLLL", P_KHLLL = "C_KHLLL", P_KRNPS = "C_KRNPS",
+ P_KRRRL = "C_KRRRL", P_LABOE = "C_LABOE", P_LAGEN = "C_LAGEN",
+ P_LBSLL = "C_LBSLL", F_LTHLA = "C_LBYRN", P_LCRYM = "C_LCRYM",
+ P_LEMBS = "C_LEMBS", F_LGNDM = "C_LGNDM", P_LGNMM = "C_LGNMM",
+ P_LGNPH = "C_LGNPHR", F_LGNSM = "C_LGNSM", P_LGYNP = "C_LGYNP",
+ P_LITTB = "C_LITTB", P_LITUL = "C_LITUL", P_LMBDN = "C_LMBDN",
+ P_LMRCK = "C_LMRCK", F_LBYRN = "C_LMYXA", P_LNGLN = "C_LNGLN",
+ P_LNTCL = "C_LNTCL", P_LOXDS = "C_LOXDS", F_LPTLG = "C_LPTLG",
+ F_LNLLA = "C_LPTLGN", F_LPTMT = "C_LPTMT", P_LRYNG = "C_LRYNG",
+ P_LTCRN = "C_LTCRN", P_LTHPL = "C_LTHPL", P_LTNTS = "C_LTNTS",
+ F_LTRST = "C_LTRST", P_LXPHY = "C_LXPHY", P_MCRTH = "C_MCRTH",
+ P_MELNS = "C_MELNS", P_MSDNM = "C_MESDNM", P_METPS = "C_METPS",
+ P_MIMSN = "C_MIMSN", P_MINCN = "C_MINCN", P_MLLNL = "C_MLLNL",
+ P_MLMMN = "C_MLMMN", F_MNDNL = "C_MNDNL", P_MNLYS = "C_MNLYS",
+ P_MNPSS = "C_MNPSS", P_MRGNL = "C_MRGNL", P_MRGNP = "C_MRGNP",
+ P_MRSPL = "C_MRSPL", P_MRTNT = "C_MRTNT", P_MSSLN = "C_MSSLN",
+ P_MSSSS = "C_MSSSS", P_MTCNT = "C_MTCNT", P_MYCHS = "C_MYCHS",
+ P_MYSCH = "C_MYSCH", F_MYZCY = "C_MYZCY", P_NASSL = "C_NASSL",
+ P_NBCLN = "C_NBCLN", P_NBCLR = "C_NBCLR", P_NCNRB = "C_NCNRB",
+ P_NDBCL = "C_NDBCL", P_NRLLA = "C_NDBCLR", P_NMMLC = "C_NMMLC",
+ F_NMTPH = "C_NMTPH", P_NNNLL = "C_NNNLL", P_NODSR = "C_NODSR",
+ P_NONIN = "C_NONIN", P_NOURI = "C_NOURI", P_OCLNA = "C_OCLNA",
+ P_OGLNA = "C_OGLNA", P_OPHTH = "C_OLMDM", F_OLPDP = "C_OLPDP",
+ P_ONYCH = "C_OMPSS", P_OOLIN = "C_OOLIN", P_OPRCL = "C_OPRCL",
+ P_ORBLN = "C_ORBLN", F_ORCAD = "C_ORCAD", P_ORDRS = "C_ORDRS",
+ P_OPHRY = "C_ORYDM", P_OSNGL = "C_OSNGL", P_OXYTR = "C_OXYTR",
+ P_PARRN = "C_PARRN", P_PATRS = "C_PATRS", P_PAVNN = "C_PAVNN",
+ P_PTYCH = "C_PCYLS", P_PDPHR = "C_PDPHR", P_PELSN = "C_PELSN",
+ F_PHGMY = "C_PHGMY", F_PSDSP = "C_PHRTA", P_PHRYG = "C_PHRYG",
+ P_PHYSL = "C_PHYSL", F_PHYTP = "C_PHYTP", P_PLACS = "C_PLACS",
+ P_PLCPS = "C_PLCPS", P_PLCPSL = "C_PLCPSL", P_PLCTN = "C_PLCTN",
+ P_PLGPH = "C_PLGPH", B_PLGTH = "C_PLGTH", P_PLMRN = "C_PLMRN",
+ P_PLNCT = "C_PLNCT", P_PLNDSC = "C_PLNDSC", P_PLNGY = "C_PLNGY",
+ P_PLNRBL = "C_PLNLLA", P_PLNLN = "C_PLNLN", P_PLNLR = "C_PLNLR",
+ P_PLNRB = "C_PLNRB", P_PLNSP = "C_PLNSPR", P_PLRNM = "C_PLRNM",
+ P_PLRST = "C_PLRST", P_PLRTR = "C_PLRTR", F_PLSMD = "C_PLSMD",
+ P_PLTYC = "C_PLTYC", P_PSDBL = "C_PLVNA", P_PLYMR = "C_PLYMR",
+ P_PLTYN = "C_PNMTM", P_PNRPL = "C_PNRPL", F_PNTSM = "C_PNTSM",
