vignettes/SPSS.Rmd
SPSS.RmdR has a huge community.
-Many R users just ask questions on websites like StackOverflow.com, the largest online community for programmers. At the time of writing, 428,733 R-related questions have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.
+Many R users just ask questions on websites like StackOverflow.com, the largest online community for programmers. At the time of writing, 429,535 R-related questions have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.
R understands any data type, including SPSS/SAS/Stata.
@@ -308,7 +308,7 @@ # 8 10011 1 1 73.1 # 9 10017 1 1 56.7 # 10 10018 0 1 66.6 -# # … with 4,193 more rows +# # ... with 4,193 more rows as_factor(SPSS_data) # # A tibble: 4,203 x 4 @@ -324,7 +324,7 @@ # 8 10011 Male alive 73.1 # 9 10017 Male alive 56.7 # 10 10018 Female alive 66.6 -# # … with 4,193 more rows +# # ... with 4,193 more rowsAMR 1.7.1.9073AMR 1.7.1.9074All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
p_symbol() and all filter_*() functions (except for filter_first_isolate()), which were all deprecated in a previous package versionkey_antibiotics() and key_antibiotics_equal() functions, which were deprecated and superseded by key_antimicrobials() and antimicrobials_equal()
get_locale() to get_AMR_locale() to prevent conflicts with other packagesSupport for the CLSI 2021 guideline for interpreting MIC/disk diffusion values, which are incorporated in the rsi_translation data set. This data set now more strictly follows the WHONET software as well.
Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for eucast_rules(), mo_is_intrinsic_resistant() and mdro(). The intrinsic_resistant data set was also updated accordingly.
Support for all antimicrobial drug (group) names and colloquial microorganism names in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish
Function ab_ddd_units() to get units of DDDs (daily defined doses), deprecating the use of ab_ddd(..., units = TRUE) to be more consistent in data types of function output
antibiotics data set now contains all ATC codes that are available through the WHOCC website, regardless of drugs being present in more than one ATC group. This means that:
scale_rsi_colours() when using ggplot2 v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)as.mo()
+random_mic()
get_episode() and is_new_episode() can now cope with NAsB_ENTRC_FAE could have been both E. faecalis and E. faecium. Its new code is B_ENTRC_FCLS and E. faecium has become B_ENTRC_FACM. Also, the Latin character æ (ae) is now preserved at the start of each genus and species abbreviation. For example, the old code for Aerococcus urinae was B_ARCCC_NAE. This is now B_AERCC_URIN. IMPORTANT: Old microorganism IDs are still supported, but support will be dropped in a future version. Use as.mo() on your old codes to transform them to the new format. Using functions from the mo_* family (like mo_name() and mo_gramstain()) on old codes, will throw a warning.B_ENTRC_FAE could have been both E. faecalis and E. faecium. Its new code is B_ENTRC_FCLS and E. faecium has become B_ENTRC_FACM. Also, the Latin character ae is now preserved at the start of each genus and species abbreviation. For example, the old code for Aerococcus urinae was B_ARCCC_NAE. This is now B_AERCC_URIN. IMPORTANT: Old microorganism IDs are still supported, but support will be dropped in a future version. Use as.mo() on your old codes to transform them to the new format. Using functions from the mo_* family (like mo_name() and mo_gramstain()) on old codes, will throw a warning.as.ab(), including bidirectional language supportmdro() function, to determine multi-drug resistant organismsAll these lead to the microbial ID of E. coli:
@@ -1414,15 +1416,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/Implemented the latest publication of Becker et al. (2019), for categorising coagulase-negative Staphylococci
All microbial IDs that found are now saved to a local file ~/.Rhistory_mo. Use the new function clean_mo_history() to delete this file, which resets the algorithms.
Incoercible results will now be considered ‘unknown’, MO code UNKNOWN. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:
-
-mo_genus("qwerty", language = "es")
-# Warning:
-# one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.
-#> [1] "(género desconocido)"Incoercible results will now be considered ‘unknown’, MO code UNKNOWN. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese.
