AMR/NAMESPACE

# Generated by roxygen2: do not edit by hand

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(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,data.table)
S3method(print,frequency_tbl)
S3method(print,mic)
S3method(print,rsi)
S3method(print,tbl)
S3method(print,tbl_df)
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(abname)
export(anti_join_microorganisms)
export(as.mic)
export(as.rsi)
export(atc_ddd)
export(atc_groups)
export(atc_property)
export(clipboard_export)
export(clipboard_import)
export(first_isolate)
export(freq)
export(frequency_tbl)
export(full_join_microorganisms)
export(g.test)
export(guess_atc)
export(guess_bactid)
export(inner_join_microorganisms)
export(interpretive_reading)
export(is.mic)
export(is.rsi)
export(key_antibiotics)
export(kurtosis)
export(left_join_microorganisms)
export(like)
export(mo_property)
export(n_rsi)
export(p.symbol)
export(ratio)
export(right_join_microorganisms)
export(rsi)
export(rsi_df)
export(rsi_predict)
export(semi_join_microorganisms)
export(skewness)
export(top_freq)
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(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.data.table)
exportMethods(print.frequency_tbl)
exportMethods(print.mic)
exportMethods(print.rsi)
exportMethods(print.tbl)
exportMethods(print.tbl_df)
exportMethods(skewness)
exportMethods(skewness.data.frame)
exportMethods(skewness.default)
exportMethods(skewness.matrix)
exportMethods(summary.mic)
exportMethods(summary.rsi)
importFrom(broom,tidy)
importFrom(clipr,read_clip_tbl)
importFrom(clipr,write_clip)
importFrom(curl,nslookup)
importFrom(data.table,data.table)
importFrom(dplyr,"%>%")
importFrom(dplyr,all_vars)
importFrom(dplyr,any_vars)
importFrom(dplyr,arrange)
importFrom(dplyr,arrange_at)
importFrom(dplyr,as_tibble)
importFrom(dplyr,between)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
importFrom(dplyr,filter_at)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_at)
importFrom(dplyr,group_size)
importFrom(dplyr,group_vars)
importFrom(dplyr,if_else)
importFrom(dplyr,lag)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n_distinct)
importFrom(dplyr,n_groups)
importFrom(dplyr,progress_estimated)
importFrom(dplyr,pull)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,summarise)
importFrom(dplyr,tibble)
importFrom(dplyr,top_n)
importFrom(dplyr,vars)
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(reshape2,dcast)
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,mad)
importFrom(stats,na.omit)
importFrom(stats,pchisq)
importFrom(stats,sd)
importFrom(tibble,tibble)
importFrom(utils,View)
importFrom(utils,browseVignettes)
importFrom(utils,installed.packages)
importFrom(utils,object.size)
importFrom(utils,packageDescription)
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`

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)`
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)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`S3method(print,data.table)`
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)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`S3method(print,tbl)`
			`S3method(print,tbl_df)`
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)`
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)`
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)`
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)`
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)`
			`export(is.mic)`
			`export(is.rsi)`
			`export(key_antibiotics)`
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)`
first commit 2018-02-21 11:52:31 +01:00			`export(mo_property)`
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)`
rename vector2ratio to ratio 2018-07-02 11:14:20 +02:00			`export(ratio)`
- 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_df)`
			`export(rsi_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(semi_join_microorganisms)`
kurtosis, skewness, start with ML 2018-07-08 22:14:55 +02:00			`export(skewness)`
top_freq 2018-06-20 14:47:37 +02:00			`export(top_freq)`
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)`
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)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`exportMethods(print.data.table)`
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)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`exportMethods(print.tbl)`
			`exportMethods(print.tbl_df)`
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)`
kurtosis, skewness, start with ML 2018-07-08 22:14:55 +02:00			`importFrom(broom,tidy)`
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)`
try to support older R versions 2018-04-18 14:50:16 +02:00			`importFrom(data.table,data.table)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(dplyr,"%>%")`
			`importFrom(dplyr,all_vars)`
			`importFrom(dplyr,any_vars)`
			`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)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`importFrom(dplyr,desc)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(dplyr,filter)`
			`importFrom(dplyr,filter_at)`
			`importFrom(dplyr,group_by)`
			`importFrom(dplyr,group_by_at)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`importFrom(dplyr,group_size)`
			`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)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`importFrom(dplyr,n_groups)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(dplyr,progress_estimated)`
			`importFrom(dplyr,pull)`
			`importFrom(dplyr,row_number)`
			`importFrom(dplyr,select)`
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)`
			`importFrom(dplyr,tibble)`
top_freq 2018-06-20 14:47:37 +02:00			`importFrom(dplyr,top_n)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(dplyr,vars)`
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)`
first commit 2018-02-21 11:52:31 +01:00			`importFrom(reshape2,dcast)`
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)`
include IQR and MAD in freq 2018-07-03 11:30:40 +02:00			`importFrom(stats,mad)`
kurtosis, skewness, start with ML 2018-07-08 22:14:55 +02:00			`importFrom(stats,na.omit)`
new g.test() and edited freq() 2018-07-01 21:40:37 +02:00			`importFrom(stats,pchisq)`
MDRO, freq tables, new print format for tibbles 2018-04-18 12:24:54 +02:00			`importFrom(stats,sd)`
new g.test() and edited freq() 2018-07-01 21:40:37 +02:00			`importFrom(tibble,tibble)`
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)`
- Added new algorithm to determine weighted isolates, can now be `points` or `keyantibiotics, see `?first_isolate` - Function `first_isolate` supports tidyverse-like evaluation of parameters (no need to quote them anymore) - Functions `as.rsi` and `as.mic` now add the package name and version as attribute 2018-03-19 20:39:23 +01:00			`importFrom(utils,packageDescription)`
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)`