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as.rsi warning, site update

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dr. M.S. (Matthijs) Berends 2019-02-10 09:13:06 +01:00
parent cbad93d92b
commit 1a1e81c5d2
2 changed files with 190 additions and 1 deletions
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2
.gitlab-ci.yml
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@ -35,7 +35,7 @@ before_script:
# install dependencies for packages
- apt-get install -y wget locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev r-base > /dev/null
# recent pandoc
- wget https://github.com/jgm/pandoc/releases/download/2.6/pandoc-2.6-1-amd64.deb
- wget --quiet https://github.com/jgm/pandoc/releases/download/2.6/pandoc-2.6-1-amd64.deb
- dpkg -i pandoc*.deb
- rm pandoc*.deb
# set R system language

189
NAMESPACE
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@ -1,5 +1,194 @@
# Generated by roxygen2: do not edit by hand
S3method(as.data.frame,atc)
S3method(as.data.frame,frequency_tbl)
S3method(as.data.frame,mo)
S3method(as.double,mic)
S3method(as.integer,mic)
S3method(as.numeric,mic)
S3method(as.vector,frequency_tbl)
S3method(as_tibble,frequency_tbl)
S3method(barplot,mic)
S3method(barplot,rsi)
S3method(diff,frequency_tbl)
S3method(droplevels,mic)
S3method(droplevels,rsi)
S3method(format,frequency_tbl)
S3method(hist,frequency_tbl)
S3method(kurtosis,data.frame)
S3method(kurtosis,default)
S3method(kurtosis,matrix)
S3method(plot,frequency_tbl)
S3method(plot,mic)
S3method(plot,resistance_predict)
S3method(plot,rsi)
S3method(print,atc)
S3method(print,frequency_tbl)
S3method(print,mic)
S3method(print,mo)
S3method(print,rsi)
S3method(pull,atc)
S3method(pull,mo)
S3method(select,frequency_tbl)
S3method(skewness,data.frame)
S3method(skewness,default)
S3method(skewness,matrix)
S3method(summary,mic)
S3method(summary,mo)
S3method(summary,rsi)
export("%like%")
export(EUCAST_rules)
export(ab_atc)
export(ab_certe)
export(ab_name)
export(ab_official)
export(ab_property)
export(ab_tradenames)
export(ab_trivial_nl)
export(ab_umcg)
export(abname)
export(age)
export(age_groups)
export(anti_join_microorganisms)
export(as.atc)
export(as.mic)
export(as.mo)
export(as.rsi)
export(atc_certe)
export(atc_ddd)
export(atc_groups)
export(atc_name)
export(atc_official)
export(atc_online_ddd)
export(atc_online_groups)
export(atc_online_property)
export(atc_property)
export(atc_tradenames)
export(atc_trivial_nl)
export(atc_umcg)
export(availability)
export(brmo)
export(count_I)
export(count_IR)
export(count_R)
export(count_S)
export(count_SI)
export(count_all)
export(count_df)
export(eucast_exceptional_phenotypes)
export(eucast_rules)
export(facet_rsi)
export(filter_first_isolate)
export(filter_first_weighted_isolate)
export(first_isolate)
export(freq)
export(frequency_tbl)
export(full_join_microorganisms)
export(g.test)
export(geom_rsi)
export(get_locale)
export(get_mo_source)
export(ggplot_rsi)
export(ggplot_rsi_predict)
export(guess_ab_col)
export(guess_atc)
export(guess_mo)
export(header)
export(inner_join_microorganisms)
export(interpretive_reading)
export(is.atc)
export(is.mic)
export(is.mo)
export(is.rsi)
export(is.rsi.eligible)
export(key_antibiotics)
export(key_antibiotics_equal)
export(kurtosis)
export(labels_rsi_count)
export(left_join_microorganisms)
export(like)
export(mdro)
export(mo_TSN)
export(mo_authors)
export(mo_class)
export(mo_failures)
export(mo_family)
export(mo_fullname)
export(mo_genus)
export(mo_gramstain)
export(mo_kingdom)
export(mo_order)
export(mo_phylum)
export(mo_property)
export(mo_ref)
export(mo_renamed)
export(mo_shortname)
export(mo_species)
export(mo_subkingdom)
export(mo_subspecies)
export(mo_taxonomy)
export(mo_type)
export(mo_uncertainties)
export(mo_year)
export(mrgn)
export(n_rsi)
export(p.symbol)
export(portion_I)
export(portion_IR)
export(portion_R)
export(portion_S)
export(portion_SI)
export(portion_df)
export(ratio)
export(read.4D)
export(resistance_predict)
export(right_join_microorganisms)
export(rsi)
export(rsi_predict)
export(scale_rsi_colours)
export(scale_y_percent)
export(semi_join_microorganisms)
export(set_mo_source)
export(skewness)
export(theme_rsi)
export(top_freq)
exportMethods(as.data.frame.atc)
exportMethods(as.data.frame.frequency_tbl)
exportMethods(as.data.frame.mo)
exportMethods(as.double.mic)
exportMethods(as.integer.mic)
exportMethods(as.numeric.mic)
exportMethods(as.vector.frequency_tbl)
exportMethods(as_tibble.frequency_tbl)
exportMethods(barplot.mic)
exportMethods(barplot.rsi)
exportMethods(diff.frequency_tbl)
exportMethods(droplevels.mic)
exportMethods(droplevels.rsi)
exportMethods(format.frequency_tbl)
exportMethods(hist.frequency_tbl)
exportMethods(kurtosis)
exportMethods(kurtosis.data.frame)
exportMethods(kurtosis.default)
exportMethods(kurtosis.matrix)
exportMethods(plot.frequency_tbl)
exportMethods(plot.mic)
exportMethods(plot.rsi)
exportMethods(print.atc)
exportMethods(print.frequency_tbl)
exportMethods(print.mic)
exportMethods(print.mo)
exportMethods(print.rsi)
exportMethods(pull.atc)
exportMethods(pull.mo)
exportMethods(select.frequency_tbl)
exportMethods(skewness)
exportMethods(skewness.data.frame)
exportMethods(skewness.default)
exportMethods(skewness.matrix)
exportMethods(summary.mic)
exportMethods(summary.mo)
exportMethods(summary.rsi)
importFrom(crayon,bgGreen)
importFrom(crayon,bgRed)
importFrom(crayon,bgYellow)