+ P_PRCNT = "C_PRCNT", P_PRFSS = "C_PRFSS", P_PRMCM = "C_PRMCUM",
+ F_PRNSP = "C_PRNSP", P_PRPND = "C_PRPND", P_PRPYX = "C_PRPYX",
+ P_PRRDN = "C_PRRDN", P_PSDDF = "C_PSDDF", P_PSDMC = "C_PSDMC",
+ P_PSDND = "C_PSDND", P_PSDNN = "C_PSDNN", P_PSDPL = "C_PSDPLY",
+ P_PSMMS = "C_PSMMS", P_PTLLN = "C_PTLLN", P_PTLLND = "C_PTLLND",
+ F_PTRSN = "C_PTRSN", P_PULLN = "C_PULLN", P_PUTLN = "C_PUTLN",
+ P_PRTTR = "C_PYMNA", P_PYRGL = "C_PYRGL", P_PYRGO = "C_PYRGO",
+ P_PYRLN = "C_PYRLN", F_PYTHM = "C_PYTHIM", F_PYTHL = "C_PYTHL",
+ P_PYXCL = "C_PYXCL", P_QNQLC = "C_QNQLC", P_RAMLN = "C_RAMLN",
+ P_RBRTN = "C_RBRTN", P_RCRVD = "C_RCRVD", P_RCTBL = "C_RCTBL",
+ P_RCTCB = "C_RCTCB", P_RCTGL = "C_RCTGL", P_RCTVG = "C_RCTVG",
+ P_RDGDR = "C_RDGDR", P_REMNC = "C_REMNC", P_REPHX = "C_REPHX",
+ P_RHBDM = "C_RHBDMM", F_RHBDS = "C_RHBDSP", P_RHPDD = "C_RHPDD",
+ F_RHPDM = "C_RHPDM", F_RHZDMY = "C_RHZDM", P_RHZMM = "C_RHZMM",
+ P_RIVRN = "C_RIVRN", P_ROSLN = "C_ROSLN", P_ROTAL = "C_ROTAL",
+ P_RPHDP = "C_RPHDP", P_RPRTN = "C_RPRTN", P_RSSLL = "C_RSSLL",
+ P_RTLMM = "C_RTLMM", P_RTYLA = "C_RTYLA", P_RUGID = "C_RUGID",
+ F_RZLLP = "C_RZLLP", P_SAGRN = "C_SAGRN", P_SCCMM = "C_SCCMM",
+ P_SCCRH = "C_SCCRH", P_SCHLM = "C_SCHLM", F_SCLRS = "C_SCLRS",
+ P_SCTLR = "C_SCTLR", P_SEBRK = "C_SEBRK", P_SGMLN = "C_SGMLN",
+ P_SGMLP = "C_SGMLP", P_SGMMR = "C_SGMMR", P_SGMVR = "C_SGMVR",
+ F_SMMRS = "C_SMMRS", P_SNNDS = "C_SNNDS", P_SORTS = "C_SORTS",
+ P_SPHGN = "C_SPHGN", P_SPHNN = "C_SPHNN", P_SNLLA = "C_SPHNNL",
+ P_SPHTR = "C_SPHTR", P_SPHTX = "C_SPHTX", P_SPHVG = "C_SPHVG",
+ P_SPRDT = "C_SPRDT", P_SPRLC = "C_SPRLC", F_SPRLG = "C_SPRLG",
+ P_SPRLL = "C_SPRLL", F_SPRMY = "C_SPRMY", P_SPRPL = "C_SPRPL",
+ P_SPRSG = "C_SPRSG", P_SPRST = "C_SPRST", P_SPHNP = "C_SPRTA",
+ P_SPRZN = "C_SPRZN", P_SPHRG = "C_SPSNA", P_STHDM = "C_SPTHD",
+ P_SRCNR = "C_SRCNR", F_SRLPD = "C_SRLPD", F_SPNGS = "C_SSPRA",
+ F_STEIN = "C_STEIN", P_SPTHD = "C_STHDDS", P_STHRP = "C_STHRP",
+ P_STNFR = "C_STNFR", P_STNSM = "C_STNSM", P_STNTR = "C_STNTR",
+ P_STRBL = "C_STRBL", P_STRMB = "C_STRMB", P_STTSN = "C_STTSN",
+ P_STYLN = "C_SYCHA", F_SCHZC = "C_SYTRM", P_TBNLL = "C_TBNLL",
+ P_TRCHL = "C_TCHLS", P_TCHNT = "C_TCHNT", P_THRCL = "C_THRCL",
+ P_THRMM = "C_THRMM", P_TIARN = "C_TIARN", P_TKPHR = "C_TKPHR",
+ P_TLNMA = "C_TLNMA", P_TLYPM = "C_TLYPM", P_TMNDS = "C_TMNDS",
+ P_TMNTA = "C_TMNTA", P_TNTNN = "C_TNNDM", P_TTNNS = "C_TNTNN",
+ P_TNPSS = "C_TNTNNP", P_TONTN = "C_TONTN", P_TOSAI = "C_TOSAI",
+ P_TPHTR = "C_TPHTR", P_TRCHH = "C_TRCHH", P_TRPHS = "C_TRCHLR",
+ P_TMMNA = "C_TRCHM", P_TRCHS = "C_TRCHSP", P_TRFRN = "C_TRFRN",
+ P_TRLCL = "C_TRLCL", P_TRTXL = "C_TRTXL", P_TRTXS = "C_TRTXS",
+ P_TTRHY = "C_TTRHY", F_TTRMY = "C_TTRMY", P_TXTLR = "C_TXTLR",
+ F_THRST = "C_TYTRM", P_URLPT = "C_ULPTS", P_UNGLT = "C_UNGLT",
+ P_URCNT = "C_URCNT", P_URONM = "C_URONM", P_UROSM = "C_UROSM",
+ P_URTRC = "C_URTRC", P_URSTY = "C_UTYLA", P_UVGRN = "C_UVGRN",
+ P_VLVLN = "C_VALVLN", P_VGNLN = "C_VGNLN", P_VGNLNP = "C_VGNLNP",
+ P_VLNRA = "C_VLVLN", P_VGNCL = "C_VNCLA", P_VRGLN = "C_VRGLN",
+ P_VRGLNP = "C_VRGLNP", P_VRTCL = "C_VRTCL", P_WBBNL = "C_WBBNL",
+ P_WEBBN = "C_WEBBN", P_WSNRL = "C_WSNRL", P_ZTHMN = "C_ZHMNM",
+ B_ZOOGL = "C_ZOOGL", F_DDSCS = "F_DPDSC", F_SCCHR = "F_SMYCS",
+ P_AMTRN = "P_ACNTH", F_AMBDM = "P_AMBDM", F_ARCYR = "P_ARCYR",
+ F_BADHM = "P_BADHM", F_BDHMP = "P_BDHMP", F_BRBYL = "P_BRBYL",
+ F_BRFLD = "P_BRFLD", F_CLMYX = "P_CLMYX", F_CLSTD = "P_CLSTD",
+ F_CMTRC = "P_CMTRC", F_CRBRR = "P_CRBRR", F_CRTMY = "P_CRTMY",
+ F_CRTRM = "P_CRTRM", F_DCTYD = "P_DCTYD", F_DDYMM = "P_DDYMM",
+ F_DIACH = "P_DIACH", F_DIANM = "P_DIANM", F_DIDRM = "P_DIDRM",
+ F_ELMYX = "P_ELMYX", F_ESTLM = "P_ESTLM", F_FULIG = "P_FULIG",
+ F_HMTRC = "P_HMTRC", F_LCRPS = "P_LCRPS", F_LICEA = "P_LICEA",
+ F_LMPRD = "P_LMPRD", F_LPTDR = "P_LPTDR", F_LSTRL = "P_LSTRL",
+ F_LYCGL = "P_LYCGL", F_MCBRD = "P_MCBRD", F_MNKTL = "P_MNKTL",
+ F_MTTRC = "P_MTTRC", F_MUCLG = "P_MUCLG", F_PHYSR = "P_PHYSR",
+ F_PRCHN = "P_PRCHN", F_PRMBD = "P_PRMBD", F_PRTPH = "P_PRTPH",
+ F_PSRNA = "P_PSRNA", F_PYSRM = "P_PYSRM", F_RTCLR = "P_RTCLR",
+ F_STMNT = "P_STMNT", F_SYMPH = "P_SYMPH", F_TRBRK = "P_TRBRK",
+ F_TRICH = "P_TRICH", F_TUBFR = "P_TUBFR")
+}
diff --git a/docs/articles/AMR.html b/docs/articles/AMR.html
index 17046f02..89199875 100644
--- a/docs/articles/AMR.html
+++ b/docs/articles/AMR.html
@@ -327,19 +327,41 @@
-2012-08-08 |
-P2 |
-Hospital B |
-Streptococcus pneumoniae |
-S |
+2010-03-19 |
+Z1 |
+Hospital A |
+Escherichia coli |
+R |
S |
S |
S |
F |
-2011-03-05 |
-D8 |
+2012-12-24 |
+Z8 |
+Hospital A |
+Klebsiella pneumoniae |
+R |
+S |
+S |
+S |
+F |
+
+
+2013-12-12 |
+Z1 |
+Hospital A |
+Staphylococcus aureus |
+R |
+S |
+S |
+S |
+F |
+
+
+2014-08-13 |
+J4 |
Hospital A |
Escherichia coli |
S |
@@ -349,20 +371,20 @@
M |
-2012-04-03 |
-D4 |
-Hospital C |
-Staphylococcus aureus |
-R |
+2012-04-09 |
+F5 |
+Hospital A |
+Escherichia coli |
+S |
+S |
S |
-R |
S |
M |
-2012-10-25 |
-I1 |
