diff --git a/.Rbuildignore b/.Rbuildignore index 210709e..193006b 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -17,3 +17,4 @@ ^docs$ ^pkgdown$ ^codecov\.yml$ +^CRAN-SUBMISSION$ diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 0000000..2f37b74 --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 2.5.0 +Date: 2023-07-16 17:41:44 UTC +SHA: 146fe539ca7632c983c246652e40f35950753b46 diff --git a/R/setstep.R b/R/setstep.R index a559e0c..1cbf05b 100644 --- a/R/setstep.R +++ b/R/setstep.R @@ -30,12 +30,14 @@ #' ## tolerance of +/- 30 minutes for matching existing data #' setstep(dat, timestep = 120, differ = 30) #' +#' \dontrun{ #' ## convert a nutrient time series to a continuous time series #' ## then remove empty rows and columns #' data(apacpnut) #' dat_nut <- apacpnut #' dat_nut <- setstep(dat_nut, timestep = 60) #' subset(dat_nut, rem_rows = TRUE, rem_cols = TRUE) +#' } setstep <- function(dat_in, ...) UseMethod('setstep') #' @rdname setstep diff --git a/man/cens_id.Rd b/man/cens_id.Rd index f0f442a..eec1654 100644 --- a/man/cens_id.Rd +++ b/man/cens_id.Rd @@ -26,7 +26,7 @@ Flag observations above/below detection limits } \details{ Censored observations are identified in swmpr objects using the CDMO flags -4 or -5, indicating outside the low or high sensor range, respectively. Additional codes are identified including A (-2007) or SUL (2007-) for above and B (-2007), SBL (2007-), SCB (2007-, calculated) for below detection limits. The QAQC columns are searched for all parameters and replaced with the appropriate value indicating the detection limit as defined by \code{flag_type}. The default argument \code{flag_type = 'both'} will recode the QAQC columns as -1, 0, or 1 indicating below, within, or above the detection limit. Setting \code{flag_type = 'below'} or \code{'above'} will convert the columns to \code{TRUE}/\code{FALSE} values indicating observations beyond the detection limit (either above or below, \code{TRUE}) or within the normal detection range \code{FALSE}. -The output includes additional columns similar to those for QAQC flags, such that the column names for censored flags include a \code{c_} prefix before the parameter name. Note that the function will of course not work if already processed with \code{\link{qaqc}}. QAQC columns are retaine for additional processing. +The output includes additional columns similar to those for QAQC flags, such that the column names for censored flags include a \code{c_} prefix before the parameter name. Note that the function will of course not work if already processed with \code{\link{qaqc}}. QAQC columns are retained for additional processing. The user should refer to the metadata or visually examine the observed data to identify the actual limit, which may change over time. } diff --git a/man/setstep.Rd b/man/setstep.Rd index 8753cce..abe2bf6 100644 --- a/man/setstep.Rd +++ b/man/setstep.Rd @@ -41,6 +41,7 @@ dat <- apaebmet ## tolerance of +/- 30 minutes for matching existing data setstep(dat, timestep = 120, differ = 30) +\dontrun{ ## convert a nutrient time series to a continuous time series ## then remove empty rows and columns data(apacpnut) @@ -48,6 +49,7 @@ dat_nut <- apacpnut dat_nut <- setstep(dat_nut, timestep = 60) subset(dat_nut, rem_rows = TRUE, rem_cols = TRUE) } +} \seealso{ \code{\link{comb}} } diff --git a/tests/testthat/test-import_local.R b/tests/testthat/test-import_local.R index 58d51c1..3dc85b8 100644 --- a/tests/testthat/test-import_local.R +++ b/tests/testthat/test-import_local.R @@ -166,4 +166,5 @@ test_that("import_local works with downstream functions when keep_qaqcstatus = T }) # Cleanup: Remove the temporary directory +file.remove(file.path(test_dir, 'apadwq.zip')) unlink(test_dir, recursive = TRUE)