R/align_TDL_Licor_times.R
In erikerhardt/isogasex: Isotopic gas exchange using TDL and Licor input. Updated version of package tdllicor
#' Find the overlapping time window of the TDL and Licor files and return the start/end indices of each file
#'
#' Unused sites (comment):
#' When sites are specified in TDL file that are not in the template file (because more than 4 sites are used),
#' then there are NAs for times for used sites. In this case, the matching times above may be different
#' from the min/max times below. In this case, we should use the matching times (that is, always use the matching times)
#' otherwise errors result from NA times in \code{\link{time_window_TDL_Licor_interp}}.
#' The logic is: use the widest matching times within the timewindow.
#'
#' Indicate first and last times for TDL and Licor.
#'
#' Report first and last times.
#'
#' Indicate the time window specified.
#'
#' Set TDL and Licor times to NA outside the time window.
#'
#' Indicate the first and last matching TDL and Licor times in time window.
#'
#' Check that TDL and Licor first and last times are identical.
#'
#' Indices for first and last times in TDL and Licor files.
#'
#' Use narrower timewindow start and end times, if specified.
#'
#' @param TDL_time xxxPARAMxxx
#' @param TDL_n xxxPARAMxxx
#' @param Licor_time xxxPARAMxxx
#' @param Licor_n xxxPARAMxxx
#' @param val_timewindow xxxPARAMxxx
#' @param sw xxxPARAMxxx
#'
#' @return TDL_Licor_times xxxRETURNxxx
#'
align_TDL_Licor_times <-
function# find the overlapping time window of the TDL and Licor files and return the start/end indices of each file
###
(TDL_time
###
, TDL_n
###
, Licor_time
###
, Licor_n
###
, val_timewindow
###
, sw
###
)
{
# DEBUGGING
# TDL_time <- TDL$time ;
# TDL_n <- TDL$n ;
# Licor_time <- Licor$time ;
# Licor_n <- Licor$n ;
# val_timewindow <- val$timewindow ;
# 10/2/2011 1:59PM
##details<<
## Unused sites (comment):
## When sites are specified in TDL file that are not in the template file (because more than 4 sites are used),
## then there are NAs for times for used sites. In this case, the matching times above may be different
## from the min/max times below. In this case, we should use the matching times (that is, always use the matching times)
## otherwise errors result from NA times in \code{\link{time_window_TDL_Licor_interp}}.
## The logic is: use the widest matching times within the timewindow.
##details<<
## Indicate first and last times for TDL and Licor.
TDL_run_time_first <- if(sw$use_TDL ) {as.POSIXct(min(TDL_time , na.rm=TRUE))} else {NA}
TDL_run_time_last <- if(sw$use_TDL ) {as.POSIXct(max(TDL_time , na.rm=TRUE))} else {NA}
Licor_run_time_first <- if(sw$use_Licor) {as.POSIXct(min(Licor_time, na.rm=TRUE))} else {NA}
Licor_run_time_last <- if(sw$use_Licor) {as.POSIXct(max(Licor_time, na.rm=TRUE))} else {NA}
##details<<
## Report first and last times.
if(sw$use_TDL ) {
p_o <- paste(" TDL first and last run times are ",
TDL_run_time_first,
" to ",
TDL_run_time_last,
"\n"); write_out(p_o);
}
if(sw$use_Licor) {
p_o <- paste(" Licor first and last run times are ",
Licor_run_time_first,
" to ",
Licor_run_time_last,
"\n"); write_out(p_o);
}
##details<<
## Indicate the time window specified.
time_window_first <-
if(!is.na(val_timewindow$start_time)) {if((val_timewindow$start_time > 0)) {as.POSIXct(val_timewindow$start_time)} else {NA}} else {NA};
time_window_last <-
if(!is.na(val_timewindow$end_time)) {if((val_timewindow$end_time > 0)) {as.POSIXct(val_timewindow$end_time)} else {NA}} else {NA};
p_o <- paste(" Specified time window times are ",
if(!is.na(time_window_first)) {time_window_first} else {"_BEGIN_"} ,
" to ",
if(!is.na(time_window_last)) {time_window_last} else {"_END_"} ,
"\n"); write_out(p_o);
if (!is.na(time_window_first) & !is.na(time_window_last)) {
if ( time_window_first >= time_window_last ) {
p_o <- paste("ERROR -- ERROR -- Time Window start time is after end time \n"); write_out(p_o);
return (NULL);
