AMR/NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(as.data.frame,atc)
S3method(as.data.frame,bactid)
S3method(as.data.frame,frequency_tbl)
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(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,rsi)
S3method(print,atc)
S3method(print,bactid)
S3method(print,frequency_tbl)
S3method(print,mic)
S3method(print,rsi)
S3method(pull,atc)
S3method(pull,bactid)
S3method(skewness,data.frame)
S3method(skewness,default)
S3method(skewness,matrix)
S3method(summary,mic)
S3method(summary,rsi)
export("%like%")
export(BRMO)
export(EUCAST_exceptional_phenotypes)
export(EUCAST_rules)
export(MDRO)
export(MRGN)
export(ab_atc)
export(ab_certe)
export(ab_official)
export(ab_official_nl)
export(ab_property)
export(ab_tradenames)
export(ab_trivial_nl)
export(ab_umcg)
export(abname)
export(anti_join_microorganisms)
export(as.atc)
export(as.bactid)
export(as.mic)
export(as.rsi)
export(atc_ddd)
export(atc_groups)
export(atc_property)
export(clipboard_export)
export(clipboard_import)
export(count_I)
export(count_IR)
export(count_R)
export(count_S)
export(count_SI)
export(count_df)
export(facet_rsi)
export(first_isolate)
export(freq)
export(frequency_tbl)
export(full_join_microorganisms)
export(g.test)
export(geom_rsi)
export(ggplot_rsi)
export(guess_atc)
export(guess_bactid)
export(inner_join_microorganisms)
export(interpretive_reading)
export(is.atc)
export(is.bactid)
export(is.mic)
export(is.rsi)
export(is.rsi.eligible)
export(key_antibiotics)
export(key_antibiotics_equal)
export(kurtosis)
export(left_join_microorganisms)
export(like)
export(mo_aerobic)
export(mo_family)
export(mo_fullname)
export(mo_genus)
export(mo_gramstain)
export(mo_gramstain_nl)
export(mo_property)
export(mo_species)
export(mo_subspecies)
export(mo_type)
export(mo_type_nl)
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(resistance_predict)
export(right_join_microorganisms)
export(rsi)
export(rsi_predict)
export(scale_rsi_colours)
export(scale_y_percent)
export(semi_join_microorganisms)
export(skewness)
export(theme_rsi)
export(top_freq)
exportMethods(as.data.frame.atc)
exportMethods(as.data.frame.bactid)
exportMethods(as.data.frame.frequency_tbl)
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(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.bactid)
exportMethods(print.frequency_tbl)
exportMethods(print.mic)
exportMethods(print.rsi)
exportMethods(pull.atc)
exportMethods(pull.bactid)
exportMethods(skewness)
exportMethods(skewness.data.frame)
exportMethods(skewness.default)
exportMethods(skewness.matrix)
exportMethods(summary.mic)
exportMethods(summary.rsi)
importFrom(clipr,read_clip_tbl)
importFrom(clipr,write_clip)
importFrom(curl,nslookup)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,arrange_at)
importFrom(dplyr,as_tibble)
importFrom(dplyr,between)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,desc)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_at)
importFrom(dplyr,group_vars)
importFrom(dplyr,if_else)
importFrom(dplyr,lag)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n_distinct)
importFrom(dplyr,progress_estimated)
importFrom(dplyr,pull)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,select_if)
importFrom(dplyr,slice)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_if)
importFrom(dplyr,tibble)
importFrom(dplyr,top_n)
importFrom(grDevices,boxplot.stats)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,hist)
importFrom(graphics,plot)
importFrom(graphics,text)
importFrom(knitr,kable)
importFrom(readr,locale)
importFrom(readr,parse_guess)
importFrom(rvest,html_children)
