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(v1.2.0.9035) as.mo() speed improvement

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dr. M.S. (Matthijs) Berends
2020-07-22 10:24:23 +02:00
parent 6ab468362d
commit 09fba38ea6
37 changed files with 174 additions and 441 deletions
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23
R/first_isolate.R
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@ -174,10 +174,6 @@ first_isolate <- function(x,
col_date <- search_type_in_df(x = x, type = "date")
stop_if(is.null(col_date), "`col_date` must be set")
}
# convert to Date
dates <- as.Date(x[, col_date, drop = TRUE])
dates[is.na(dates)] <- as.Date("1970-01-01")
x[, col_date] <- dates
# -- patient id
if (is.null(col_patient_id)) {
@ -223,12 +219,17 @@ first_isolate <- function(x,
check_columns_existance(col_icu)
check_columns_existance(col_keyantibiotics)
# convert dates to Date
dates <- as.Date(x[, col_date, drop = TRUE])
dates[is.na(dates)] <- as.Date("1970-01-01")
x[, col_date] <- dates
# create original row index
x$newvar_row_index <- seq_len(nrow(x))
x$newvar_mo <- x %>% pull(col_mo) %>% as.mo()
x$newvar_mo <- x[, col_mo, drop = TRUE]
x$newvar_genus_species <- paste(mo_genus(x$newvar_mo), mo_species(x$newvar_mo))
x$newvar_date <- x %>% pull(col_date)
x$newvar_patient_id <- x %>% pull(col_patient_id)
x$newvar_date <- x[, col_date, drop = TRUE]
x$newvar_patient_id <- x[, col_patient_id, drop = TRUE]
if (is.null(col_testcode)) {
testcodes_exclude <- NULL
@ -317,10 +318,10 @@ first_isolate <- function(x,
}
# Analysis of first isolate ----
x$other_pat_or_mo <- if_else(x$newvar_patient_id == lag(x$newvar_patient_id) &
x$newvar_genus_species == lag(x$newvar_genus_species),
FALSE,
TRUE)
x$other_pat_or_mo <- ifelse(x$newvar_patient_id == lag(x$newvar_patient_id) &
x$newvar_genus_species == lag(x$newvar_genus_species),
FALSE,
TRUE)
x$episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
x$more_than_episode_ago <- unlist(lapply(unique(x$episode_group),
function(g,