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AMR
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AMR/NAMESPACE

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first commit
2018-02-21 11:52:31 +01:00
# Generated by roxygen2: do not edit by hand
S3method(as.double,mic)
S3method(as.integer,mic)
S3method(as.numeric,mic)
add barplots
2018-03-13 14:34:10 +01:00
S3method(barplot,mic)
S3method(barplot,rsi)
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)
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)
first commit
2018-02-21 11:52:31 +01:00
S3method(summary,mic)
S3method(summary,rsi)
MDRO, freq tables, new print format for tibbles
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export("%like%")
export(BRMO)
EUCAST rules for MDRO
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export(EUCAST_exceptional_phenotypes)
first commit
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export(EUCAST_rules)
MDRO, freq tables, new print format for tibbles
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export(MDRO)
export(MRGN)
abname, logo
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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`
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export(anti_join_microorganisms)
first commit
2018-02-21 11:52:31 +01:00
export(as.mic)
export(as.rsi)
export(atc_property)
export first_isolate
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export(first_isolate)
MDRO, freq tables, new print format for tibbles
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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)
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)
- 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)
first commit
2018-02-21 11:52:31 +01:00
export(mo_property)
- 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)
first commit
2018-02-21 11:52:31 +01:00
exportMethods(as.double.mic)
exportMethods(as.integer.mic)
exportMethods(as.numeric.mic)
add barplots
2018-03-13 14:34:10 +01:00
exportMethods(barplot.mic)
exportMethods(barplot.rsi)
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)
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)
first commit
2018-02-21 11:52:31 +01:00
exportMethods(summary.mic)
exportMethods(summary.rsi)
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)
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
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importFrom(dplyr,slice)
first commit
2018-02-21 11:52:31 +01:00
importFrom(dplyr,summarise)
importFrom(dplyr,tibble)
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
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importFrom(graphics,axis)
importFrom(graphics,barplot)
first commit
2018-02-21 11:52:31 +01:00
importFrom(graphics,plot)
importFrom(graphics,text)
importFrom(reshape2,dcast)
importFrom(rvest,html_nodes)
importFrom(rvest,html_table)
MDRO, freq tables, new print format for tibbles
2018-04-18 12:24:54 +02:00
importFrom(stats,fivenum)
importFrom(stats,quantile)
importFrom(stats,sd)
- 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)
first commit
2018-02-21 11:52:31 +01:00
importFrom(xml2,read_html)