importFrom(rvest,html_node)
importFrom(rvest,html_nodes)
importFrom(rvest,html_table)
importFrom(stats,complete.cases)
importFrom(stats,fivenum)
importFrom(stats,glm)
importFrom(stats,lm)
importFrom(stats,mad)
importFrom(stats,pchisq)
importFrom(stats,predict)
importFrom(stats,sd)
importFrom(utils,View)
importFrom(utils,browseVignettes)
importFrom(utils,installed.packages)
importFrom(utils,object.size)
importFrom(utils,read.delim)
importFrom(utils,write.table)
importFrom(xml2,read_html)
first commit 2018-02-21 11:52:31 +01:00			`# Generated by roxygen2: do not edit by hand`

atc and bactid functions, readme update 2018-08-25 22:01:14 +02:00			`S3method(as.data.frame,atc)`
new class bactid 2018-07-23 14:14:03 +02:00			`S3method(as.data.frame,bactid)`
include IQR and MAD in freq 2018-07-03 11:30:40 +02:00			`S3method(as.data.frame,frequency_tbl)`
first commit 2018-02-21 11:52:31 +01:00			`S3method(as.double,mic)`
			`S3method(as.integer,mic)`
			`S3method(as.numeric,mic)`
freq: support for table 2018-07-09 14:02:58 +02:00			`S3method(as.vector,frequency_tbl)`
			`S3method(as_tibble,frequency_tbl)`
add barplots 2018-03-13 14:34:10 +01:00			`S3method(barplot,mic)`
			`S3method(barplot,rsi)`
support format.freq 2018-07-16 16:41:48 +02:00			`S3method(format,frequency_tbl)`
kurtosis, skewness, start with ML 2018-07-08 22:14:55 +02:00			`S3method(hist,frequency_tbl)`
			`S3method(kurtosis,data.frame)`
			`S3method(kurtosis,default)`
			`S3method(kurtosis,matrix)`
			`S3method(plot,frequency_tbl)`
first commit 2018-02-21 11:52:31 +01:00			`S3method(plot,mic)`
			`S3method(plot,rsi)`
atc and bactid functions, readme update 2018-08-25 22:01:14 +02:00			`S3method(print,atc)`
new class bactid 2018-07-23 14:14:03 +02:00			`S3method(print,bactid)`
top_freq 2018-06-20 14:47:37 +02:00			`S3method(print,frequency_tbl)`
first commit 2018-02-21 11:52:31 +01:00			`S3method(print,mic)`
			`S3method(print,rsi)`
atc and bactid functions, readme update 2018-08-25 22:01:14 +02:00			`S3method(pull,atc)`
new functions R, RI, SI, S 2018-07-29 22:14:51 +02:00			`S3method(pull,bactid)`
kurtosis, skewness, start with ML 2018-07-08 22:14:55 +02:00			`S3method(skewness,data.frame)`
			`S3method(skewness,default)`
			`S3method(skewness,matrix)`
first commit 2018-02-21 11:52:31 +01:00			`S3method(summary,mic)`
			`S3method(summary,rsi)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`export("%like%")`
			`export(BRMO)`
EUCAST rules for MDRO 2018-04-25 15:33:58 +02:00			`export(EUCAST_exceptional_phenotypes)`
first commit 2018-02-21 11:52:31 +01:00			`export(EUCAST_rules)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`export(MDRO)`
			`export(MRGN)`
ab_* functions, mo_* functions, 180 new microorganisms, speed improvement for bactid 2018-08-28 13:51:13 +02:00			`export(ab_atc)`
			`export(ab_certe)`
			`export(ab_official)`
			`export(ab_official_nl)`
			`export(ab_property)`
163 new trade names, added ab_tradenames 2018-08-29 12:27:37 +02:00			`export(ab_tradenames)`
ab_* functions, mo_* functions, 180 new microorganisms, speed improvement for bactid 2018-08-28 13:51:13 +02:00			`export(ab_trivial_nl)`
			`export(ab_umcg)`
abname, logo 2018-02-21 12:10:00 +01:00			`export(abname)`
- For functions `first_isolate`, `EUCAST_rules` the antibiotic column names are case-insensitive - Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore) - Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS - Renamed dataset `bactlist` to `microorganisms` 2018-03-23 14:46:02 +01:00			`export(anti_join_microorganisms)`
