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renamed year columns to ref

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-10-01 14:44:40 +02:00
parent 3119a221e5
commit ed17db0263
16 changed files with 78 additions and 66 deletions
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6
man/freq.Rd
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@ -119,7 +119,7 @@ years <- format(years)
# print a histogram of numeric values
septic_patients \%>\%
freq(age) \%>\%
hist() # prettier: ggplot(septic_patients, aes(age)) + geom_histogram()
hist()
# or print all points to a regular plot
septic_patients \%>\%
@ -147,6 +147,10 @@ table(septic_patients$gender,
septic_patients$age) \%>\%
freq(sep = " **sep** ")
# check differences between frequency tables
diff(freq(septic_patients$trim),
freq(septic_patients$trsu))
\dontrun{
# send frequency table to clipboard (e.g. for pasting in Excel)
septic_patients \%>\%

5
man/microorganisms.Rd
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@ -4,7 +4,7 @@
\name{microorganisms}
\alias{microorganisms}
\title{Data set with taxonomic data from ITIS}
\format{A \code{\link{data.frame}} with 18,833 observations and 16 variables:
\format{A \code{\link{data.frame}} with 18,833 observations and 15 variables:
\describe{
\item{\code{mo}}{ID of microorganism}
\item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
@ -20,8 +20,7 @@
\item{\code{gramstain}}{Gram of microorganism, like \code{"Gram negative"}}
\item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungi"}}
\item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
\item{\code{authors}}{Author(s) that published this taxonomic name as found in ITIS, see Source}
\item{\code{year}}{Year in which the author(s) published this taxonomic name as found in ITIS, see Source}
\item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
}}
\source{
[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.

5
man/microorganisms.old.Rd
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@ -4,13 +4,12 @@
\name{microorganisms.old}
\alias{microorganisms.old}
\title{Data set with old taxonomic data from ITIS}
\format{A \code{\link{data.frame}} with 2,383 observations and 5 variables:
\format{A \code{\link{data.frame}} with 2,383 observations and 4 variables:
\describe{
\item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS}
\item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source}
\item{\code{tsn_new}}{New Taxonomic Serial Number (TSN), as defined by ITIS}
\item{\code{authors}}{Authors responsible for renaming as found in ITIS, see Source}
\item{\code{year}}{Year in which the literature was published about the renaming as found in ITIS, see Source}
\item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
}}
\source{
[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.

10
man/mo_property.Rd
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@ -12,8 +12,7 @@
\alias{mo_class}
\alias{mo_phylum}
\alias{mo_subkingdom}
\alias{mo_authors}
\alias{mo_year}
\alias{mo_ref}
\alias{mo_type}
\alias{mo_TSN}
\alias{mo_gramstain}
@ -40,9 +39,7 @@ mo_phylum(x, ...)
mo_subkingdom(x, ...)
mo_authors(x, ...)
mo_year(x, ...)
mo_ref(x, ...)
mo_type(x, language = NULL, ...)
@ -103,8 +100,7 @@ mo_shortname("E. coli") # "E. coli"
mo_gramstain("E. coli") # "Gram negative"
mo_TSN("E. coli") # 285
mo_type("E. coli") # "Bacteria"
mo_authors("E. coli") # "Castellani and Chalmers"
mo_year("E. coli") # 1919
mo_ref("E. coli") # "Castellani and Chalmers, 1919"
# Abbreviations known in the field