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RMHDR-244 Fix Device Summaries De-duplication #15

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merged 3 commits into from
Mar 18, 2024
Merged

RMHDR-244 Fix Device Summaries De-duplication #15

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66e36c0
Convert dataset column names to lowercase more efficiently
pranavanba Mar 18, 2024
e03eaac
RMHDR-244 Participant device type is "Apple" if "Apple" among other n…
pranavanba Mar 18, 2024
02740aa
RMHDR-243 Exclude records where device_model is "iPhone" and where a …
pranavanba Mar 18, 2024
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19 changes: 9 additions & 10 deletions scripts/process-data/participant_devices.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,18 +13,14 @@ vars <- list(fitbitdevices = c("ParticipantIdentifier",

# Load the desired subset of this dataset in memory
df <-
sapply(dataset, function(x) {
lapply(dataset, function(x) {
tmp <- vars[[x]]
arrow::open_dataset(file.path(downloadLocation, glue::glue("dataset_{x}"))) %>%
select(all_of(tmp)) %>%
dplyr::rename_with(tolower) %>%
collect()
})

df <-
lapply(df, function(x) {
colnames(x) <- tolower(colnames(x))
return(x)
})
}) %>%
setNames(dataset)

# Get lists of participants that i2b2 summaries are already generated for and
# add a variable to indicate device type
Expand All @@ -33,14 +29,15 @@ fitbit_participants <- read.csv(file.path(outputConceptsDir, "fitbit_participant
df$fitbitdevices <-
df$fitbitdevices %>%
dplyr::filter(participantidentifier %in% fitbit_participants$participantidentifier) %>%
dplyr::mutate(type = ifelse(is.na(device) | device == "", NA, "fitbit"))
dplyr::mutate(type = ifelse(is.na(device) | device == "", NA, "Fitbit"))

hk_participants <- read.csv(file.path(outputConceptsDir, "hk_participants.csv"))

df$healthkitv2samples <-
df$healthkitv2samples %>%
dplyr::filter(participantidentifier %in% hk_participants$participantidentifier) %>%
mutate(type = case_when(device_manufacturer %in% c("Apple", "Apple Inc.") ~ "Apple",
dplyr::filter(device_model != "iPhone") %>%
mutate(type = case_when(device_manufacturer %in% c("Apple", "Apple Inc.") ~ "Apple Watch",
device_manufacturer %in% c("Garmin") ~ "Garmin",
device_manufacturer %in% c("Polar Electro Oy") ~ "Polar",
device_model %in% c("HRM808S") ~ "HRM808S",
Expand All @@ -57,6 +54,8 @@ df_joined <-
summarise(type = toString(sort(unique(type)))) %>%
mutate(concept = "mhp:device") %>%
rename(value = type) %>%
mutate(value = ifelse({grepl(", Apple Watch|Apple Watch, ", value)}, "Apple Watch", value)) %>%
filter(value != "Other") %>%
select(all_of(c("participantidentifier", "concept", "value"))) %>%
ungroup()

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