Commit validated bk, 118922 Feb 7
This commit is contained in:
Gerolf de Boer
299
interfaces/4D/src/4D_archive.R
Normal file
299
interfaces/4D/src/4D_archive.R
Normal file
@ -0,0 +1,299 @@
|
||||
require(tidyverse)
|
||||
if (!require(lubridate)) {
|
||||
install.packages('lubridate')
|
||||
require(lubridate)
|
||||
}
|
||||
require(crayon)
|
||||
require(stringr)
|
||||
|
||||
# TODO: check wat ProcessAndMergeDailyFiles ingaat: Monsternummer is.character?
|
||||
# TODO: min # rows = bijv. 10 i.v.m. privacy
|
||||
# TODO: 2 versies: MMBI & 'Algemeen'
|
||||
|
||||
memSize = function() {
|
||||
result = tibble(object='', size=0, sizeMB=0)
|
||||
objs = ls(envir = globalenv())
|
||||
for (i in 1:length(objs) ) {
|
||||
objName = objs[i]
|
||||
sizeBytes = as.numeric(object.size(get(objName)))
|
||||
result = result %>%
|
||||
add_row(object = objName, size = sizeBytes, sizeMB = sizeBytes / 1024^2)
|
||||
}
|
||||
result = result %>%
|
||||
arrange(desc(size))
|
||||
return(list(result, sum(result$sizeMB)))
|
||||
}
|
||||
|
||||
gatherAbIds = function() {
|
||||
archFolders = list.dirs(file.path(dataFolder, 'archive'), full.names = F)
|
||||
archFolders = archFolders[str_length(archFolders) == 26]
|
||||
for (archFolder in archFolders) {
|
||||
folder = archFolder
|
||||
abFiles = list.files(file.path(dataFolder, 'archive', folder), pattern = 'AB-*')
|
||||
for (abFileName in abFiles) {
|
||||
abFile = read_4D_file(file.path(dataFolder, 'archive', folder, abFileName))
|
||||
abNamesDict = tibble(name4d = abFile %>% pull(AB) %>% unique())
|
||||
newNamesDict = abNamesDict %>% filter(!name4d %in% a$name4d, !is.na(name4d))
|
||||
tNewNames = tibble(name4d = newNamesDict$name4d,
|
||||
nameAMR = as.ab(newNamesDict$name4d),
|
||||
nameAMRlong = ab_name(newNamesDict$name4d))
|
||||
a = a %>% add_row(tNewNames)
|
||||
}
|
||||
}
|
||||
return(a)
|
||||
}
|
||||
|
||||
source('4D_day.R')
|
||||
|
||||
useCachedFileInfo = T
|
||||
|
||||
archivePath = './data/archive'
|
||||
folders = list.files(path = archivePath, pattern = 'ImportedFromGlimms-*', full.names = T)
|
||||
|
||||
addFileInfo = function(x, filePath, fileName) {
|
||||
mtime = file.mtime(filePath)
|
||||
|
||||
x = x %>%
|
||||
add_row(filePath = filePath,
|
||||
fileName = fileName,
|
||||
fileType = str_sub(fileName, 1, 2),
|
||||
fileDate = fileName %>% str_sub(4, 9) %>% ymd(),
|
||||
modified = mtime,
|
||||
# mdate = as.Date(ymd_hms(modified)),
|
||||
size = file.size(filePath)) %>%
|
||||
group_by(fileDate) %>%
|
||||
mutate(nFilesPerDate = n()) %>%
|
||||
ungroup() %>%
|
||||
arrange(desc(fileDate))
|
||||
|
||||
return(x)
|
||||
}
|
||||
|
||||
deriveFileOverview = function(tFiles) {
|
||||
tFiles %>%
|
||||
group_by(fileDate) %>%
|
||||
mutate(AB = cur_data() %>%
|
||||
filter(str_sub(fileName, 1, 2) == 'AB') %>%
|
||||
nrow(),
|
||||
MS = cur_data() %>%
|
||||
filter(str_sub(fileName, 1, 2) == 'MS') %>%
|
||||
nrow(),
|
||||
ST = cur_data() %>%
|
||||
filter(str_sub(fileName, 1, 2) == 'ST') %>%
|
||||
nrow(),
|
||||
TM = cur_data() %>%
|