}
}
##details<<
## Set TDL and Licor times to NA outside the time window.
TDL_time_window <- TDL_time;
TDL_time_window [(TDL_time_window < time_window_first)] <- NA;
TDL_time_window [(TDL_time_window > time_window_last )] <- NA;
Licor_time_window <- Licor_time;
Licor_time_window[(Licor_time_window < time_window_first)] <- NA;
Licor_time_window[(Licor_time_window > time_window_last )] <- NA;
##details<<
## Indicate the first and last matching TDL and Licor times in time window.
if (sw$use_TDL & sw$use_Licor) {
# clumbsy: running these min/max lines repeatedly matches them up
for (ii in 1:20) {
# Set TDL and Licor times to NA outside the other (Licor and TDL) times
Licor_time_window[(Licor_time_window < min(TDL_time_window,na.rm=TRUE) )] <- NA;
Licor_time_window[(Licor_time_window > max(TDL_time_window,na.rm=TRUE) )] <- NA;
TDL_time_window [(TDL_time_window < min(Licor_time_window,na.rm=TRUE))] <- NA;
TDL_time_window [(TDL_time_window > max(Licor_time_window,na.rm=TRUE))] <- NA;
}
## The above code works (looping over min/max), but something like below would be better.
## Want to match the lowest common time and the highest common time
# TinL <- TDL_time_window %in% Licor_time_window; # indices in TDL also in Licor
# LinT <- Licor_time_window %in% TDL_time_window;
#
# # indices of first and last in overlap window
# temp_TDL_time_ind_first <- min(seq(1,TDL_n)[TinL]) ;
# temp_TDL_time_ind_last <- max(seq(1,TDL_n)[TinL]) ;
# temp_Licor_time_ind_first <- min(seq(1,Licor_n)[LinT]);
# temp_Licor_time_ind_last <- max(seq(1,Licor_n)[LinT]);
#
# # report first and last matching times
# p_o <- paste(" First matching time TDL=",
# TDL_time[temp_TDL_time_ind_first],
# ", Licor=",
# Licor_time[temp_Licor_time_ind_first], "\n"); write_out(p_o);
# p_o <- paste(" Last matching time TDL=",
# TDL_time[temp_TDL_time_ind_last],
# ", Licor=",
# Licor_time[temp_Licor_time_ind_last], "\n"); write_out(p_o);
}
if (sw$use_TDL) {
if (sum(!is.na(TDL_time_window))==0) {
p_o <- paste("ERROR -- ERROR -- no TDL times overlapping with Licor and time window \n"); write_out(p_o);
return (NULL);
} else {
TDL_time_window_first <- min(TDL_time_window,na.rm=TRUE);
TDL_time_window_last <- max(TDL_time_window,na.rm=TRUE);
}
}
if (sw$use_Licor) {
if (sum(!is.na(Licor_time_window))==0) {
p_o <- paste("ERROR -- ERROR -- no Licor times overlapping with TDL and time window \n"); write_out(p_o);
return (NULL);
} else {
Licor_time_window_first <- min(Licor_time_window,na.rm=TRUE);
Licor_time_window_last <- max(Licor_time_window,na.rm=TRUE);
}
}
if (sw$use_TDL & sw$use_Licor) {
##details<<
## Check that TDL and Licor first and last times are identical.
if (!(TDL_time_window_first == Licor_time_window_first)) {
p_o <- paste("WARNING: first time window times don't match, are - ",
"TDL:", TDL_time_window_first,
", Licor:", Licor_time_window_first,
"\n"); write_out(p_o);
}
if (!(TDL_time_window_last == Licor_time_window_last)) {
p_o <- paste("WARNING: last time window times don't match, are - ",
"TDL:", TDL_time_window_last,
", Licor:", Licor_time_window_last,
"\n"); write_out(p_o);
}
}
##details<<
## Indices for first and last times in TDL and Licor files.
if (sw$use_TDL) {
TDL_time_ind_first <- seq(1,TDL_n )[(!is.na(TDL_time ) & (TDL_time == TDL_time_window_first ))];
TDL_time_ind_last <- seq(1,TDL_n )[(!is.na(TDL_time ) & (TDL_time == TDL_time_window_last ))];
p_o <- paste(" TDL first and last times used are ",
"index ", TDL_time_ind_first, " time ", TDL_time_window_first,
" to ",
"index ", TDL_time_ind_last, " time ", TDL_time_window_last,
"\n"); write_out(p_o);
} else {
TDL_time_ind_first <- NA;
TDL_time_ind_last <- NA;
}
if (sw$use_Licor) {
Licor_time_ind_first <- seq(1,Licor_n)[(!is.na(Licor_time) & (Licor_time == Licor_time_window_first))];
Licor_time_ind_last <- seq(1,Licor_n)[(!is.na(Licor_time) & (Licor_time == Licor_time_window_last ))];
p_o <- paste(" Licor first and last times used are ",
"index ", Licor_time_ind_first, " time ", Licor_time_window_first,
" to ",
"index ", Licor_time_ind_last, " time ", Licor_time_window_last,
"\n"); write_out(p_o);
} else {
Licor_time_ind_first <- NA;
Licor_time_ind_last <- NA;
}
if (sw$use_TDL & sw$use_Licor) {
TDL_time_points <- TDL_time_ind_last - TDL_time_ind_first ;
Licor_time_points <- Licor_time_ind_last - Licor_time_ind_first;
p_o <- paste(" On average there are roughly", format(TDL_time_points/Licor_time_points, digits=4), "TDL timepoints per Licor timepoint.", "\n"); write_out(p_o);
