diff --git a/.Rbuildignore b/.Rbuildignore index 7e567125..6b4a446a 100755 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -13,9 +13,7 @@ ^CRAN-RELEASE$ ^doc$ ^docs$ -^git_merge\.sh$ -^git_premaster\.sh$ -^git_siteonly\.sh$ +^git_.*\.sh$ ^index\.md$ ^installed_deps$ ^Meta$ diff --git a/R/catalogue_of_life.R b/R/catalogue_of_life.R index 812e5e0d..e37da8f8 100755 --- a/R/catalogue_of_life.R +++ b/R/catalogue_of_life.R @@ -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: diff --git a/man/as.mo.Rd b/man/as.mo.Rd index 1bd977fa..fa970206 100644 --- a/man/as.mo.Rd +++ b/man/as.mo.Rd @@ -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}()}. } diff --git a/man/catalogue_of_life.Rd b/man/catalogue_of_life.Rd index 7daee1ac..74327fa9 100644 --- a/man/catalogue_of_life.Rd +++ b/man/catalogue_of_life.Rd @@ -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}()}. } diff --git a/man/catalogue_of_life_version.Rd b/man/catalogue_of_life_version.Rd index 9decac39..3207b130 100644 --- a/man/catalogue_of_life_version.Rd +++ b/man/catalogue_of_life_version.Rd @@ -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}()}. } diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd index c85f8eaf..e0d29d5a 100755 --- a/man/microorganisms.Rd +++ b/man/microorganisms.Rd @@ -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}()}. } diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd index 46252cac..561fb16d 100644 --- a/man/microorganisms.codes.Rd +++ b/man/microorganisms.codes.Rd @@ -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}()}. } diff --git a/man/microorganisms.old.Rd b/man/microorganisms.old.Rd index f8e470b8..b926bfe5 100644 --- a/man/microorganisms.old.Rd +++ b/man/microorganisms.old.Rd @@ -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}()}. } diff --git a/man/mo_property.Rd b/man/mo_property.Rd index 86092391..e917ea5e 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -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}()}. } diff --git a/vignettes/benchmarks.Rmd b/vignettes/benchmarks.Rmd index 24e07e4e..46ebf8b0 100755 --- a/vignettes/benchmarks.Rmd +++ b/vignettes/benchmarks.Rmd @@ -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