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(v1.8.1.9011) update prevalence of some genera

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dr. M.S. (Matthijs) Berends
2022-06-03 12:43:25 +02:00
parent 70a07bad39
commit 1b84564d36
35 changed files with 278 additions and 429 deletions
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18
man/proportion.Rd
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@ -89,7 +89,9 @@ The function \code{\link[=proportion_df]{proportion_df()}} takes any variable fr
}
\section{Combination Therapy}{
When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:\preformatted{--------------------------------------------------------------------
When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:
\if{html}{\out{<div class="sourceCode">}}\preformatted{--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as
@ -105,15 +107,19 @@ When using more than one variable for \code{...} (= combination therapy), use \c
R <NA> - - - -
<NA> <NA> - - - -
--------------------------------------------------------------------
}
}\if{html}{\out{</div>}}
Please note that, in combination therapies, for \code{only_all_tested = TRUE} applies that:\preformatted{ count_S() + count_I() + count_R() = count_all()
Please note that, in combination therapies, for \code{only_all_tested = TRUE} applies that:
\if{html}{\out{<div class="sourceCode">}}\preformatted{ count_S() + count_I() + count_R() = count_all()
proportion_S() + proportion_I() + proportion_R() = 1
}
}\if{html}{\out{</div>}}
and that, in combination therapies, for \code{only_all_tested = FALSE} applies that:\preformatted{ count_S() + count_I() + count_R() >= count_all()
and that, in combination therapies, for \code{only_all_tested = FALSE} applies that:
\if{html}{\out{<div class="sourceCode">}}\preformatted{ count_S() + count_I() + count_R() >= count_all()
proportion_S() + proportion_I() + proportion_R() >= 1
}
}\if{html}{\out{</div>}}
Using \code{only_all_tested} has no impact when only using one antibiotic as input.
}