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replaced bactid by mo

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dr. M.S. (Matthijs) Berends
2018-08-31 13:36:19 +02:00
parent 98ff131680
commit 5965d3c794
41 changed files with 786 additions and 411 deletions
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R/data.R
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@ -125,7 +125,7 @@
#' A dataset containing 2,646 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}.
#' @format A data.frame with 2,646 observations and 12 variables:
#' \describe{
#' \item{\code{bactid}}{ID of microorganism}
#' \item{\code{mo}}{ID of microorganism}
#' \item{\code{bactsys}}{Bactsyscode of microorganism}
#' \item{\code{family}}{Family name of microorganism}
#' \item{\code{genus}}{Genus name of microorganism, like \code{"Echerichia"}}
@ -140,27 +140,27 @@
#' }
# source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
# new <- microorganisms %>% filter(genus == "Bacteroides") %>% .[1,]
# new[1, 'bactid'] <- "DIAPNU"
# new[1, 'mo'] <- "DIAPNU"
# new[1, 'bactsys'] <- "DIAPNU"
# new[1, 'family'] <- "Veillonellaceae"
# new[1, 'genus'] <- "Dialister"
# new[1, 'species'] <- "pneumosintes"
# new[1, 'subspecies'] <- NA
# new[1, 'fullname'] <- paste(new[1, 'genus'], new[1, 'species'])
# microorganisms <- microorganisms %>% bind_rows(new) %>% arrange(bactid)
#' @seealso \code{\link{guess_bactid}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}
# microorganisms <- microorganisms %>% bind_rows(new) %>% arrange(mo)
#' @seealso \code{\link{guess_mo}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}
"microorganisms"
#' Translation table for UMCG with ~1100 microorganisms
#'
#' A dataset containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$bactid} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{bactid}'s with \code{\link{guess_bactid}}.
#' A dataset containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{mo}'s with \code{\link{guess_mo}}.
#' @format A data.frame with 1090 observations and 2 variables:
#' \describe{
#' \item{\code{mocode}}{Code of microorganism according to UMCG MMB}
#' \item{\code{bactid}}{Code of microorganism in \code{\link{microorganisms}}}
#' \item{\code{umcg}}{Code of microorganism according to UMCG MMB}
#' \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
#' }
# source MOLIS (LIS of Certe) - \url{https://www.certe.nl} \cr \cr GLIMS (LIS of UMCG) - \url{https://www.umcg.nl}
#' @seealso \code{\link{guess_bactid}} \code{\link{microorganisms}}
#' @seealso \code{\link{guess_mo}} \code{\link{microorganisms}}
"microorganisms.umcg"
#' Dataset with 2000 blood culture isolates of septic patients
@ -176,7 +176,7 @@
#' \item{\code{age}}{age of the patient}
#' \item{\code{sex}}{sex of the patient}
#' \item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
#' \item{\code{bactid}}{ID of microorganism, see \code{\link{microorganisms}}}
#' \item{\code{mo}}{ID of microorganism, see \code{\link{microorganisms}}}
#' \item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}}
#' }
# source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
@ -193,7 +193,7 @@
#'
#' # Add first isolates to our dataset:
#' my_data <- my_data %>%
#' mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "bactid"))
#' mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "mo"))
#'
#' # -------- #
#' # ANALYSIS #
@ -203,7 +203,7 @@
#' # and numbers (n) of E. coli, divided by hospital:
#'
#' my_data %>%
#' filter(bactid == guess_bactid("E. coli"),
#' filter(mo == guess_mo("E. coli"),
#' first_isolates == TRUE) %>%
#' group_by(hospital_id) %>%
#' summarise(n = n_rsi(amox),
@ -214,7 +214,7 @@
#' # percentages of E. coli, trend over the years:
#'
#' my_data %>%
#' filter(bactid == guess_bactid("E. coli"),
#' filter(mo == guess_mo("E. coli"),
#' first_isolates == TRUE) %>%
#' group_by(year = format(date, "%Y")) %>%
#' summarise(n = n_rsi(amcl),