atc and bactid functions, readme update 2018-08-25 22:01:14 +02:00			`export(as.atc)`
new class bactid 2018-07-23 14:14:03 +02:00			`export(as.bactid)`
first commit 2018-02-21 11:52:31 +01:00			`export(as.mic)`
			`export(as.rsi)`
atc_groups 2018-06-19 10:05:38 +02:00			`export(atc_ddd)`
			`export(atc_groups)`
first commit 2018-02-21 11:52:31 +01:00			`export(atc_property)`
add clipboard functions again 2018-06-27 15:54:56 +02:00			`export(clipboard_export)`
			`export(clipboard_import)`
count_* functions 2018-08-22 00:02:26 +02:00			`export(count_I)`
			`export(count_IR)`
			`export(count_R)`
			`export(count_S)`
			`export(count_SI)`
			`export(count_df)`
new ggplot enhancement 2018-08-11 21:30:00 +02:00			`export(facet_rsi)`
export first_isolate 2018-02-26 12:15:52 +01:00			`export(first_isolate)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`export(freq)`
			`export(frequency_tbl)`
- For functions `first_isolate`, `EUCAST_rules` the antibiotic column names are case-insensitive - Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore) - Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS - Renamed dataset `bactlist` to `microorganisms` 2018-03-23 14:46:02 +01:00			`export(full_join_microorganisms)`
new g.test() and edited freq() 2018-07-01 21:40:37 +02:00			`export(g.test)`
new ggplot enhancement 2018-08-11 21:30:00 +02:00			`export(geom_rsi)`
			`export(ggplot_rsi)`
EUCAST rules for MDRO 2018-04-25 15:33:58 +02:00			`export(guess_atc)`
- Added new function `guess_bactid` to determine the ID of a microorganism based on genus/species - Renamed `ablist` to `antibiotics` - Added support for character vector in join functions - Altered `%like%` to make it case insensitive 2018-03-19 12:43:22 +01:00			`export(guess_bactid)`
- For functions `first_isolate`, `EUCAST_rules` the antibiotic column names are case-insensitive - Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore) - Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS - Renamed dataset `bactlist` to `microorganisms` 2018-03-23 14:46:02 +01:00			`export(inner_join_microorganisms)`
first commit 2018-02-21 11:52:31 +01:00			`export(interpretive_reading)`
atc and bactid functions, readme update 2018-08-25 22:01:14 +02:00			`export(is.atc)`
new class bactid 2018-07-23 14:14:03 +02:00			`export(is.bactid)`
first commit 2018-02-21 11:52:31 +01:00			`export(is.mic)`
			`export(is.rsi)`
count_* functions 2018-08-22 00:02:26 +02:00			`export(is.rsi.eligible)`
first commit 2018-02-21 11:52:31 +01:00			`export(key_antibiotics)`
new algorithm key abs 2018-07-17 13:02:05 +02:00			`export(key_antibiotics_equal)`
kurtosis, skewness, start with ML 2018-07-08 22:14:55 +02:00			`export(kurtosis)`
- For functions `first_isolate`, `EUCAST_rules` the antibiotic column names are case-insensitive - Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore) - Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS - Renamed dataset `bactlist` to `microorganisms` 2018-03-23 14:46:02 +01:00			`export(left_join_microorganisms)`
addins and small improvements to microorganisms dataset 2018-07-04 17:20:03 +02:00			`export(like)`
ab_* functions, mo_* functions, 180 new microorganisms, speed improvement for bactid 2018-08-28 13:51:13 +02:00			`export(mo_aerobic)`
			`export(mo_family)`
			`export(mo_fullname)`
			`export(mo_genus)`
			`export(mo_gramstain)`
			`export(mo_gramstain_nl)`
			`export(mo_property)`
			`export(mo_species)`
			`export(mo_subspecies)`
			`export(mo_type)`
			`export(mo_type_nl)`
Added function `n_rsi` 2018-05-02 14:56:25 +02:00			`export(n_rsi)`
new g.test() and edited freq() 2018-07-01 21:40:37 +02:00			`export(p.symbol)`
