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eucast rules fix, 1st isolate fix, website update

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-12-31 01:48:53 +01:00
parent 469b145d8c
commit 2e4d703338
51 changed files with 1473 additions and 1760 deletions
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49
R/first_isolate.R
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@ -380,7 +380,7 @@ first_isolate <- function(tbl,
)
}
# suppress warnings because dplyr want us to use library(dplyr) when using filter(row_number())
# suppress warnings because dplyr wants us to use library(dplyr) when using filter(row_number())
suppressWarnings(
scope.size <- tbl %>%
filter(
@ -391,17 +391,46 @@ first_isolate <- function(tbl,
nrow()
)
identify_new_year = function(x, episode_days) {
# I asked on StackOverflow:
# https://stackoverflow.com/questions/42122245/filter-one-row-every-year
if (length(x) == 1) {
return(TRUE)
}
indices = integer(0)
start = x[1]
ind = 1
indices[ind] = ind
for (i in 2:length(x)) {
if (as.numeric(x[i] - start >= episode_days)) {
ind = ind + 1
indices[ind] = i
start = x[i]
}
}
result <- rep(FALSE, length(x))
result[indices] <- TRUE
return(result)
}
# Analysis of first isolate ----
all_first <- tbl %>%
mutate(other_pat_or_mo = if_else(patient_id == lag(patient_id)
& genus == lag(genus)
& species == lag(species),
FALSE,
TRUE),
days_diff = 0) %>%
mutate(days_diff = if_else(other_pat_or_mo == FALSE,
(date_lab - lag(date_lab)) + lag(days_diff),
0))
TRUE)) %>% #,
# days_diff = 0) %>%
# mutate(days_diff = if_else(other_pat_or_mo == FALSE,
# as.integer((date_lab - lag(date_lab)) + lag(days_diff)),
# as.integer(0))) %>%
# mutate(r = days_diff) %>%
group_by_at(vars(patient_id,
genus,
species)) %>%
mutate(more_than_episode_ago = identify_new_year(x = date_lab,
episode_days = episode_days)) %>%
ungroup()
weighted.notice <- ''
if (!is.null(col_keyantibiotics)) {
@ -436,13 +465,12 @@ first_isolate <- function(tbl,
between(row_number(), row.start, row.end)
& genus != ""
& species != ""
& (other_pat_or_mo
| days_diff >= episode_days
| key_ab_other),
& (other_pat_or_mo | more_than_episode_ago | key_ab_other),
TRUE,
FALSE))
)
} else {
# no key antibiotics
# suppress warnings because dplyr want us to use library(dplyr) when using filter(row_number())
suppressWarnings(
all_first <- all_first %>%
@ -452,8 +480,7 @@ first_isolate <- function(tbl,
between(row_number(), row.start, row.end)
& genus != ""
& species != ""
& (other_pat_or_mo
| days_diff >= episode_days),
& (other_pat_or_mo | more_than_episode_ago),
TRUE,
FALSE))
)