||||
filter(str_sub(fileName, 1, 2) == 'TM') %>%
|
||||
nrow(),
|
||||
TS = cur_data() %>%
|
||||
filter(str_sub(fileName, 1, 2) == 'TS') %>%
|
||||
nrow()
|
||||
) %>%
|
||||
slice(1) %>%
|
||||
select(fileDate, AB, MS, ST, TM, TS)
|
||||
}
|
||||
|
||||
getFilesInfo = function() {
|
||||
tFiles = tibble(filePath = 'deleteme',
|
||||
fileName = '',
|
||||
fileType = '',
|
||||
fileDate = ymd('2022-01-01'),
|
||||
modified = ymd('2022-01-01'),
|
||||
size = 0
|
||||
)
|
||||
for (folder in folders) {
|
||||
# if (folder == 'ImportedFromGlimms-2014-09') {
|
||||
folderPath = folder #file.path(archivePath, folder)
|
||||
files = list.files(folderPath, pattern = '*')
|
||||
for (file in files) {
|
||||
filePath = file.path(folderPath, file)
|
||||
tFiles = tFiles %>%
|
||||
addFileInfo(filePath = filePath, fileName = file)
|
||||
}
|
||||
}
|
||||
tFiles = tFiles %>%
|
||||
mutate(mdate = as.Date(ymd_hms(modified))) %>%
|
||||
filter(filePath != 'deleteme') %>%
|
||||
arrange(fileDate, fileName)
|
||||
tFiles = tFiles %>%
|
||||
left_join(tFiles %>% count(fileDate, name = 'nFilesPerDate'), by = 'fileDate')
|
||||
|
||||
return(tFiles)
|
||||
}
|
||||
|
||||
addFileInfoOfDay = function(x, folders, ymdDate, overwrite = F) {
|
||||
datePattern = format(ymdDate, format = '%y%m%d')
|
||||
dirPattern = format(today(), format = '%Y-%m')
|
||||
folder = folders[which(folders %>% str_detect(dirPattern))]
|
||||
dayFiles = list.files(path = folder, pattern = datePattern)
|
||||
for (fileName in dayFiles) {
|
||||
cat(paste0('Processing ', fileName, '\n'))
|
||||
x = x %>% addFileInfo(filePath = file.path(folder, fileName),
|
||||
fileName = fileName)
|
||||
}
|
||||
|
||||
return(x)
|
||||
}
|
||||
|
||||
addFileInfoOfToday = function(tFiles, folders) {
|
||||
browser()
|
||||
dirPattern = format(today(), format = '%Y-%m')
|
||||
folder = folders[which(folders %>% str_detect(dirPattern))]
|
||||
tFiles = tFiles %>%
|
||||
addFileInfoOfDay(folderPath = file.path(archivePath, folder),
|
||||
ymdDate = today(),
|
||||
overwrite = F)
|
||||
return(tFiles)
|
||||
}
|
||||
|
||||
plotFileSize = function(tFiles) {
|
||||
tFiles %>%
|
||||
filter(fileDate > ymd('2014-10-01'),
|
||||
fileDate <= ymd('2014-10-31'),
|
||||
fileType != 'Ee') %>%
|
||||
mutate(dayOfWeek = wday(fileDate),
|
||||
dayOfWeekName = weekdays(fileDate),
|
||||
size = size / (1024)
|
||||
) %>%
|
||||
ggplot(aes(x = dayOfWeek, y = size, group = dayOfWeek)) +
|
||||
geom_boxplot(aes(fill = fileType)) +
|
||||
scale_y_continuous(limits = c(0, 1250)) +
|
||||
facet_wrap(facets = c(~fileType)) +
|
||||
labs(y = 'size [KB]') +
|
||||
theme_light() +
|
||||
theme(
|
||||
plot.title = element_text(face = 'bold')
|
||||
)
|
||||
}
|
||||
|
||||
if (useCachedFileInfo) {
|
||||
tFiles = read_rds('./data/tFiles_2022-10-13.rds')
|
||||
tFileOvw = read_rds('./data/tFileOvw_2022-10-13.rds')
|
||||
} else {
|
||||
tFiles = getFilesInfo()
|
||||
tFileOvw = deriveFileOverview(tFiles)
|
||||
|
||||
write_rds(tFiles, paste0('./data/tFiles_', today(), '.rds'))
|
||||