new portion functions 2018-08-10 15:01:05 +02:00			`export(portion_I)`
			`export(portion_IR)`
			`export(portion_R)`
			`export(portion_S)`
			`export(portion_SI)`
new ggplot enhancement 2018-08-11 21:30:00 +02:00			`export(portion_df)`
Welcome C++! 2018-07-13 17:23:46 +02:00			`export(resistance_predict)`
- For functions `first_isolate`, `EUCAST_rules` the antibiotic column names are case-insensitive - Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore) - Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS - Renamed dataset `bactlist` to `microorganisms` 2018-03-23 14:46:02 +01:00			`export(right_join_microorganisms)`
first commit 2018-02-21 11:52:31 +01:00			`export(rsi)`
			`export(rsi_predict)`
new ggplot enhancement 2018-08-11 21:30:00 +02:00			`export(scale_rsi_colours)`
			`export(scale_y_percent)`
- For functions `first_isolate`, `EUCAST_rules` the antibiotic column names are case-insensitive - Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore) - Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS - Renamed dataset `bactlist` to `microorganisms` 2018-03-23 14:46:02 +01:00			`export(semi_join_microorganisms)`
kurtosis, skewness, start with ML 2018-07-08 22:14:55 +02:00			`export(skewness)`
new ggplot enhancement 2018-08-11 21:30:00 +02:00			`export(theme_rsi)`
top_freq 2018-06-20 14:47:37 +02:00			`export(top_freq)`
atc and bactid functions, readme update 2018-08-25 22:01:14 +02:00			`exportMethods(as.data.frame.atc)`
new class bactid 2018-07-23 14:14:03 +02:00			`exportMethods(as.data.frame.bactid)`
include IQR and MAD in freq 2018-07-03 11:30:40 +02:00			`exportMethods(as.data.frame.frequency_tbl)`
first commit 2018-02-21 11:52:31 +01:00			`exportMethods(as.double.mic)`
			`exportMethods(as.integer.mic)`
			`exportMethods(as.numeric.mic)`
freq: support for table 2018-07-09 14:02:58 +02:00			`exportMethods(as.vector.frequency_tbl)`
			`exportMethods(as_tibble.frequency_tbl)`
add barplots 2018-03-13 14:34:10 +01:00			`exportMethods(barplot.mic)`
			`exportMethods(barplot.rsi)`
support format.freq 2018-07-16 16:41:48 +02:00			`exportMethods(format.frequency_tbl)`
kurtosis, skewness, start with ML 2018-07-08 22:14:55 +02:00			`exportMethods(hist.frequency_tbl)`
			`exportMethods(kurtosis)`
			`exportMethods(kurtosis.data.frame)`
			`exportMethods(kurtosis.default)`
			`exportMethods(kurtosis.matrix)`
			`exportMethods(plot.frequency_tbl)`
first commit 2018-02-21 11:52:31 +01:00			`exportMethods(plot.mic)`
			`exportMethods(plot.rsi)`
atc and bactid functions, readme update 2018-08-25 22:01:14 +02:00			`exportMethods(print.atc)`
new class bactid 2018-07-23 14:14:03 +02:00			`exportMethods(print.bactid)`
top_freq 2018-06-20 14:47:37 +02:00			`exportMethods(print.frequency_tbl)`
first commit 2018-02-21 11:52:31 +01:00			`exportMethods(print.mic)`
			`exportMethods(print.rsi)`
atc and bactid functions, readme update 2018-08-25 22:01:14 +02:00			`exportMethods(pull.atc)`
new functions R, RI, SI, S 2018-07-29 22:14:51 +02:00			`exportMethods(pull.bactid)`
kurtosis, skewness, start with ML 2018-07-08 22:14:55 +02:00			`exportMethods(skewness)`
			`exportMethods(skewness.data.frame)`
			`exportMethods(skewness.default)`
			`exportMethods(skewness.matrix)`
first commit 2018-02-21 11:52:31 +01:00			`exportMethods(summary.mic)`
			`exportMethods(summary.rsi)`
add clipboard functions again 2018-06-27 15:54:56 +02:00			`importFrom(clipr,read_clip_tbl)`
			`importFrom(clipr,write_clip)`
atc_groups 2018-06-19 10:05:38 +02:00			`importFrom(curl,nslookup)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(dplyr,"%>%")`
			`importFrom(dplyr,arrange)`
			`importFrom(dplyr,arrange_at)`
add clipboard functions again 2018-06-27 15:54:56 +02:00			`importFrom(dplyr,as_tibble)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(dplyr,between)`
support groups for portion_df, update README 2018-08-12 22:34:03 +02:00			`importFrom(dplyr,bind_rows)`
small fixes 2018-07-28 09:34:03 +02:00			`importFrom(dplyr,case_when)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`importFrom(dplyr,desc)`
support groups for portion_df, update README 2018-08-12 22:34:03 +02:00			`importFrom(dplyr,everything)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(dplyr,filter)`
			`importFrom(dplyr,group_by)`
			`importFrom(dplyr,group_by_at)`
support groups for portion_df, update README 2018-08-12 22:34:03 +02:00			`importFrom(dplyr,group_vars)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(dplyr,if_else)`
			`importFrom(dplyr,lag)`
			`importFrom(dplyr,left_join)`
			`importFrom(dplyr,mutate)`
			`importFrom(dplyr,n_distinct)`
			`importFrom(dplyr,progress_estimated)`
			`importFrom(dplyr,pull)`
			`importFrom(dplyr,row_number)`
			`importFrom(dplyr,select)`
count_* functions 2018-08-22 00:02:26 +02:00			`importFrom(dplyr,select_if)`
abname, logo 2018-02-21 12:10:00 +01:00			`importFrom(dplyr,slice)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(dplyr,summarise)`
new ggplot enhancement 2018-08-11 21:30:00 +02:00			`importFrom(dplyr,summarise_if)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(dplyr,tibble)`
top_freq 2018-06-20 14:47:37 +02:00			`importFrom(dplyr,top_n)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`importFrom(grDevices,boxplot.stats)`
import from graphics 2018-03-13 15:40:10 +01:00			`importFrom(graphics,axis)`
			`importFrom(graphics,barplot)`
kurtosis, skewness, start with ML 2018-07-08 22:14:55 +02:00			`importFrom(graphics,hist)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(graphics,plot)`
			`importFrom(graphics,text)`
new g.test() and edited freq() 2018-07-01 21:40:37 +02:00			`importFrom(knitr,kable)`
add clipboard functions again 2018-06-27 15:54:56 +02:00			`importFrom(readr,locale)`
			`importFrom(readr,parse_guess)`
atc_groups 2018-06-19 10:05:38 +02:00			`importFrom(rvest,html_children)`
			`importFrom(rvest,html_node)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(rvest,html_nodes)`
			`importFrom(rvest,html_table)`
new g.test, extra unit tests 2018-07-10 12:27:07 +02:00			`importFrom(stats,complete.cases)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`importFrom(stats,fivenum)`
improvement for forecasting resistance 2018-07-26 16:30:42 +02:00			`importFrom(stats,glm)`
			`importFrom(stats,lm)`
include IQR and MAD in freq 2018-07-03 11:30:40 +02:00			`importFrom(stats,mad)`
new g.test() and edited freq() 2018-07-01 21:40:37 +02:00			`importFrom(stats,pchisq)`
improvement for forecasting resistance 2018-07-26 16:30:42 +02:00			`importFrom(stats,predict)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`importFrom(stats,sd)`
addins and small improvements to microorganisms dataset 2018-07-04 17:20:03 +02:00			`importFrom(utils,View)`
top_freq 2018-06-20 14:47:37 +02:00			`importFrom(utils,browseVignettes)`
freq: support for table 2018-07-09 14:02:58 +02:00			`importFrom(utils,installed.packages)`
Added function `n_rsi` 2018-05-02 14:56:25 +02:00			`importFrom(utils,object.size)`
add clipboard functions again 2018-06-27 15:54:56 +02:00			`importFrom(utils,read.delim)`
			`importFrom(utils,write.table)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(xml2,read_html)`