NEWS.md
- AMR 1.6.0.9062AMR 1.6.0.9063betalactams() as additional antbiotic column selector and function filter_betalactams() as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.ggplot() method for resistance_predict()
+ggplot() method for resistance_predict()
Support for custom MDRO guidelines, using the new custom_mdro_guideline() function, please see mdro() for additional info
ggplot() generics for classes <mic> and <disk>
ggplot() generics for classes <mic> and <disk>
Function mo_is_yeast(), which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:
@@ -444,7 +444,7 @@
translate)plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion valuesplot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion valuesmicroorganisms data setis.rsi.eligible() now detects if the column name resembles an antibiotic name or code and now returns TRUE immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.
get_episode() and is_new_episode() now support less than a day as value for argument episode_days (e.g., to include one patient/test per hour)ampc_cephalosporin_resistance in eucast_rules() now also applies to value “I” (not only “S”)print() and summary() on a Principal Components Analysis object (pca()) now print additional group info if the original data was grouped using dplyr::group_by()
+print() and summary() on a Principal Components Analysis object (pca()) now print additional group info if the original data was grouped using dplyr::group_by()
guess_ab_col(). As this also internally improves the reliability of first_isolate() and mdro(), this might have a slight impact on the results of those functions.mo_name() when used in other languages than Englishsummary(example_isolates) # see all R/SI results at a glance - +# \donttest{ if (require("skimr")) { # class <rsi> supported in skim() too: skim(example_isolates) } - +# } # For INTERPRETING disk diffusion and MIC values ----------------------- # a whole data set, even with combined MIC values and disk zones diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html index dbe0d59b9..dee60e497 100644 --- a/docs/reference/atc_online.html +++ b/docs/reference/atc_online.html @@ -82,7 +82,7 @@ @@ -327,7 +327,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!@@ -397,6 +397,7 @@ The lifecycle of this function is stable# See ?example_isolates. # See ?pca for more info about Principal Component Analysis (PCA). +# \donttest{ if (require("dplyr")) { pca_model <- example_isolates %>% filter(mo_genus(mo) == "Staphylococcus") %>% @@ -416,6 +417,7 @@ The lifecycle of this function is stablelabs(title = "Title here") } } +# } @@ -429,7 +429,8 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!Examples
-# \donttest{ +if (FALSE) { # oral DDD (Defined Daily Dose) of amoxicillin atc_online_property("J01CA04", "DDD", "O") @@ -335,7 +335,7 @@ The lifecycle of this function is stableatc_online_property("J01CA04", "DDD", "P") atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin -# } +}@@ -90,14 +90,14 @@
if (require("ggplot2") & require("dplyr")) { +@@ -406,6 +406,7 @@ A microorganism is categorised as Susceptible, Increased exposure when proportion_IR(example_isolates$AMX) proportion_R(example_isolates$AMX) +# \donttest{ if (require("dplyr")) { example_isolates %>% group_by(hospital_id) %>% @@ -464,6 +465,7 @@ A microorganism is categorised as Susceptible, Increased exposure when group_by(hospital_id) %>% proportion_df(translate = FALSE) } +# } @@ -404,6 +404,7 @@ A microorganism is categorised as Susceptible, Increased exposure when year_min = 2010, model = "binomial") plot(x) +# \donttest{ if (require("ggplot2")) { ggplot_rsi_predict(x) } @@ -448,6 +449,7 @@ A microorganism is categorised as Susceptible, Increased exposure when x = "Year") + theme_minimal(base_size = 13) } +# } diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd index 181cc9bbb..7257e8c89 100644 --- a/man/antibiotic_class_selectors.Rd +++ b/man/antibiotic_class_selectors.Rd @@ -115,7 +115,7 @@ example_isolates[any(carbapenems() == "R"), penicillins()] # dplyr ------------------------------------------------------------------- - +\donttest{ if (require("dplyr")) { # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem): @@ -165,3 +165,4 @@ if (require("dplyr")) { example_isolates \%>\% filter(across(carbapenems(), ~.x == "R")) } } +} diff --git a/man/as.ab.Rd b/man/as.ab.Rd index 936a441cb..50673d094 100644 --- a/man/as.ab.Rd +++ b/man/as.ab.Rd @@ -102,13 +102,14 @@ ab_atc("seephthriaaksone") # and even this works # they use as.ab() internally: ab_name("J01FA01") # "Erythromycin" ab_name("eryt") # "Erythromycin" - +\donttest{ if (require("dplyr")) { # you can quickly rename# \donttest{ +if (require("ggplot2") & require("dplyr")) { # get antimicrobial results for drugs against a UTI: ggplot(example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)) + @@ -478,7 +479,6 @@ The lifecycle of this function is stablescale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R") } -# \donttest{ # resistance of ciprofloxacine per age group example_isolates %>% mutate(first_isolate = first_isolate(.)) %>% diff --git a/docs/reference/index.html b/docs/reference/index.html index 4029fbd27..466b2f313 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ diff --git a/docs/reference/intrinsic_resistant.html b/docs/reference/intrinsic_resistant.html index e0d7698f1..23b0a5af1 100644 --- a/docs/reference/intrinsic_resistant.html +++ b/docs/reference/intrinsic_resistant.html @@ -82,7 +82,7 @@ @@ -90,14 +90,14 @@@@ -329,7 +329,6 @@ The lifecycle of this function is stable# See ?example_isolates. # \donttest{ - if (require("dplyr")) { # calculate the resistance per group first resistance_data <- example_isolates %>% diff --git a/docs/reference/plot.html b/docs/reference/plot.html index 6d811391f..f46e7e89d 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -82,7 +82,7 @@ @@ -408,11 +408,13 @@ The lifecycle of this function is stableplot(some_mic_values, mo = "S. aureus", ab = "ampicillin") plot(some_disk_values, mo = "Escherichia coli", ab = "cipro") +# \donttest{ if (require("ggplot2")) { ggplot(some_mic_values) ggplot(some_disk_values, mo = "Escherichia coli", ab = "cipro") ggplot(some_rsi_values) } +# }