write_rds(tFileOvw, paste0('./data/tFileOvw_', today(), '.rds'))
|
||||
}
|
||||
|
||||
readDailyFile = function(tFiles, date, prefix) {
|
||||
result = NULL
|
||||
fileNames = tFiles %>%
|
||||
filter(fileDate == date,
|
||||
fileType == prefix) %>%
|
||||
pull(filePath)
|
||||
if (length(fileNames) > 0) {
|
||||
for (f in 1:length(fileNames)) {
|
||||
fileName = fileNames[f]
|
||||
cat(silver(paste0('Reading ', fileName)), '\n')
|
||||
fileContent = read_4D_file(fileName)
|
||||
if (f == 1) {
|
||||
result = fileContent
|
||||
} else {
|
||||
result = result %>%
|
||||
add_row(fileContent)
|
||||
}
|
||||
}
|
||||
}
|
||||
return(result)
|
||||
}
|
||||
|
||||
readDailyMSFile = function(tFiles, date) {
|
||||
result = NULL
|
||||
fileNames = tFiles %>%
|
||||
filter(fileDate == date,
|
||||
fileType == 'MS') %>%
|
||||
pull(filePath)
|
||||
if (length(fileNames) > 0) {
|
||||
for (f in 1:length(fileNames)) {
|
||||
fileName = fileNames[f]
|
||||
cat(silver(paste0('Reading ', fileName)), '\n')
|
||||
msFileContent = read_4D_MS_file(fileName)
|
||||
if (f == 1) {
|
||||
result = msFileContent
|
||||
} else {
|
||||
result = result %>%
|
||||
add_row(msFileContent)
|
||||
}
|
||||
}
|
||||
}
|
||||
return(result)
|
||||
|
||||
}
|
||||
|
||||
readDailyFiles = function(tFiles, date) {
|
||||
abFile = readDailyFile(tFiles, date, 'AB')
|
||||
msFile = readDailyMSFile(tFiles, date)
|
||||
stFile = readDailyFile(tFiles, date, 'ST')
|
||||
tmFile = readDailyFile(tFiles, date, 'TM')
|
||||
tsFile = readDailyFile(tFiles, date, 'TS')
|
||||
|
||||
return(list(abFile, msFile, stFile, tmFile, tsFile))
|
||||
}
|
||||
|
||||
readArchive = function(tFileInfo, tFileOvw, createDebugList = FALSE) {
|
||||
tMergeDates = NULL
|
||||
tsDates = NULL
|
||||
tMergeDatesDebugList = list()
|
||||
dates = tFileInfo %>% filter(!is.na(fileDate)) %>% pull(fileDate) %>% unique()
|
||||
for (d in 1:length(dates)) {
|
||||
currDate = dates[d]
|
||||
cat(paste0('\nd = ', d, ', date: ', currDate, '\n'))
|
||||
print(tFileOvw %>% filter(fileDate == currDate))
|
||||
|
||||
dateFiles = readDailyFiles(tFileInfo, currDate)
|
||||
|
||||
if (!is.null(dateFiles[[1]])) {
|
||||
processed = ProcessAndMergeDailyFiles(
|
||||
dateFiles[[1]] %>% select(-...15),
|
||||
dateFiles[[2]],
|
||||
dateFiles[[3]],
|
||||
dateFiles[[4]],
|
||||
dateFiles[[5]]
|
||||
)
|
||||
|
||||
if (!is.null(processed$merged)) {
|
||||
tMergeDate = processed$merged %>% # abFile, stFile and msFile joined
|
||||
mutate(date = currDate, .before = 1)
|
||||
if (createDebugList) tMergeDatesDebugList[[d]] = tMergeDate
|
||||
|
||||
# separate tables of (ab|st|ms|ts|tm)File of the current day can be found
|
||||
# in processed$(ab|st|ms|ts|tm)File, for instance:
|
||||
if (!is.null(processed$tsFile)) {
|
||||
tsDate = processed$tsFile %>%
|
||||
mutate(date = currDate, .before = 1)
|
||||
}
|
||||
|
||||
if (is.null(tMergeDates)) {
|
||||
if (nrow(tMergeDate) > 0) {
|
||||
tMergeDates = tMergeDate
|
||||
}
|
||||
if (exists('tsDate')) {
|
||||
if (nrow(tsDate) > 0) {
|
||||
