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dr. M.S. (Matthijs) Berends 2018-03-19 21:03:23 +01:00
parent dd2517ecb7
commit c765f424ab
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2 changed files with 6 additions and 5 deletions
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9
R/first_isolates.R
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@ -321,11 +321,12 @@ first_isolate <- function(tbl,
, points_threshold, ')...\n')) , points_threshold, ')...\n'))
} }
} }
type_param <- type
all_first <- all_first %>% all_first <- all_first %>%
mutate(key_ab_lag = lag(key_ab)) %>% mutate(key_ab_lag = lag(key_ab)) %>%
mutate(key_ab_other = !key_antibiotics_equal(x = key_ab, mutate(key_ab_other = !key_antibiotics_equal(x = key_ab,
y = key_ab_lag, y = key_ab_lag,
type = type, type = type_param,
ignore_I = ignore_I, ignore_I = ignore_I,
points_threshold = points_threshold, points_threshold = points_threshold,
info = info)) %>% info = info)) %>%
@ -524,9 +525,9 @@ key_antibiotics_equal <- function(x,
points_threshold = 2, points_threshold = 2,
info = FALSE) { info = FALSE) {
# x is active row, y is lag # x is active row, y is lag
type <- type[1]
type <- type[1]
if (length(x) != length(y)) { if (length(x) != length(y)) {
stop('Length of `x` and `y` must be equal.') stop('Length of `x` and `y` must be equal.')
} }
@ -594,7 +595,7 @@ key_antibiotics_equal <- function(x,
result[i] <- all(x2 == y2) result[i] <- all(x2 == y2)
} else { } else {
stop('No valid value for type, must be `points` or `keyantibiotics`. See ?first_isolate.') stop('`', type, '` is not a valid value for type, must be `points` or `keyantibiotics`. See ?first_isolate.')
} }
} }
} }

2
README.md
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@ -20,7 +20,7 @@ This package is available on CRAN and also here on GitHub.
[![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](http://cran.r-project.org/package=AMR) [![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](http://cran.r-project.org/package=AMR)
[![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/AMR)](http://cran.r-project.org/package=AMR) [![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/AMR)](http://cran.r-project.org/package=AMR)
- <img src="https://cran.r-project.org/favicon.ico" alt="R favicon" height="20px">In R: - <img src="https://cran.r-project.org/favicon.ico" alt="R favicon" height="20px"> In R:
- `install.packages("AMR")` - `install.packages("AMR")`
- <img src="http://www.rstudio.com/favicon.ico" alt="RStudio favicon" height="20px"> In RStudio: - <img src="http://www.rstudio.com/favicon.ico" alt="RStudio favicon" height="20px"> In RStudio: