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Multiple design_link handling #60

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merged 10 commits into from
Dec 2, 2023
Merged

Multiple design_link handling #60

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0992167
Create design_link_shift_example.R
bpbond Dec 2, 2023
e4b105e
Update design_link_shift_example.R
bpbond Dec 2, 2023
115caa1
Works except for two-shift cases
bpbond Dec 2, 2023
896d9e7
Much simpler and clearer!
bpbond Dec 2, 2023
d91a1df
Update design_link_shift_example.R
bpbond Dec 2, 2023
8262e4e
Update design_link_shift_example.R
bpbond Dec 2, 2023
5320e9d
Update design_link_shift_example.R
bpbond Dec 2, 2023
21e6beb
Move code into helpers.R
bpbond Dec 2, 2023
c8ba045
Integrate the multiple-design link code into L1_normalize
bpbond Dec 2, 2023
8525134
Remove unneeded valid_until column
bpbond Dec 2, 2023
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20 changes: 16 additions & 4 deletions synoptic/L1_normalize.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ if(packageVersion("compasstools") < "0.2") {

# Read the design table (everything must have an entry)
DESIGN_TABLE <- file.path(params$DATA_ROOT, params$DESIGN_TABLE)
dt <- read_csv(DESIGN_TABLE, col_types = "ccccccc")
dt <- read_csv(DESIGN_TABLE, col_types = "cccccDcc")
dt$note <- NULL
# For compactness, the design table may have expansions. For example,
# "DiffVoltA_Avg({1:8})" -> "DiffVoltA_Avg(1)", "DiffVoltA_Avg(2)", etc., with
Expand All @@ -56,7 +56,7 @@ dt_ex <- compasstools::expand_df(dt)

# Read the variable metadata table
METADATA_VARS_TABLE <- file.path(params$DATA_ROOT, params$METADATA_VARS_TABLE)
mt <- read_csv(METADATA_VARS_TABLE, col_types = "ccccccccddc")
mt <- read_csv(METADATA_VARS_TABLE, col_types = "ccccccddc")
# ...and create the units table (everything must have an entry)
ut <- mt[!is.na(mt$research_name),] # filter
ut$new_unit = ut$final_units # rename
Expand Down Expand Up @@ -128,8 +128,20 @@ f <- function(fn, out_dir, design_table) {
dat <- merge(dat, design_table,
by = c("Logger", "Table", "loggernet_variable"),
sort = FALSE)
# This is a left join, and should not have changed number of rows;
# i.e., there must be exactly one match for every loggernet variable
# This is a left join, and normally should not have changed the number of rows
# The exception would be if a sensor has been reassigned; in that case it will have
# >1 entry in the design table, with the "valid_until" column controlling when the
# old assignment becomes invalid and the new one takes over. Call valid_entries()
# (in helpers.R) to figure out which mappings should apply.
message("\tChecking for multiple-match design links...")
dat_retain <- valid_entries(objects = dat$loggernet_variable,
times = ymd_hms(dat$TIMESTAMP, tz = "EST"),
valid_until = dat$valid_until)
message("\tDropping ", sum(!dat_retain), " out-of-date design links")
dat <- dat[dat_retain,]
dat$valid_until <- NULL

# At this point, there should be exactly one match for every loggernet variable
if(nrow(dat) > old_rows) {
counts <- aggregate(design_link ~ loggernet_variable, data = test,
FUN = function(x) length(unique(x)))
Expand Down
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