tsDates = tsDate
|
||||
}
|
||||
}
|
||||
} else {
|
||||
if (nrow(tMergeDates) > 0) {
|
||||
tMergeDates = tMergeDates %>% add_row(tMergeDate)
|
||||
}
|
||||
if (exists('tsDates')) {
|
||||
if (!is.null(tsDates)) {
|
||||
if (nrow(tsDates)) {
|
||||
tsDates = tsDates %>% add_row(tsDate)
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
tMergeDates = tMergeDates %>%
|
||||
mutate(Monsternummer = str_trim(Monsternummer))
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (createDebugList) {
|
||||
return(list(tMergeDates, tMergeDatesDebugList))
|
||||
} else {
|
||||
return(tMergeDates)
|
||||
}
|
||||
}
|
||||
268
interfaces/4D/src/4D_day.R
Normal file
268
interfaces/4D/src/4D_day.R
Normal file
@ -0,0 +1,268 @@
|
||||
# initially only interfacing 4D data
|
||||
|
||||
# TODO loggen zoveel mogelijk over ontvangen data (nieuwe GLIMS data)
|
||||
# TODO pushen R scripts naar git server waar Gerhard en Kornelis bij kunnen
|
||||
|
||||
# require(stringr)
|
||||
require(tidyverse)
|
||||
require(AMR)
|
||||
|
||||
dataFolder = './data'
|
||||
|
||||
get_most_recent_4D_file = function(path, prefix) {
|
||||
files = list.files(dataFolder, paste0('^', prefix, '*'))
|
||||
tFiles = tibble(name = files,
|
||||
mtime = file.mtime(file.path(dataFolder, files))) %>%
|
||||
arrange(desc(mtime))
|
||||
|
||||
tmpFilename = tFiles$name[1]
|
||||
|
||||
return(tmpFilename)
|
||||
}
|
||||
|
||||
read_4D_file = function(path) {
|
||||
tFile = read_tsv(path, col_types = paste0(rep('c', 30), collapse = ''))
|
||||
|
||||
# remove comment lines
|
||||
if (nrow(tFile) > 0) {
|
||||
tFile = tFile %>%
|
||||
slice( seq(4, nrow(tFile)) ) %>%
|
||||
filter(str_sub(ID, 1, 3) != '___')
|
||||
}
|
||||
|
||||
if (colnames(tFile)[1] == 'X1') {
|
||||
if (str_detect(path, 'AB-')) {
|
||||
tFile = tibble(ID = '0',
|
||||
Monsternummer = '',
|
||||
IsolNr = '',
|
||||
AB = '',
|
||||
V = '',
|
||||
PrefMIC ='',
|
||||
MIC = '',
|
||||
D = '',
|
||||
DIF = '',
|
||||
PrefEtest = '',
|
||||
E = '',
|
||||
ETEST = '',
|
||||
RIS = '',
|
||||
RAP = '',
|
||||
...15 = '')
|
||||
} else if (str_detect(path, 'MS-')) {
|
||||
tFile = tibble(UMCG.Monster= '0',
|
||||
PIN.Lot= '0',
|
||||
TypeObject= '0',
|
||||
Lot= '0',Echtgenoot= '0',
|
||||
AchternNaam= '0',
|
||||
Geboortedatum= '0',
|
||||
Geslacht= '0',
|
||||
OntvOLabDatum= '0',
|
||||
Tijdstip.materiaal.afgenomen= '0',
|
||||
PC= '0',
|
||||
Aanvrager= '0',
|
||||
ligafdeling= '0',
|
||||
A= '0',
|
||||
B= '0',
|
||||
C= '0',
|
||||
Materiaal= '0',
|
||||
Materiaal.variabelen= '0',
|
||||
X = F)
|
||||
} else if (str_detect(path, 'ST-')) {
|
||||
tFile = tibble(ID = '0',
|
||||
Monsternummer = '',
|
||||
MMBProc = '',
|
||||
Isolnr = '',
|
||||
MO = '',
|
||||
Waarde = '',
|
||||
Pos = '',
|
||||
Rap = '')
|
||||
} else if (str_detect(path, 'TM-')) {
|
||||
tFile = tibble(ID = '0',
|
||||
Monsternummer = '',
|
||||
Test = '',
|
||||
Uitslag = '')
|
||||
} else if (str_detect(path, 'TS-')) {
|
||||
tFile = tibble(ID = '0',
|
||||
Monsternummer = '',
|
||||
Isolnr = '',
|
||||
Test = '',
|
||||
Waarde = '',
|
||||
Rapport = '')
|
||||
}
|
||||
}
|
||||
if ('ID' %in% colnames(tFile)) {
|
||||
tFile = tFile %>%
|
||||
filter(ID != '0')
|
||||
} else if ('UMCG.Monster' %in% colnames(tFile)) {
|
||||
tFile = tFile %>%
|
||||
filter(UMCG.Monster != '0')
|
||||
}
|
||||
|
||||
return(tFile)
|
||||
}
|
||||
|
||||
read_4D_TM_file = function(path) {
|
||||
tmFilename = str_remove(path, paste0(dirname(path), '/'))
|
||||
tmFileL = readLines(path)
|
||||
tmFileL = tmFileL[c(5:length(tmFileL))]
|
||||
for (l in 1:length(tmFileL)) {
|
||||
if (str_count(tmFileL[l], '\t') == 3) {
|
||||
tmFileL = paste0(tmFileL, '\t')
|
||||
}
|
||||
}
|
||||
newTmFilename = file.path(dirname(path),
|
||||
tmFilename %>% str_replace('TM', 'bTM'))
|
||||
if (file.exists(newTmFilename)) file.remove(newTmFilename)
|
||||
writeLines(tmFileL, newTmFilename)
|
||||
|
||||
tFile = read_tsv(newTmFilename,
|
||||
col_names = c('ID','Monsternummer','Test','Status.test.tm','Uitslag'),
|
||||
col_types = 'ccccc')
|
||||
|
||||
# remove comment lines
|
||||
tFile = tFile %>%
|
||||
slice(c(5:(tFile %>% nrow()))) %>%
|
||||
mutate(
|
||||
Monsternummer = as.character(Monsternummer)
|
||||
)
|
||||
return(tFile)
|
||||
}
|
||||
|
||||
get_most_recent_4D_MS_file = function(path) {
|
||||
# get files
|
||||
msFiles = list.files(path, '^MS*')
|
||||
# create table with modification datetimes, for selection of the most recent one
|
||||
tmsFiles = tibble(name = msFiles,
|
||||
mtime = file.mtime(file.path(path, msFiles))) %>%
|
||||
arrange(desc(mtime))
|
||||
# get the name of the most recently modified file
|
||||
msFilename = tmsFiles$name[1]
|
||||
|
||||
return(msFilename)
|
||||
}
|
||||
|
||||
read_4D_MS_file = function(path) {
|
||||
# print(path)
|
||||
msFilename = str_remove(path, paste0(dirname(path), '/'))
|
||||
# read content
|
||||
msFileL = readLines(path)
|
||||
# remove lines with repeated '_', useful for the human eye only
|
||||
msFileL = msFileL[str_sub(msFileL, 1, 5) != '_____']
|
||||
# replace (real) header
|
||||
msHeader = readLines(file.path(dataFolder, 'headerMS.txt'))
|
||||
msFileL[1] = paste0(msHeader, '\t')
|
||||
# replace tabs within a date time combination with a space in line 2 and further,
|
||||
# for example: replace '29/09/2021 14:05' by '29/09/2021 14:05'
|
||||
# ↑ = '\t' ↑ = ' '
|
||||
for (i in 2:length(msFileL)) {
|
||||
msFileL[i] = msFileL[i] %>% str_replace_all('(?<=[:digit:]{4})\t(?=[:digit:]{2}:[:digit:]{2})', ' ')
|
||||
}
|
||||
# write to new machine readable file
|
||||
newMsFilename = file.path(dirname(path),
|
||||
msFilename %>% str_replace('MS', 'bMS'))
|
||||
if (file.exists(newMsFilename)) file.remove(newMsFilename)
|
||||
writeLines(msFileL, newMsFilename)
|
||||
# finally: read the machine readable file
|
||||
result = read.delim(file = newMsFilename, sep = '\t') %>%
|
||||
as_tibble() %>%
|
||||
mutate(
|
||||
UMCG.Monster = as.character(UMCG.Monster),
|
||||
PIN.Lot = as.character(PIN.Lot),
|
||||
Aanvrager = as.character(Aanvrager),
|
||||
C = as.character(C)
|
||||
)
