P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 22:21:52 +02:00
Code Releases Activity

(v2.1.1.9049) new 2024 breakpoints, add AMO, set NI instead of N

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-06-14 22:39:01 +02:00
parent de17de1be9
commit 9bf7584d58
57 changed files with 4375 additions and 135 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
R/bug_drug_combinations.R
View File

@ -124,7 +124,7 @@ bug_drug_combinations <- function(x,
# turn and merge everything
pivot <- lapply(x_mo_filter, function(x) {
m <- as.matrix(table(as.sir(x)))
data.frame(S = m["S", ], SDD = m["SDD", ], I = m["I", ], R = m["R", ], N = m["N", ], stringsAsFactors = FALSE)
data.frame(S = m["S", ], SDD = m["SDD", ], I = m["I", ], R = m["R", ], NI = m["NI", ], stringsAsFactors = FALSE)
})
merged <- do.call(rbind_AMR, pivot)
out_group <- data.frame(
@ -134,8 +134,8 @@ bug_drug_combinations <- function(x,
SDD = merged$SDD,
I = merged$I,
R = merged$R,
N = merged$N,
total = merged$S + merged$SDD + merged$I + merged$R + merged$N,
NI = merged$NI,
total = merged$S + merged$SDD + merged$I + merged$R + merged$NI,
stringsAsFactors = FALSE
)
if (data_has_groups) {
@ -210,13 +210,13 @@ format.bug_drug_combinations <- function(x,
SDD = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$SDD[i], na.rm = TRUE)),
I = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$I[i], na.rm = TRUE)),
R = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$R[i], na.rm = TRUE)),
N = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$R[i], na.rm = TRUE)),
NI = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$NI[i], na.rm = TRUE)),
total = vapply(FUN.VALUE = double(1), idx, function(i) {
sum(x$S[i], na.rm = TRUE) +
sum(x$SDD[i], na.rm = TRUE) +
sum(x$I[i], na.rm = TRUE) +
sum(x$R[i], na.rm = TRUE) +
sum(x$N[i], na.rm = TRUE)
sum(x$NI[i], na.rm = TRUE)
}),
stringsAsFactors = FALSE
)