Fix for vector containing only empty values
Finds better results when input is in other languages
Better handling for subspecies
freq() function):
Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
-+# Determine genus of microorganisms (mo) in `septic_patients` data set: # OLD WAY @@ -1530,7 +1524,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/Fewer than 3 characters as input for
as.mowill return NAFunction
-as.mo(and allmo_*wrappers) now supports genus abbreviations with “species” attached+as.mo("E. species") # B_ESCHR mo_fullname("E. spp.") # "Escherichia species" @@ -1546,7 +1540,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/Frequency tables -
freq():
Support for grouping variables, test with:
-+septic_patients %>% group_by(hospital_id) %>% @@ -1554,7 +1548,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/Support for (un)selecting columns:
-+septic_patients %>% freq(hospital_id) %>% @@ -1621,7 +1615,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/- Author and year:
mo_refThey also come with support for German, Dutch, French, Italian, Spanish and Portuguese:
-+mo_gramstain("E. coli") # [1] "Gram negative" @@ -1632,7 +1626,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ mo_fullname("S. group A", language = "pt") # Portuguese # [1] "Streptococcus grupo A"Furthermore, former taxonomic names will give a note about the current taxonomic name:
-+mo_gramstain("Esc blattae") # Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010) @@ -1645,7 +1639,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/Function
is.rsi.eligibleto check for columns that have valid antimicrobial results, but do not have thersiclass yet. Transform the columns of your raw data with:data %>% mutate_if(is.rsi.eligible, as.rsi)Functions
-as.moandis.moas replacements foras.bactidandis.bactid(since themicrooganismsdata set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. Theas.mofunction determines microbial IDs using intelligent rules:+as.mo("E. coli") # [1] B_ESCHR_COL @@ -1654,7 +1648,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ as.mo("S group A") # [1] B_STRPTC_GRAAnd with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:
-+thousands_of_E_colis <- rep("E. coli", 25000) microbenchmark::microbenchmark(as.mo(thousands_of_E_colis), unit = "s") @@ -1683,7 +1677,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
Added three antimicrobial agents to the
antibioticsdata set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)Added 163 trade names to the
-antibioticsdata set, it now contains 298 different trade names in total, e.g.:+ab_official("Bactroban") # [1] "Mupirocin" @@ -1700,7 +1694,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/Added arguments
minimumandas_percenttoportion_dfSupport for quasiquotation in the functions series
-count_*andportions_*, andn_rsi. This allows to check for more than 2 vectors or columns.+septic_patients %>% select(amox, cipr) %>% count_IR() # which is the same as: @@ -1720,12 +1714,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/Added longest en shortest character length in the frequency table (
freq) header of classcharacterSupport for types (classes) list and matrix for
-freq@@ -188,15 +188,13 @@+For lists, subsetting is possible:
-@@ -199,7 +199,7 @@+@@ -267,10 +267,10 @@my_list = list(age = septic_patients$age, gender = septic_patients$gender) my_list %>% freq(age) @@ -1769,7 +1763,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/- New Lancefield classification for Streptococcus to categorise them into Lancefield groups
- For convience, new descriptive statistical functions
-kurtosisandskewnessthat are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices- Function
g.testto perform the Χ2 distributed G-test, which use is the same aschisq.test+- Function
g.testto perform the X2 distributed G-test, which use is the same aschisq.testFunctiondiff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html index 48d7be17..b85ff781 100644 --- a/docs/reference/as.mo.html +++ b/docs/reference/as.mo.html @@ -17,7 +17,7 @@ratioto transform a vector of values to a preset ratioSource
-
- +
Becker K et al. Coagulase-Negative Staphylococci. 2014. Clin Microbiol Rev. 27(4): 870–926; doi: 10.1128/CMR.00109-13
Becker K et al. Coagulase-Negative Staphylococci. 2014. Clin Microbiol Rev. 27(4): 870-926; doi: 10.1128/CMR.00109-13
Becker K et al. Implications of identifying the recently defined members of the S. aureus complex, S. argenteus and S. schweitzeri: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS). 2019. Clin Microbiol Infect; doi: 10.1016/j.cmi.2019.02.028
- -
Becker K et al. Emergence of coagulase-negative staphylococci 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: 10.1080/14787210.2020.1730813
- +
Lancefield RC A serological differentiation of human and other groups of hemolytic streptococci. 1933. J Exp Med. 57(4): 571–95; doi: 10.1084/jem.57.4.571
Lancefield RC A serological differentiation of human and other groups of hemolytic streptococci. 1933. J Exp Med. 57(4): 571-95; doi: 10.1084/jem.57.4.571
Catalogue of Life: 2019 Annual Checklist, http://www.catalogueoflife.org
List of Prokaryotic names with Standing in Nomenclature (5 October 2021), doi: 10.1099/ijsem.0.004332
- diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index bce19cb8..37bed60d 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -18,7 +18,7 @@
US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009
Source
Methodology of this function is strictly based on:
- -
M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition, 2014, Clinical and Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/.
- +
Hindler JF and Stelling J (2007). Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute. Clinical Infectious Diseases, 44(6), 867–873. doi: 10.1086/511864
Hindler JF and Stelling J (2007). Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute. Clinical Infectious Diseases, 44(6), 867-873. doi: 10.1086/511864
diff --git a/docs/reference/intrinsic_resistant.html b/docs/reference/intrinsic_resistant.html index 95614cb2..623576d7 100644 --- a/docs/reference/intrinsic_resistant.html +++ b/docs/reference/intrinsic_resistant.html @@ -17,7 +17,7 @@Arguments
diff --git a/docs/reference/index.html b/docs/reference/index.html index aeb36b61..85f434ca 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@@@ -173,7 +173,7 @@Examples
-diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index a514af42..0852e1ad 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -17,7 +17,7 @@subset(intrinsic_resistant, - antibiotic == "Vancomycin" & microorganism %like% "Enterococcus")$microorganism -#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" - -# \donttest{ +@@ -179,8 +179,8 @@# \donttest{ if (require("dplyr")) { intrinsic_resistant %>% - filter(antibiotic == "Vancomycin" & microorganism %like% "Enterococcus") %>% - pull(microorganism) + mutate(mo = mo_name(mo), + ab = ab_name(mo)) + filter(ab == "Vancomycin" & mo %like% "Enterococcus") %>% + pull(mo) #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" } # } diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index 9402453b..99bd6974 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -17,7 +17,7 @@Source
Catalogue of Life: 2019 Annual Checklist as currently implemented in this
AMRpackage:
Annual Checklist (public online taxonomic database), http://www.catalogueoflife.org
List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this
AMRpackage:
- -
Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi: 10.1099/ijsem.0.004332
- -
Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
- +
Parte, A.C. (2014). LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613–D616; doi: 10.1093/nar/gkt1111
- +
Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; doi: 10.1093/nar/gkt1111
Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; doi: 10.1099/00207713-47-2-590
US Edition of SNOMED CT from 1 September 2020 as currently implemented in this
AMRpackage:
Retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009
Source
Catalogue of Life: Annual Checklist (public online taxonomic database), http://www.catalogueoflife.org (check included annual version with
-catalogue_of_life_version()).Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
+Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
@@ -292,10 +292,10 @@ This package contains the complete taxonomic tree of almost all microorganisms (Catalogue of Life
diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index ad8567ae..c5cf5f2a 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -17,7 +17,7 @@Source
-
- +
Becker K et al. Coagulase-Negative Staphylococci. 2014. Clin Microbiol Rev. 27(4): 870–926; doi: 10.1128/CMR.00109-13
Becker K et al. Coagulase-Negative Staphylococci. 2014. Clin Microbiol Rev. 27(4): 870-926; doi: 10.1128/CMR.00109-13
Becker K et al. Implications of identifying the recently defined members of the S. aureus complex, S. argenteus and S. schweitzeri: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS). 2019. Clin Microbiol Infect; doi: 10.1016/j.cmi.2019.02.028
- -
Becker K et al. Emergence of coagulase-negative staphylococci 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: 10.1080/14787210.2020.1730813
- +
Lancefield RC A serological differentiation of human and other groups of hemolytic streptococci. 1933. J Exp Med. 57(4): 571–95; doi: 10.1084/jem.57.4.571
Lancefield RC A serological differentiation of human and other groups of hemolytic streptococci. 1933. J Exp Med. 57(4): 571-95; doi: 10.1084/jem.57.4.571
Catalogue of Life: 2019 Annual Checklist, http://www.catalogueoflife.org
List of Prokaryotic names with Standing in Nomenclature (5 October 2021), doi: 10.1099/ijsem.0.004332
- diff --git a/inst/tinytest/test-data.R b/inst/tinytest/test-data.R index 1480e993..8828e4cb 100644 --- a/inst/tinytest/test-data.R +++ b/inst/tinytest/test-data.R @@ -92,3 +92,36 @@ expect_true(NROW(uncategorised) == 0, "All staphylococcal species categorised as CoNS/CoPS.", paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ", uncategorised$species, " (", uncategorised$mo, ")"))) + +# THIS WILL CHECK NON-ASCII STRINGS IN ALL FILES: + +# check_non_ascii <- function() { +# purrr::map_df( +# .id = "file", +# # list common text files +# .x = fs::dir_ls( +# recurse = TRUE, +# type = "file", +# # ignore images, compressed +# regexp = "\\.(png|ico|rda|ai|tar.gz|zip|xlsx|csv|pdf|psd)$", +# invert = TRUE +# ), +# .f = function(path) { +# x <- readLines(path, warn = FALSE) +# # from tools::showNonASCII() +# asc <- iconv(x, "latin1", "ASCII") +# ind <- is.na(asc) | asc != x +# # make data frame +# if (any(ind)) { +# tibble::tibble( +# row = which(ind), +# line = iconv(x[ind], "latin1", "ASCII", sub = "byte") +# ) +# } else { +# tibble::tibble() +# } +# } +# ) +# } +# x <- check_non_ascii() %>% +# filter(file %unlike% "^(data-raw|docs|git_)") diff --git a/man/as.mo.Rd b/man/as.mo.Rd index a3ed10ec..d0e4a128 100644 --- a/man/as.mo.Rd +++ b/man/as.mo.Rd @@ -126,10 +126,10 @@ The intelligent rules consider the prevalence of microorganisms in humans groupe \section{Source}{ \enumerate{ -\item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926; \doi{10.1128/CMR.00109-13} +\item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870-926; \doi{10.1128/CMR.00109-13} \item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028} \item Becker K \emph{et al.} \strong{Emergence of coagulase-negative staphylococci} 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813} -\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95; \doi{10.1084/jem.57.4.571} +\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571-95; \doi{10.1084/jem.57.4.571} \item Catalogue of Life: 2019 Annual Checklist, \url{http://www.catalogueoflife.org} \item List of Prokaryotic names with Standing in Nomenclature (5 October 2021), \doi{10.1099/ijsem.0.004332} \item US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: \url{https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009} diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd index 60f6edbf..44e6828d 100755 --- a/man/first_isolate.Rd +++ b/man/first_isolate.Rd @@ -8,7 +8,7 @@ Methodology of this function is strictly based on: \itemize{ \item \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}. -\item Hindler JF and Stelling J (2007). \strong{Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.} Clinical Infectious Diseases, 44(6), 867–873. \doi{10.1086/511864} +\item Hindler JF and Stelling J (2007). \strong{Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.} Clinical Infectious Diseases, 44(6), 867-873. \doi{10.1086/511864} } } \usage{ diff --git a/man/intrinsic_resistant.Rd b/man/intrinsic_resistant.Rd index 692df98f..6859d0d0 100644 --- a/man/intrinsic_resistant.Rd +++ b/man/intrinsic_resistant.Rd @@ -33,15 +33,13 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/ } \examples{ -subset(intrinsic_resistant, - antibiotic == "Vancomycin" & microorganism \%like\% "Enterococcus")$microorganism -#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" - \donttest{ if (require("dplyr")) { intrinsic_resistant \%>\% - filter(antibiotic == "Vancomycin" & microorganism \%like\% "Enterococcus") \%>\% - pull(microorganism) + mutate(mo = mo_name(mo), + ab = ab_name(mo)) + filter(ab == "Vancomycin" & mo \%like\% "Enterococcus") \%>\% + pull(mo) #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" } } diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd index 9afb6f38..e3b82800 100755 --- a/man/microorganisms.Rd +++ b/man/microorganisms.Rd @@ -27,8 +27,8 @@ Catalogue of Life: 2019 Annual Checklist as currently implemented in this \code{ List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this \code{AMR} package: \itemize{ \item Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332} -\item Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786} -\item Parte, A.C. (2014). LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613–D616; \doi{10.1093/nar/gkt1111} +\item Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786} +\item Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; \doi{10.1093/nar/gkt1111} \item Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; \doi{10.1099/00207713-47-2-590} } diff --git a/man/microorganisms.old.Rd b/man/microorganisms.old.Rd index e88b7c2d..58ed4ca4 100644 --- a/man/microorganisms.old.Rd +++ b/man/microorganisms.old.Rd @@ -16,7 +16,7 @@ A \link{data.frame} with 14,338 observations and 4 variables: \source{ Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}). -Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786} +Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786} } \usage{ microorganisms.old diff --git a/man/mo_property.Rd b/man/mo_property.Rd index 1c57aefe..188e14f0 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -181,10 +181,10 @@ This package contains the complete taxonomic tree of almost all microorganisms ( \section{Source}{ \enumerate{ -\item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926; \doi{10.1128/CMR.00109-13} +\item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870-926; \doi{10.1128/CMR.00109-13} \item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028} \item Becker K \emph{et al.} \strong{Emergence of coagulase-negative staphylococci} 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813} -\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95; \doi{10.1084/jem.57.4.571} +\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571-95; \doi{10.1084/jem.57.4.571} \item Catalogue of Life: 2019 Annual Checklist, \url{http://www.catalogueoflife.org} \item List of Prokaryotic names with Standing in Nomenclature (5 October 2021), \doi{10.1099/ijsem.0.004332} \item US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: \url{https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009} diff --git a/vignettes/SPSS.Rmd b/vignettes/SPSS.Rmd index 01e1e31b..5e276e29 100755 --- a/vignettes/SPSS.Rmd +++ b/vignettes/SPSS.Rmd @@ -126,7 +126,7 @@ SPSS_data # 8 10011 1 1 73.1 # 9 10017 1 1 56.7 # 10 10018 0 1 66.6 -# # … with 4,193 more rows +# # ... with 4,193 more rows as_factor(SPSS_data) # # A tibble: 4,203 x 4 @@ -142,7 +142,7 @@ as_factor(SPSS_data) # 8 10011 Male alive 73.1 # 9 10017 Male alive 56.7 # 10 10018 Female alive 66.6 -# # … with 4,193 more rows +# # ... with 4,193 more rows ``` ### Base R
US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009