-Hospital B |
+2010-08-11 |
+N1 |
+Hospital A |
Klebsiella pneumoniae |
S |
S |
@@ -370,28 +392,6 @@
S |
M |
-
-2017-04-18 |
-X3 |
-Hospital B |
-Streptococcus pneumoniae |
-S |
-I |
-S |
-R |
-F |
-
-
-2013-03-18 |
-C4 |
-Hospital A |
-Streptococcus pneumoniae |
-S |
-I |
-S |
-S |
-M |
-
Now, let’s start the cleaning and the analysis!
@@ -411,8 +411,8 @@
#>
#> Item Count Percent Cum. Count Cum. Percent
#> --- ----- ------- -------- ----------- -------------
-#> 1 M 10,458 52.3% 10,458 52.3%
-#> 2 F 9,542 47.7% 20,000 100.0%
+#> 1 M 10,436 52.2% 10,436 52.2%
+#> 2 F 9,564 47.8% 20,000 100.0%
So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values M
and F
. From a researcher perspective: there are slightly more men. Nothing we didn’t already know.
The data is already quite clean, but we still need to transform some variables. The bacteria
column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The mutate()
function of the dplyr
package makes this really easy:
data <- data %>%
@@ -443,10 +443,10 @@
#> Kingella kingae (no changes)
#>
#> EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
-#> Table 1: Intrinsic resistance in Enterobacteriaceae (1342 changes)
+#> Table 1: Intrinsic resistance in Enterobacteriaceae (1333 changes)
#> Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)
#> Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes)
-#> Table 4: Intrinsic resistance in Gram-positive bacteria (2761 changes)
+#> Table 4: Intrinsic resistance in Gram-positive bacteria (2733 changes)
#> Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)
#> Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)
#> Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)
@@ -462,9 +462,9 @@
#> Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)
#> Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)
#>
-#> => EUCAST rules affected 7,471 out of 20,000 rows
+#> => EUCAST rules affected 7,452 out of 20,000 rows
#> -> added 0 test results
-#> -> changed 4,103 test results (0 to S; 0 to I; 4,103 to R)
+#> -> changed 4,066 test results (0 to S; 0 to I; 4,066 to R)
-So only 28.4% is suitable for resistance analysis! We can now filter on it with the filter()
function, also from the dplyr
package:
+#> => Found 5,692 first isolates (28.5% of total)
+So only 28.5% is suitable for resistance analysis! We can now filter on it with the filter()
function, also from the dplyr
package:
For future use, the above two syntaxes can be shortened with the filter_first_isolate()
