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(v0.7.0.9010) mo_synonyms, plot/barplot fixes

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dr. M.S. (Matthijs) Berends
2019-06-16 21:42:40 +02:00
parent 980be2b22d
commit 9c39c35f86
72 changed files with 595 additions and 802 deletions
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2
man/count.Rd
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@ -62,7 +62,7 @@ The function \code{n_rsi} is an alias of \code{count_all}. They can be used to c
The function \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of S, I and R. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
The function \code{rsi_df} works exactly like \code{count_df}, but add the percentage of S, I and R.
The function \code{rsi_df} works exactly like \code{count_df}, but adds the percentage of S, I and R.
}
\section{Interpretation of S, I and R}{

4
man/mo_property.Rd
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@ -20,6 +20,7 @@
\alias{mo_year}
\alias{mo_rank}
\alias{mo_taxonomy}
\alias{mo_synonyms}
\alias{mo_info}
\alias{mo_url}
\title{Property of a microorganism}
@ -60,6 +61,8 @@ mo_rank(x, ...)
mo_taxonomy(x, language = get_locale(), ...)
mo_synonyms(x, ...)
mo_info(x, language = get_locale(), ...)
mo_url(x, open = FALSE, ...)
@ -147,6 +150,7 @@ mo_gramstain("E. coli") # "Gram-negative"
mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
mo_rank("E. coli") # "species"
mo_url("E. coli") # get the direct url to the online database entry
mo_synonyms("E. coli") # get previously accepted taxonomic names
## scientific reference
mo_ref("E. coli") # "Castellani et al., 1919"

2
man/portion.Rd
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@ -73,7 +73,7 @@ These functions are not meant to count isolates, but to calculate the portion of
The function \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each group and each variable with class \code{"rsi"}.
The function \code{rsi_df} works exactly like \code{portion_df}, but add the number of isolates.
The function \code{rsi_df} works exactly like \code{portion_df}, but adds the number of isolates.
\if{html}{
\cr\cr
To calculate the probability (\emph{p}) of susceptibility of one antibiotic, we use this formula: