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Subdaily EGRET plots #223

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Subdaily EGRET plots #223

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b7bbee3
don't force Date class
Aug 17, 2017
082d912
Merge branch 'master' of github.com:USGS-R/loadflex
Aug 17, 2017
cb3b5d5
get rid of interactive=FALSE warnings
Aug 17, 2017
47f7ae8
drop dateTime col & allow posix to carry through
Aug 18, 2017
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20 changes: 9 additions & 11 deletions R/convertToEGRET.R
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Original file line number Diff line number Diff line change
Expand Up @@ -91,9 +91,7 @@ convertToEGRETSample <- function(data = NULL, meta = NULL, dailydat = NULL) {
sample_data <- sample_data %>% # use transform b/c mutate breaks with smwrQW columns
mutate(Uncen = as.numeric(!is.na(ConcLow) & !is.na(ConcHigh) & ConcHigh == ConcLow)) %>%
populateSampleColumns() %>%
mutate(
dateTime = data[[date_col]],
Date = as.Date(Date))
mutate(Date = data[[date_col]])

# Format the flow info
flow_col <- getInfo(meta, 'flow', TRUE)
Expand All @@ -103,11 +101,11 @@ convertToEGRETSample <- function(data = NULL, meta = NULL, dailydat = NULL) {
flow.colname = flow_col,
date.colname = date_col,
flow.units = getUnits(meta, 'flow', 'EGRET')) %>%
select(Date, Q, dateTime)
select(Date, Q)

# Combine the sample and flow info
sample_df <- sample_data %>%
left_join(flow_data, by=c('dateTime', 'Date'))
left_join(flow_data, by=c('Date'))

# Add in predictions if available. The sample-specific model predictions
# created by EGRET are actually leave-one-out estimates where yHat, SE, and
Expand All @@ -120,8 +118,8 @@ convertToEGRETSample <- function(data = NULL, meta = NULL, dailydat = NULL) {
if(!is.null(dailydat) && all(c('yHat','SE','ConcDay') %in% names(dailydat))) {
sample_df <- left_join(
sample_df,
select(dailydat, dateTime, yHat, SE, ConcHat=ConcDay),
by='dateTime')
select(dailydat, Date, yHat, SE, ConcHat=ConcDay),
by='Date')
}

return(sample_df)
Expand Down Expand Up @@ -200,8 +198,8 @@ convertToEGRETDaily <- function(newdata, load.model = NULL, meta = NULL) {
# (3) is the estimated concentration (ConcHat).
fit <- se.pred <- '.dplyr.var'
daily_df <- daily_df %>%
left_join(select(preds_log, date, yHat = fit, SE = se.pred), by=c("dateTime" = "date")) %>%
left_join(select(preds_lin, date, ConcDay = fit), by=c("dateTime" = "date"))
left_join(select(preds_log, date, yHat = fit, SE = se.pred), by=c("Date" = "date")) %>%
left_join(select(preds_lin, date, ConcDay = fit), by=c("Date" = "date"))

# Fill in the Flux preds based on the Conc preds
meta.conv <- updateMetadata(meta, flow='Q', flow.units='cms', load.rate.units='kg d^-1')
Expand Down Expand Up @@ -241,8 +239,8 @@ expandFlowForEGRET <- function(flowdat, flow.colname, date.colname, flow.units)
rename_("value" = flow.colname,
"dateTime" = date.colname) %>%
mutate(code = "") %>%
populateDaily(qConvert = qconvert, interactive = FALSE) %>%
mutate(dateTime = flowdat[[date.colname]])
populateDaily(qConvert = qconvert, verbose = FALSE) %>%
mutate(Date = flowdat[[date.colname]])

return(flowdat_corrected)
}
14 changes: 7 additions & 7 deletions tests/testthat/test-51-EGRET.R
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Expand Up @@ -78,11 +78,11 @@ test_that("convertToEGRETSample returns NA without fitdat", {
test_that("convertToEGRETSample correctly converts", {
Sample <- loadflex:::convertToEGRETSample(meta = meta, data = fitdat)
expect_equal(nrow(Sample), nrow(fitdat))
expect_equal(ncol(Sample), 15)
expect_equal(ncol(Sample), 14)

expected_cols <- c("Date", "ConcLow", "ConcHigh", "Uncen", "ConcAve", "Julian",
"Month", "Day", "DecYear", "MonthSeq", "waterYear", "SinDY",
"CosDY", "dateTime", "Q")
"CosDY", "Q")
expect_equal(sort(names(Sample)), sort(expected_cols))
})

Expand All @@ -95,16 +95,16 @@ test_that("convertToEGRETDaily returns NA without estdat or preds", {

test_that("convertToEGRETDaily returns partial info without preds", {
Daily <- loadflex:::convertToEGRETDaily(meta = meta, newdata = estdat)
expect_equal(ncol(Daily), 14)
expect_equal(ncol(Daily), 13)
})

test_that("convertToEGRETDaily correctly converts", {
Daily <- loadflex:::convertToEGRETDaily(newdata = estdat, load.model = conc_lm)
expect_equal(nrow(Daily), nrow(estdat))
expect_equal(ncol(Daily), 18)
expect_equal(ncol(Daily), 17)

expected_cols <- c("Date", "Q", "Julian", "Month", "Day", "DecYear", "MonthSeq",
"waterYear", "Qualifier", "i", "LogQ", "Q7", "Q30", "dateTime",
"waterYear", "Qualifier", "i", "LogQ", "Q7", "Q30",
"ConcDay", "SE", "FluxDay", "yHat")
expect_equal(sort(names(Daily)), sort(expected_cols))
})
Expand All @@ -115,8 +115,8 @@ context("expandFlowForEGRET")
test_that("expandFlowForEGRET returns correct columns", {
corrected_flow_df <- loadflex:::expandFlowForEGRET(estdat, 'DISCHARGE', 'DATE', 'ft^3 s^-1')
expect_equal(nrow(corrected_flow_df), nrow(estdat))
expect_equal(ncol(corrected_flow_df), 14)
expect_equal(ncol(corrected_flow_df), 13)
expected_cols <- c("Date", "Q", "Julian", "Month", "Day", "DecYear", "MonthSeq",
"waterYear", "Qualifier", "i", "LogQ", "Q7", "Q30", "dateTime")
"waterYear", "Qualifier", "i", "LogQ", "Q7", "Q30")
expect_equal(sort(names(corrected_flow_df)), sort(expected_cols))
})