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(v1.5.0.9015) unit test fix, grouped first isolates

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dr. M.S. (Matthijs) Berends
2021-02-04 16:48:16 +01:00
parent 2eca8c3f01
commit 8fda473e49
44 changed files with 239 additions and 168 deletions
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10
vignettes/datasets.Rmd
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@ -29,8 +29,8 @@ options(knitr.kable.NA = '')
structure_txt <- function(dataset) {
paste0("A data set with ",
format(nrow(dataset), big.mark = ","), " rows and ",
ncol(dataset), " columns, containing the following column names: \n*",
paste0("'", colnames(dataset), "'", collapse = ", "), "*.")
ncol(dataset), " columns, containing the following column names: \n",
AMR:::vector_or(colnames(dataset), quotes = "*", last_sep = " and "), ".")
}
download_txt <- function(filename) {
@ -172,7 +172,7 @@ This data set is in R available as `antibiotics`, after you load the `AMR` packa
This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.
* [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is frelly available from the WHO CC website for personal use)
* [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)
* [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
* [WHONET software 2019](https://whonet.org)
@ -197,7 +197,7 @@ This data set is in R available as `antivirals`, after you load the `AMR` packag
This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.
* [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is frelly available from the WHO CC website for personal use)
* [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)
* [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
### Example content
@ -218,7 +218,7 @@ This data set is in R available as `intrinsic_resistant`, after you load the `AM
### Source
This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on '`r AMR:::EUCAST_VERSION_EXPERT_RULES[["3.2"]]$title`', `r AMR:::EUCAST_VERSION_EXPERT_RULES[["3.2"]]$version_txt` from `r AMR:::EUCAST_VERSION_EXPERT_RULES[["3.2"]]$year`.
This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on `r AMR:::format_eucast_version_nr("3.2")`.
### Example content