function:
@@ -516,19 +516,19 @@
1 |
-2010-01-23 |
-A4 |
+2010-01-14 |
+O6 |
B_ESCHR_COL |
-S |
-S |
-S |
+R |
+I |
+R |
S |
TRUE |
2 |
-2010-03-13 |
-A4 |
+2010-02-22 |
+O6 |
B_ESCHR_COL |
S |
S |
@@ -538,8 +538,8 @@
3 |
-2010-04-19 |
-A4 |
+2010-04-01 |
+O6 |
B_ESCHR_COL |
S |
S |
@@ -549,21 +549,21 @@
4 |
-2010-06-11 |
-A4 |
+2010-04-25 |
+O6 |
B_ESCHR_COL |
S |
S |
-R |
+S |
S |
FALSE |
5 |
-2010-07-04 |
-A4 |
+2010-05-09 |
+O6 |
B_ESCHR_COL |
-R |
+S |
S |
S |
S |
@@ -571,52 +571,52 @@
6 |
-2010-07-05 |
-A4 |
+2010-05-29 |
+O6 |
B_ESCHR_COL |
S |
-S |
-S |
+I |
+R |
S |
FALSE |
7 |
-2011-03-21 |
-A4 |
+2010-06-27 |
+O6 |
B_ESCHR_COL |
S |
S |
-R |
S |
-TRUE |
+S |
+FALSE |
8 |
-2011-04-02 |
-A4 |
+2010-06-27 |
+O6 |
B_ESCHR_COL |
-R |
S |
-R |
+S |
+S |
S |
FALSE |
9 |
-2011-04-05 |
-A4 |
+2011-02-01 |
+O6 |
B_ESCHR_COL |
-S |
-S |
-S |
R |
-FALSE |
+S |
+S |
+S |
+TRUE |
10 |
-2011-04-13 |
-A4 |
+2011-03-20 |
+O6 |
B_ESCHR_COL |
S |
S |
@@ -637,7 +637,7 @@
#> NOTE: Using column `patient_id` as input for `col_patient_id`.
#> NOTE: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.
#> [Criterion] Inclusion based on key antibiotics, ignoring I.
-#> => Found 15,801 first weighted isolates (79.0% of total)
+#> => Found 15,851 first weighted isolates (79.3% of total)
1 |
-2010-01-23 |
-A4 |
+2010-01-14 |
+O6 |
B_ESCHR_COL |
-S |
-S |
-S |
+R |
+I |
+R |
S |
TRUE |
TRUE |
2 |
-2010-03-13 |
-A4 |
+2010-02-22 |
+O6 |
B_ESCHR_COL |
S |
S |
S |
S |
FALSE |
-FALSE |
+TRUE |
3 |
-2010-04-19 |
-A4 |
+2010-04-01 |
+O6 |
B_ESCHR_COL |
S |
S |
@@ -690,80 +690,80 @@
4 |
-2010-06-11 |
-A4 |
+2010-04-25 |
+O6 |
B_ESCHR_COL |
S |
S |
-R |
+S |
S |
FALSE |
-TRUE |
+FALSE |
5 |
-2010-07-04 |
-A4 |
+2010-05-09 |
+O6 |
B_ESCHR_COL |
-R |
+S |
S |
S |
S |
FALSE |
-TRUE |
+FALSE |
6 |
-2010-07-05 |
-A4 |
+2010-05-29 |
+O6 |
B_ESCHR_COL |
S |
-S |
-S |
+I |
+R |
S |
FALSE |
TRUE |
7 |
-2011-03-21 |
-A4 |
+2010-06-27 |
+O6 |
B_ESCHR_COL |
S |
S |
-R |
S |
-TRUE |
+S |
+FALSE |
TRUE |
8 |
-2011-04-02 |
-A4 |
+2010-06-27 |
+O6 |
B_ESCHR_COL |
-R |
S |
-R |
+S |
+S |
S |
FALSE |
-TRUE |
+FALSE |
9 |
-2011-04-05 |
-A4 |
+2011-02-01 |
+O6 |
B_ESCHR_COL |
-S |
-S |
-S |
R |
-FALSE |
+S |
+S |
+S |
+TRUE |
TRUE |
10 |
-2011-04-13 |
-A4 |
+2011-03-20 |
+O6 |
B_ESCHR_COL |
S |
S |
@@ -774,11 +774,11 @@
-Instead of 2, now 8 isolates are flagged. In total, 79% of all isolates are marked ‘first weighted’ - 50.6% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.
