diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 7e7283be..2243b2bc 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -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 diff --git a/NAMESPACE b/NAMESPACE index a45e7b30..79cac6fa 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -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)