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AMR
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(v0.6.1.9047) ggplot fix

This commit is contained in:
dr. M.S. (Matthijs) Berends 2019-05-31 20:48:22 +02:00
parent 4ed27c7e7a
commit 0a6580b4eb
13 changed files with 44 additions and 52 deletions
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1
.gitignore vendored
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@ -20,3 +20,4 @@ vignettes/*.R
^CRAN-RELEASE$
packrat/lib*/
packrat/src/
cran-comments.md

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 0.6.1.9046
Version: 0.6.1.9047
Date: 2019-05-31
Title: Antimicrobial Resistance Analysis
Authors@R: c(

41
R/zzz.R
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@ -29,10 +29,6 @@
microorganisms.oldDT$fullname_lower <- tolower(microorganisms.oldDT$fullname)
setkey(microorganisms.oldDT, col_id, fullname)
assign(x = "microorganisms",
value = make(),
envir = asNamespace("AMR"))
assign(x = "microorganismsDT",
value = make_DT(),
envir = asNamespace("AMR"))
@ -55,44 +51,9 @@
}
#' @importFrom dplyr mutate case_when
make <- function() {
AMR::microorganisms %>%
mutate(prevalence = case_when(
class == "Gammaproteobacteria"
| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
| mo == "UNKNOWN"
~ 1,
phylum %in% c("Proteobacteria",
"Firmicutes",
"Actinobacteria",
"Sarcomastigophora")
| genus %in% c("Aspergillus",
"Bacteroides",
"Candida",
"Capnocytophaga",
"Chryseobacterium",
"Cryptococcus",
"Elisabethkingia",
"Flavobacterium",
"Fusobacterium",
"Giardia",
"Leptotrichia",
"Mycoplasma",
"Prevotella",
"Rhodotorula",
"Treponema",
"Trichophyton",
"Ureaplasma")
| rank %in% c("kingdom", "phylum", "class", "order", "family")
~ 2,
TRUE ~ 3
))
}
#' @importFrom data.table as.data.table setkey
make_DT <- function() {
microorganismsDT <- as.data.table(make())
microorganismsDT <- as.data.table(AMR::microorganisms)
microorganismsDT$fullname_lower <- tolower(microorganismsDT$fullname)
setkey(microorganismsDT,
prevalence,

BIN
data/microorganisms.rda
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2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
</span>
</div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
</span>
</div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
</span>
</div>

2
docs/index.html
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@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
</span>
</div>

2
docs/news/index.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
</span>
</div>

4
docs/reference/ggplot_rsi.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
</span>
</div>
@ -485,7 +485,7 @@
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Top Three Microorganisms In Blood Culture Isolates"</span>,
<span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/expression'>expression</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Only First Isolates, CoNS grouped according to Becker "</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/grDevices/topics/plotmath'>italic</a></span>(<span class='st'>"et al."</span>), <span class='st'>" (2014)"</span>)),
<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antibiotic (Ears-Net code)"</span>)
<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antibiotic (EARS-Net code)"</span>)
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span>
</span>
</div>

33
reproduction_of_microorganisms.R
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@ -452,6 +452,39 @@ MOs <- MOs %>%
sum(duplicated(MOs$mo))
colnames(MOs)
# set prevalence per species
MOs <- MOs %>%
mutate(prevalence = case_when(
class == "Gammaproteobacteria"
| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
| mo == "UNKNOWN"
~ 1,
phylum %in% c("Proteobacteria",
"Firmicutes",
"Actinobacteria",
"Sarcomastigophora")
| genus %in% c("Aspergillus",
"Bacteroides",
"Candida",
"Capnocytophaga",
"Chryseobacterium",
"Cryptococcus",
"Elisabethkingia",
"Flavobacterium",
"Fusobacterium",
"Giardia",
"Leptotrichia",
"Mycoplasma",
"Prevotella",
"Rhodotorula",
"Treponema",
"Trichophyton",
"Ureaplasma")
| rank %in% c("kingdom", "phylum", "class", "order", "family")
~ 2,
TRUE ~ 3
))
# save it
MOs <- as.data.frame(MOs %>% arrange(fullname), stringsAsFactors = FALSE)
MOs.old <- as.data.frame(MOs.old, stringsAsFactors = FALSE)

3
tests/testthat/test-ggplot_rsi.R
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@ -59,9 +59,6 @@ test_that("ggplot_rsi works", {
summarise_all(count_IR) %>% as.double()
)
expect_equal(colnames(getlbls(septic_patients %>% select(AMC, CIP))),
c("Interpretation", "Antibiotic", "Value", "lbl"))
expect_error(ggplot_rsi(septic_patients, fun = "invalid"))
expect_error(geom_rsi(septic_patients, fun = "invalid"))