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edited g.test

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dr. M.S. (Matthijs) Berends
2019-01-12 11:06:58 +01:00
parent 641d866db2
commit 5aad26035c
62 changed files with 703 additions and 845 deletions
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2
man/ITIS.Rd
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@ -11,7 +11,7 @@ All taxonomic names of all microorganisms are included in this package, using th
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

6
man/age.Rd
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@ -9,13 +9,13 @@ age(x, reference = Sys.Date())
\arguments{
\item{x}{date(s), will be coerced with \code{\link{as.POSIXlt}}}
\item{reference}{reference date(s) (defaults to today), will be coerced with \code{\link{as.POSIXlt}}}
\item{reference}{reference date(s) (defaults to today), will be coerced with \code{\link{as.POSIXlt}} and cannot be lower than \code{x}}
}
\value{
Integer (no decimals)
}
\description{
Calculates age in years based on a reference date, which is the sytem time at default.
Calculates age in years based on a reference date, which is the sytem date at default.
}
\section{Read more on our website!}{
@ -24,5 +24,5 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
}
\seealso{
\code{\link{age_groups}} to splits age into groups
\code{\link{age_groups}} to split age into age groups
}

2
man/age_groups.Rd
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@ -20,7 +20,7 @@ Split ages into age groups defined by the \code{split} parameter. This allows fo
\details{
To split ages, the input can be:
\itemize{
\item{A numeric vector. A vector of \code{c(10, 20)} will split on 0-9, 10-19 and 20+. A value of only \code{50} will split on 0-49 and 50+.
\item{A numeric vector. A vector of e.g. \code{c(10, 20)} will split on 0-9, 10-19 and 20+. A value of only \code{50} will split on 0-49 and 50+.
The default is to split on young children (0-11), youth (12-24), young adults (26-54), middle-aged adults (55-74) and elderly (75+).}
\item{A character:}
\itemize{

2
man/as.mo.Rd
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@ -88,7 +88,7 @@ When using \code{allow_uncertain = TRUE} (which is the default setting), it will
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

2
man/g.test.Rd
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@ -78,7 +78,7 @@ Use the \emph{G}-test of independence when you have two nominal variables, each
It is also possible to do a \emph{G}-test of independence with more than two nominal variables. For example, Jackson et al. (2013) also had data for children under 3, so you could do an analysis of old vs. young, thigh vs. arm, and reaction vs. no reaction, all analyzed together.
Fisher's exact test (\code{\link{fisher.test}}) is more accurate than the \emph{G}-test of independence when the expected numbers are small, so it is recommend to only use the \emph{G}-test if your total sample size is greater than 1000.
Fisher's exact test (\code{\link{fisher.test}}) is an \strong{exact} test, where the \emph{G}-test is still only an \strong{approximation}. For any 2x2 table, Fisher's Exact test may be slower but will still run in seconds, even if the sum of your observations is multiple millions.
The \emph{G}-test of independence is an alternative to the chi-square test of independence (\code{\link{chisq.test}}), and they will give approximately the same results.
}

2
man/microorganisms.Rd
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@ -36,7 +36,7 @@ A data set containing the complete microbial taxonomy of the kingdoms Bacteria,
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

2
man/microorganisms.old.Rd
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@ -25,7 +25,7 @@ A data set containing old (previously valid or accepted) taxonomic names accordi
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

2
man/mo_property.Rd
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@ -97,7 +97,7 @@ Supported languages are \code{"en"} (English), \code{"de"} (German), \code{"nl"}
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}