# taxonomic tree -----------------------------------------------------------
mo_kingdom("Klebsiella pneumoniae")
-#> [1] "Bacteria"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_phylum("Klebsiella pneumoniae")
-#> [1] "Pseudomonadota"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_class("Klebsiella pneumoniae")
-#> [1] "Gammaproteobacteria"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_order("Klebsiella pneumoniae")
-#> [1] "Enterobacterales"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_family("Klebsiella pneumoniae")
-#> [1] "Enterobacteriaceae"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_genus("Klebsiella pneumoniae")
-#> [1] "Klebsiella"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_species("Klebsiella pneumoniae")
-#> [1] "pneumoniae"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_subspecies("Klebsiella pneumoniae")
-#> [1] ""
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# full names and short names -----------------------------------------------
mo_name("Klebsiella pneumoniae")
-#> [1] "Klebsiella pneumoniae"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_fullname("Klebsiella pneumoniae")
-#> [1] "Klebsiella pneumoniae"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_shortname("Klebsiella pneumoniae")
-#> [1] "K. pneumoniae"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# other properties ---------------------------------------------------------
mo_pathogenicity("Klebsiella pneumoniae")
-#> [1] Pathogenic
-#> Levels: Pathogenic < Potentially pathogenic < Non-pathogenic < Unknown
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_gramstain("Klebsiella pneumoniae")
-#> [1] "Gram-negative"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_snomed("Klebsiella pneumoniae")
-#> [[1]]
-#> [1] "1098101000112102" "446870005" "1098201000112108" "409801009"
-#> [5] "56415008" "714315002" "713926009"
-#>
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_type("Klebsiella pneumoniae")
-#> [1] "Bacteria"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_rank("Klebsiella pneumoniae")
-#> [1] "species"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_url("Klebsiella pneumoniae")
-#> Klebsiella pneumoniae
-#> "https://lpsn.dsmz.de/species/klebsiella-pneumoniae"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
-#> [1] TRUE FALSE FALSE
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# scientific reference -----------------------------------------------------
mo_ref("Klebsiella aerogenes")
-#> [1] "Tindall et al., 2017"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_authors("Klebsiella aerogenes")
-#> [1] "Tindall et al."
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_year("Klebsiella aerogenes")
-#> [1] 2017
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_lpsn("Klebsiella aerogenes")
-#> [1] "777146"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_gbif("Klebsiella aerogenes")
-#> [1] "9281703"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_synonyms("Klebsiella aerogenes")
-#> Hormaeche et al., 1960 Bascomb et al., 1971
-#> "Enterobacter aerogenes" "Klebsiella mobilis"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# abbreviations known in the field -----------------------------------------
mo_genus("MRSA")
-#> [1] "Staphylococcus"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_species("MRSA")
-#> [1] "aureus"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_shortname("VISA")
-#> [1] "S. aureus"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_gramstain("VISA")
-#> [1] "Gram-positive"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_genus("EHEC")
-#> [1] "Escherichia"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_species("EIEC")
-#> [1] "coli"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_name("UPEC")
-#> [1] "Escherichia coli"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# known subspecies ---------------------------------------------------------
mo_fullname("K. pneu rh")
-#> [1] "Klebsiella pneumoniae rhinoscleromatis"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_shortname("K. pneu rh")
-#> [1] "K. pneumoniae"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# \donttest{
# Becker classification, see ?as.mo ----------------------------------------
mo_fullname("Staph epidermidis")
-#> [1] "Staphylococcus epidermidis"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_fullname("Staph epidermidis", Becker = TRUE)
-#> [1] "Coagulase-negative Staphylococcus (CoNS)"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_shortname("Staph epidermidis")
-#> [1] "S. epidermidis"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_shortname("Staph epidermidis", Becker = TRUE)
-#> [1] "CoNS"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# Lancefield classification, see ?as.mo ------------------------------------
mo_fullname("Strep agalactiae")
-#> [1] "Streptococcus agalactiae"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_fullname("Strep agalactiae", Lancefield = TRUE)
-#> [1] "Streptococcus Group B"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_shortname("Strep agalactiae")
-#> [1] "S. agalactiae"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_shortname("Strep agalactiae", Lancefield = TRUE)
-#> [1] "GBS"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# language support --------------------------------------------------------
mo_gramstain("Klebsiella pneumoniae", language = "de") # German
-#> [1] "Gramnegativ"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch
-#> [1] "Gram-negatief"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish
-#> [1] "Gram negativo"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
-#> [1] "Αρνητικό κατά Gram"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
-#> [1] "Грамнегативні"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
mo_kingdom("Klebsiella pneumoniae")
-#> [1] "Bacteria"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_type("Klebsiella pneumoniae")
-#> [1] "Bacteria"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
-#> [1] "Bacteria"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
-#> [1] "细菌"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")
-#> [1] "Streptococcus Gruppe A"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk")
-#> [1] "Streptococcus Група A"
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# other --------------------------------------------------------------------
@@ -664,145 +658,28 @@
filter(mo_is_gram_positive()) %>%
count(mo_genus(), sort = TRUE)
}
-#> ℹ Using column 'mo' as input for mo_is_gram_positive()
-#> ℹ Using column 'mo' as input for mo_genus()
-#> # A tibble: 18 × 2
-#> `mo_genus()` n
-#> <chr> <int>
-#> 1 Staphylococcus 840
-#> 2 Streptococcus 275
-#> 3 Enterococcus 83
-#> 4 Corynebacterium 17
-#> 5 Micrococcus 6
-#> 6 Gemella 3
-#> 7 Aerococcus 2
-#> 8 Cutibacterium 1
-#> 9 Dermabacter 1
-#> 10 Fusibacter 1
-#> 11 Globicatella 1
-#> 12 Granulicatella 1
-#> 13 Lactobacillus 1
-#> 14 Leuconostoc 1
-#> 15 Listeria 1
-#> 16 Paenibacillus 1
-#> 17 Rothia 1
-#> 18 Schaalia 1
+#> Error in filter(., mo_is_gram_positive()): ℹ In argument: `mo_is_gram_positive()`.
