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documentation update

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dr. M.S. (Matthijs) Berends 2019-04-07 22:40:02 +02:00
parent e76114f394
commit 30b559827c
10 changed files with 15 additions and 16 deletions
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4
.Rbuildignore
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@ -13,9 +13,7 @@
^CRAN-RELEASE$
^doc$
^docs$
^git_merge\.sh$
^git_premaster\.sh$
^git_siteonly\.sh$
^git_.*\.sh$
^index\.md$
^installed_deps$
^Meta$

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R/catalogue_of_life.R
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@ -24,7 +24,7 @@
#' This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life.
#' @section Catalogue of Life:
#' \if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
#' This package contains the complete taxonomic tree of almost all microorganisms (~60,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
#' This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
#'
#' \link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
#' @section Included taxa:

2
man/as.mo.Rd
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@ -140,7 +140,7 @@ Group 2 probably contains all other microbial pathogens ever found in humans.
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~60,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
}

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man/catalogue_of_life.Rd
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@ -9,7 +9,7 @@ This package contains the complete taxonomic tree of almost all microorganisms f
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~60,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
}

2
man/catalogue_of_life_version.Rd
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@ -20,7 +20,7 @@ For DSMZ, see \code{?microorganisms}.
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~60,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
}

2
man/microorganisms.Rd
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@ -53,7 +53,7 @@ From: \url{https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloa
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~60,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
}

2
man/microorganisms.codes.Rd
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@ -18,7 +18,7 @@ A data set containing commonly used codes for microorganisms, from laboratory sy
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~60,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
}

2
man/microorganisms.old.Rd
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@ -23,7 +23,7 @@ A data set containing old (previously valid or accepted) taxonomic names accordi
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~60,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
}

2
man/mo_property.Rd
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@ -102,7 +102,7 @@ Supported languages are \code{"en"} (English), \code{"de"} (German), \code{"nl"}
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~60,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
}

11
vignettes/benchmarks.Rmd
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@ -85,9 +85,10 @@ boxplot(microbenchmark(as.mo("Thermus islandicus"),
main = "Benchmarks per prevalence")
```
In reality, the `as.mo()` functions **learns from its own output to speed up determinations for next times**. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use `as.mo()` yourself:
```{r, echo = FALSE}
```{r, echo = FALSE, eval = FALSE}
# In reality, the `as.mo()` functions **learns from its own output to speed up determinations for next times**. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use `as.mo()` yourself:
clean_mo_history()
par(mar = c(5, 16, 4, 2))
boxplot(microbenchmark(
@ -101,11 +102,11 @@ boxplot(microbenchmark(
horizontal = TRUE, las = 1, unit = "s", log = FALSE,
xlab = "", ylab = "Time in seconds", ylim = c(0, 0.5),
main = "Benchmarks per prevalence")
# The highest outliers are the first times. All next determinations were done in only thousands of seconds. For now, learning only works per session. If R is closed or terminated, the algorithms reset. This will probably be resolved in a next version.
```
The highest outliers are the first times. All next determinations were done in only thousands of seconds. For now, learning only works per session. If R is closed or terminated, the algorithms reset. This will probably be resolved in a next version.
Still, uncommon microorganisms take a lot more time than common microorganisms, especially the first time. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: **repetitive results** and **already precalculated results**.
Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: **repetitive results** and **already precalculated results**.
### Repetitive results