diff --git a/NEWS.md b/NEWS.md index 78d52f3c..4c25f10c 100755 --- a/NEWS.md +++ b/NEWS.md @@ -4,14 +4,14 @@ * Functions `count_R`, `count_IR`, `count_I`, `count_SI` and `count_S` to selectively count resistant or susceptible isolates * Extra function `count_df` (which works like `portion_df`) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables * Function `is.rsi.eligible` to check for columns that have valid antimicrobial results, but do not have the `rsi` class yet. Transform the columns of your raw data with: `data %>% mutate_if(is.rsi.eligible, as.rsi)` -* Functions `as.mo` and `is.mo` as replacements for `as.bactid` and `is.bactid`. These last two functions are deprecated and will be removed in a future release. +* Functions `as.mo` and `is.mo` as replacements for `as.bactid` and `is.bactid` (since the `microoganisms` data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. * Renamed all previous references to `bactid` to `mo`, like: * Column names inputs of `EUCAST_rules`, `first_isolate` and `key_antibiotics` * Column names of datasets `microorganisms` and `septic_patients` * All old syntaxes will still work with this version, but will throw warnings * Functions `as.atc` and `is.atc` to transform/look up antibiotic ATC codes as defined by the WHO. The existing function `guess_atc` is now an alias of `as.atc`. -* Aliases for existing function `mo_property`: `mo_aerobic`, `mo_family`, `mo_fullname`, `mo_genus`, `mo_gramstain`, `mo_gramstain_nl`, `mo_property`, `mo_species`, `mo_subspecies`, `mo_type`, `mo_type_nl` -* Function `ab_property` and its aliases: `ab_certe`, `ab_official`, `ab_official_nl`, `ab_property`, `ab_trivial_nl`, `ab_umcg`, `ab_tradenames` +* Aliases for existing function `mo_property`: `mo_family`, `mo_genus`, `mo_species`, `mo_subspecies`, `mo_fullname`, `mo_type`, `mo_gramstain`, `mo_aerobic`, `mo_type_nl` and `mo_gramstain_nl` +* Function `ab_property` and its aliases: `ab_official`, `ab_tradenames`, `ab_certe`, `ab_umcg`, `ab_official_nl` and `ab_trivial_nl` * Introduction to AMR as a vignette #### Changed @@ -32,7 +32,10 @@ * Added parameters `minimum` and `as_percent` to `portion_df` * Support for quasiquotation in the functions series `count_*` and `portions_*`, and `n_rsi`. This allows to check for more than 2 vectors or columns. ```r - septic_patients %>% select(amox, cipr) %>% count_R() + septic_patients %>% select(amox, cipr) %>% count_IR() + # which is the same as: + septic_patients %>% count_IR(amox, cipr) + septic_patients %>% portion_S(amcl) septic_patients %>% portion_S(amcl, gent) septic_patients %>% portion_S(amcl, gent, pita)