+Instead of 2, now 6 isolates are flagged. In total, 79.3% of all isolates are marked ‘first weighted’ - 50.8% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.
As with filter_first_isolate()
, there’s a shortcut for this new algorithm too:
-So we end up with 15,801 isolates for analysis.
+So we end up with 15,851 isolates for analysis.
We can remove unneeded columns:
@@ -786,6 +786,7 @@
-2012-08-08 |
-P2 |
-Hospital B |
-B_STRPT_PNE |
-S |
-S |
-S |
+3 |
+2013-12-12 |
+Z1 |
+Hospital A |
+B_STPHY_AUR |
R |
+S |
+S |
+S |
F |
Gram positive |
-Streptococcus |
-pneumoniae |
+Staphylococcus |
+aureus |
TRUE |
-2011-03-05 |
-D8 |
+4 |
+2014-08-13 |
+J4 |
Hospital A |
B_ESCHR_COL |
S |
@@ -832,24 +835,26 @@
TRUE |
-2012-04-03 |
-D4 |
-Hospital C |
-B_STPHY_AUR |
-R |
+5 |
+2012-04-09 |
+F5 |
+Hospital A |
+B_ESCHR_COL |
+S |
+S |
S |
-R |
S |
M |
-Gram positive |
-Staphylococcus |
-aureus |
+Gram negative |
+Escherichia |
+coli |
TRUE |
-2012-10-25 |
-I1 |
-Hospital B |
+6 |
+2010-08-11 |
+N1 |
+Hospital A |
B_KLBSL_PNE |
R |
S |
@@ -862,33 +867,35 @@
TRUE |
-2017-04-18 |
-X3 |
-Hospital B |
-B_STRPT_PNE |
-S |
-I |
-S |
+7 |
+2010-02-25 |
+E9 |
+Hospital A |
+B_KLBSL_PNE |
R |
-F |
-Gram positive |
-Streptococcus |
+R |
+S |
+S |
+M |
+Gram negative |
+Klebsiella |
pneumoniae |
TRUE |
-2013-03-18 |
-C4 |
+8 |
+2013-04-09 |
+N1 |
Hospital A |
-B_STRPT_PNE |
-S |
+B_STPHY_AUR |
I |
S |
R |
+S |
M |
Gram positive |
-Streptococcus |
-pneumoniae |
+Staphylococcus |
+aureus |
TRUE |
@@ -908,9 +915,9 @@
Or can be used like the dplyr
way, which is easier readable:
-Frequency table of genus
and species
from a data.frame
(15,801 x 13)
+Frequency table of genus
and species
from a data.frame
(15,851 x 13)
Columns: 2
-Length: 15,801 (of which NA: 0 = 0.00%)
+Length: 15,851 (of which NA: 0 = 0.00%)
Unique: 4
Shortest: 16
Longest: 24
@@ -927,33 +934,33 @@ Longest: 24
1 |
Escherichia coli |
-7,850 |
-49.7% |
-7,850 |
-49.7% |
+7,853 |
+49.5% |
+7,853 |
+49.5% |
2 |
Staphylococcus aureus |
-3,918 |
-24.8% |
-11,768 |
-74.5% |
+3,943 |
+24.9% |
+11,796 |
+74.4% |
3 |
Streptococcus pneumoniae |
-2,446 |
-15.5% |
-14,214 |
-90.0% |
+2,432 |
+15.3% |
+14,228 |
+89.8% |
4 |
Klebsiella pneumoniae |
-1,587 |
-10.0% |
-15,801 |
+1,623 |
+10.2% |
+15,851 |
100.0% |
@@ -964,7 +971,7 @@ Longest: 24
Resistance percentages
The functions portion_R
, portion_RI
, portion_I
, portion_IS
and portion_S
can be used to determine the portion of a specific antimicrobial outcome. They can be used on their own:
+#> [1] 0.4764368
Or can be used in conjuction with group_by()
and summarise()
, both from the dplyr
package:
@@ -1007,23 +1014,23 @@ Longest: 24
Hospital A |
-0.4696939 |
-4867 |
+0.4722165 |
+4841 |
Hospital B |
-0.4782930 |
-5413 |
+0.4788707 |
+5490 |
Hospital C |
-0.4683438 |
-2385 |
+0.4670535 |
+2413 |
Hospital D |
-0.4815051 |
-3136 |
+0.4859994 |
+3107 |
@@ -1043,27 +1050,27 @@ Longest: 24