|
||||
# Hurray!
|
||||
return(result)
|
||||
}
|
||||
|
||||
# abFile = read_4D_file(dataFolder, 'AB')
|
||||
# msFile = read_4D_MS_file(dataFolder)
|
||||
# stFile = read_4D_file(dataFolder, 'ST')
|
||||
# tmFile = read_4D_file(dataFolder, 'TM')
|
||||
# tsFile = read_4D_file(dataFolder, 'TS')
|
||||
|
||||
ProcessAndMergeDailyFiles = function(abFile, msFile, stFile, tmFile, tsFile) {
|
||||
if (!is.null(abFile))
|
||||
abFile = abFile %>%
|
||||
filter(!is.na(RAP)) #%>%
|
||||
# mutate(
|
||||
# #Monsternummer = as.character(Monsternummer)
|
||||
# AB.amr = AMR::ab_property(AB, 'ab') %>% as.character()
|
||||
# )
|
||||
|
||||
if (!is.null(stFile))
|
||||
stFile = stFile %>%
|
||||
filter(!is.na(Rap)) %>%
|
||||
# mutate(Monsternummer = as.character(Monsternummer) %>% str_trim()) %>%
|
||||
rename(IsolNr = Isolnr)
|
||||
|
||||
if (!is.null(msFile))
|
||||
msFile = msFile %>%
|
||||
rename(Monsternummer = UMCG.Monster) %>%
|
||||
# mutate(Monsternummer = as.character(Monsternummer) %>% str_trim()) %>%
|
||||
select(-X)
|
||||
|
||||
# if (!is.null(tmFile))
|
||||
# tmFile = tmFile %>%
|
||||
# mutate(Monsternummer = as.character(Monsternummer) %>% str_trim())
|
||||
|
||||
if (!is.null(tsFile))
|
||||
tsFile = tsFile %>%
|
||||
filter(!is.na(Rapport))
|
||||
# mutate(Monsternummer = as.character(Monsternummer) %>% str_trim())
|
||||
|
||||
if (!is.null(abFile) & !is.null(stFile))
|
||||
t_ab_st = abFile %>%
|
||||
full_join(stFile,
|
||||
by = c('Monsternummer', 'IsolNr'),
|
||||
suffix = c('.ab', '.st'))
|
||||
|
||||
if (exists('t_ab_st')) {
|
||||
if (!is.null(t_ab_st) & !is.null(msFile)) {
|
||||
t_ab_st_ms = t_ab_st %>%
|
||||
full_join(msFile, by = 'Monsternummer') %>%
|
||||
rename(Waarde.st = Waarde)
|
||||
|
||||
return(
|
||||
list(
|
||||
merged = t_ab_st_ms,
|
||||
abFile = abFile,
|
||||
stFile = stFile,
|
||||
msFile = msFile,
|
||||
tsFile = tsFile,
|
||||
tmFile = tmFile
|
||||
)
|
||||
)
|
||||
|
||||
# t_ab_st_ms_ts = t_ab_st_ms %>%
|
||||
# full_join(tsFile, by = c('Monsternummer', 'IsolNr' = 'Isolnr'))
|
||||
#
|
||||
# t_ab_st_ms_ts_tm = t_ab_st_ms_ts %>%
|
||||
# add_column(Uitslag = NA,
|
||||
# is_sampleResult = F) %>%
|
||||
# add_row(Monsternummer = tmFile$Monsternummer,
|
||||
# Test = tmFile$Test,
|
||||
# Uitslag = tmFile$Uitslag,
|
||||
# is_sampleResult = T)
|
||||
#
|
||||
# t_ab_st_ms_ts_tm = t_ab_st_ms_ts_tm %>%
|
||||
# rename(Waarde.ts = Waarde) %>%
|
||||
# filter(!Test %in% c('no_filter_yet'))
|
||||
#
|
||||
# # if ('X' %in% colnames(t_ab_st_ms_ts_tm)) {
|
||||
# # t_ab_st_ms_ts_tm = t_ab_st_ms_ts_tm %>%
|
||||
# # select(-'X')
|
||||
# # print('Dit statement is voor debugging')
|
||||
# # }
|
||||
}
|
||||
}
|
||||
return(
|
||||
list(
|
||||
merged = NULL,
|
||||
abFile = abFile,
|
||||
stFile = stFile,
|
||||
msFile = msFile,
|
||||
tsFile = tsFile,
|
||||
tmFile = tmFile
|
||||
)
|
||||
)
|
||||
}
|
||||
26
interfaces/4D/src/debug weergave patho_plot.R
Normal file
26
interfaces/4D/src/debug weergave patho_plot.R
Normal file
@ -0,0 +1,26 @@
|
||||
require(tidyverse)
|
||||
require(readr)
|
||||
|
||||
v171 = read_rds('v171.rds')
|
||||
v180 = read_rds('v180.rds')
|
||||
|
||||
new_v180 = v180 %>% anti_join(v171 %>% left_join(v180))
|
||||
|
||||
source('interfaces.R')
|
||||
|
||||
d = readGlimsArchive(NULL, NULL, T, NULL, NULL)
|
||||
d %>% filter(str_starts(mo, 'B_ES')) %>% count(mo, CXM)
|
||||
# deze aantallen zie ik niet terug in wat de applicatie presenteert:
|
||||
# Ceftazidim: R (705), SI (2705), totaal dus 3410
|
||||
|
||||
# misschien dat data_select() voor andere aantallen zorgt?
|
||||
data_select = d %>%
|
||||
# filter(specialty_shiny %in% input$specialtyInput & department %in% input$departmentInput) %>%
|
||||
filter_first_isolate(col_patient_id = "patientid", episode_days = 30) %>%
|
||||
mutate(mo = as.mo(mo, Becker = TRUE))
|
||||
|
||||
data_select %>% filter(str_starts(mo, 'B_ES')) %>% count(mo, CXM)
|
||||
|
||||
# Ja dus!
|
||||
|
||||
|
||||
37
interfaces/4D/src/debug_inspect for data validation.R
Normal file
37
interfaces/4D/src/debug_inspect for data validation.R
Normal file
@ -0,0 +1,37 @@
|
||||
require(tidyverse)
|
||||
|
||||
inspectRead = 10
|
||||
dataPath = 'data'
|
||||
|
||||
abNames = read_rds('data/abNames.rds')
|
||||
|
||||
filename = list.files(dataPath, paste0('read_', inspectRead, '_*'))
|
||||
d = read_rds(file.path(dataPath, filename)) #%>%
|
||||
# left_join(abNames, by = c('ab.amr' = 'nameAMR'))
|
||||
# list a sampleid that occurs more often but not too often
|
||||
examples = d %>% count(sampleid) %>% arrange(desc(n)) %>% filter(n < 50)
|
||||
|
||||
view_d = d %>%
|
||||
select(sampleid, date, IsolNr, MIC, mo, RIS, ab.amr, RAP) %>% #, name4d, nameAMRlong) %>%
|
||||
mutate(asmo = suppressWarnings(as.mo(mo))) %>%
|
||||
arrange(sampleid, IsolNr) #%>%
|
||||
# filter(sampleid == examples$sampleid[i])
|
||||
|
||||
has_ecoli = view_d %>% filter(str_starts(asmo, 'B_ES'))
|
||||
examples_having_ecoli = has_ecoli %>%
|
||||
filter(sampleid %in% examples$sampleid) %>%
|
||||
pull(sampleid) %>%
|
||||
unique()
|
||||
|
||||
e = 2
|
||||
view(view_d %>%
|
||||
filter(sampleid == examples_having_ecoli[e]) %>%
|
||||
mutate(IsolNr = as.numeric(IsolNr)) %>%
|
||||
arrange(IsolNr),# %>%
|
||||
#distinct(sampleid, date, IsolNr, mo, ab.amr, .keep_all = T),
|
||||
title = 'example')
|
||||
|
||||
if (F) {
|
||||
view(view_d)
|
||||
view_d %>% filter(!is.na(mo)) %>% pull(mo) %>% unique()
|
||||
}
|
||||
Reference in New Issue
Block a user