+#> Caused by error:
+#> ! in mo_is_gram_positive(): argument x is missing and no column with info
+#> about microorganisms could be found.
if (require("dplyr")) {
example_isolates %>%
filter(mo_is_intrinsic_resistant(ab = "vanco")) %>%
count(mo_genus(), sort = TRUE)
}
-#> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()
-#> ℹ Using column 'mo' as input for mo_genus()
-#> # A tibble: 20 × 2
-#> `mo_genus()` n
-#> <chr> <int>
-#> 1 Escherichia 467
-#> 2 Klebsiella 77
-#> 3 Proteus 39
-#> 4 Pseudomonas 30
-#> 5 Serratia 25
-#> 6 Enterobacter 23
-#> 7 Citrobacter 11
-#> 8 Haemophilus 8
-#> 9 Acinetobacter 6
-#> 10 Morganella 6
-#> 11 Pantoea 4
-#> 12 Salmonella 3
-#> 13 Neisseria 2
-#> 14 Stenotrophomonas 2
-#> 15 Campylobacter 1
-#> 16 Enterococcus 1
-#> 17 Hafnia 1
-#> 18 Lactobacillus 1
-#> 19 Leuconostoc 1
-#> 20 Pseudescherichia 1
+#> Error in filter(., mo_is_intrinsic_resistant(ab = "vanco")): ℹ In argument: `mo_is_intrinsic_resistant(ab = "vanco")`.
+#> Caused by error:
+#> ! in mo_is_intrinsic_resistant(): argument x is missing and no column with
+#> info about microorganisms could be found.
# get a list with the complete taxonomy (from kingdom to subspecies)
mo_taxonomy("Klebsiella pneumoniae")
-#> $kingdom
-#> [1] "Bacteria"
-#>
-#> $phylum
-#> [1] "Pseudomonadota"
-#>
-#> $class
-#> [1] "Gammaproteobacteria"
-#>
-#> $order
-#> [1] "Enterobacterales"
-#>
-#> $family
-#> [1] "Enterobacteriaceae"
-#>
-#> $genus
-#> [1] "Klebsiella"
-#>
-#> $species
-#> [1] "pneumoniae"
-#>
-#> $subspecies
-#> [1] ""
-#>
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# get a list with the taxonomy, the authors, Gram-stain,
# SNOMED codes, and URL to the online database
mo_info("Klebsiella pneumoniae")
-#> $mo
-#> [1] "B_KLBSL_PNMN"
-#>
-#> $kingdom
-#> [1] "Bacteria"
-#>
-#> $phylum
-#> [1] "Pseudomonadota"
-#>
-#> $class
-#> [1] "Gammaproteobacteria"
-#>
-#> $order
-#> [1] "Enterobacterales"
-#>
-#> $family
-#> [1] "Enterobacteriaceae"
-#>
-#> $genus
-#> [1] "Klebsiella"
-#>
-#> $species
-#> [1] "pneumoniae"
-#>
-#> $subspecies
-#> [1] ""
-#>
-#> $status
-#> [1] "accepted"
-#>
-#> $synonyms
-#> NULL
-#>
-#> $gramstain
-#> [1] "Gram-negative"
-#>
-#> $oxygen_tolerance
-#> [1] "aerobe"
-#>
-#> $url
-#> [1] "https://lpsn.dsmz.de/species/klebsiella-pneumoniae"
-#>
-#> $ref
-#> [1] "Trevisan, 1887"
-#>
-#> $snomed
-#> [1] "1098101000112102" "446870005" "1098201000112108" "409801009"
-#> [5] "56415008" "714315002" "713926009"
-#>
-#> $lpsn
-#> [1] "777151"
-#>
-#> $gbif
-#> [1] "3221874"
-#>
+#> Error in .Call(Cchin, x, table): NULL value passed as symbol address
# }