} # if TDL & Licor
# Time overlap 9/8/2011
##details<<
## Use narrower timewindow start and end times, if specified.
window_start <-
max(c(
if(sw$use_TDL ) {as.POSIXct(TDL_time_window_first )} else {NA}
, if(sw$use_Licor) {as.POSIXct(Licor_time_window_first)} else {NA}
), na.rm=TRUE);
window_end <-
min(c(
if(sw$use_TDL ) {as.POSIXct(TDL_time_window_last )} else {NA}
, if(sw$use_Licor) {as.POSIXct(Licor_time_window_last)} else {NA}
), na.rm=TRUE);
p_o <- paste(" Time window used for analysis is: ", window_start, " to ", window_end, ".", "\n"); write_out(p_o);
## all new code above, 10/4/2011
## commented code (at bottom) was removed from here on 10/4/2011
TDL_Licor_times <- list(); # create a list to return with data
TDL_Licor_times$TDL_time_ind_first <- TDL_time_ind_first ;
TDL_Licor_times$TDL_time_ind_last <- TDL_time_ind_last ;
TDL_Licor_times$Licor_time_ind_first <- Licor_time_ind_first ;
TDL_Licor_times$Licor_time_ind_last <- Licor_time_ind_last ;
return( TDL_Licor_times );
### TDL_Licor_times
}
## commented 10/4/2011, new code is above
# if (sw$use_TDL & sw$use_Licor) {
#
# ## pre-timewindow way of finding start/end times 9/8/2011
# # indices of overlap window for each file
# TinL <- TDL_time %in% Licor_time; # indices in TDL also in Licor
# LinT <- Licor_time %in% TDL_time;
#
# if ( (sum(TinL) == 0) || (sum(LinT) == 0) ) {
# p_o <- paste("ERROR -- ERROR -- TDL and Licor times do not overlap \n"); write_out(p_o);
# return (NULL);
# }
#
# # indices of first and last in overlap window
# temp_TDL_time_ind_first <- min(seq(1,TDL_n)[TinL]) ;
# temp_TDL_time_ind_last <- max(seq(1,TDL_n)[TinL]) ;
# temp_Licor_time_ind_first <- min(seq(1,Licor_n)[LinT]);
# temp_Licor_time_ind_last <- max(seq(1,Licor_n)[LinT]);
#
# # report first and last matching times
# p_o <- paste(" First matching time TDL=",
# TDL_time[temp_TDL_time_ind_first],
# ", Licor=",
# Licor_time[temp_Licor_time_ind_first], "\n"); write_out(p_o);
# p_o <- paste(" Last matching time TDL=",
# TDL_time[temp_TDL_time_ind_last],
# ", Licor=",
# Licor_time[temp_Licor_time_ind_last], "\n"); write_out(p_o);
#
# TDL_time_points <- temp_TDL_time_ind_last - temp_TDL_time_ind_first ;
# Licor_time_points <- temp_Licor_time_ind_last - temp_Licor_time_ind_first;
# p_o <- paste(" On average there are roughly", format(TDL_time_points/Licor_time_points, digits=4), "TDL timepoints per Licor timepoint.", "\n"); write_out(p_o);
#
# # # Time overlap 9/8/2011
# # # use timewindow start time
# # if ((val_timewindow$start_time > 0) & !is.na(val_timewindow$start_time)) {
# # window_start <-
# # max(c(
# # as.POSIXct(min(TDL_time, na.rm=TRUE))
# # , as.POSIXct(min(Licor_time, na.rm=TRUE))
# # , as.POSIXct(val_timewindow$start_time)
# # ));
# # } else {
# # window_start <-
# # max(c(
# # as.POSIXct(min(TDL_time, na.rm=TRUE))
# # , as.POSIXct(min(Licor_time, na.rm=TRUE))
# # ));
# # };
# #
# # if ((val_timewindow$end_time > 0) & !is.na(val_timewindow$end_time)) {
# # window_end <-
# # min(c(
# # as.POSIXct(max(TDL_time, na.rm=TRUE))
# # , as.POSIXct(max(Licor_time, na.rm=TRUE))
# # , as.POSIXct(val_timewindow$end_time)
# # ));
# # } else {
# # window_end <-
# # min(c(
# # as.POSIXct(max(TDL_time, na.rm=TRUE))
# # , as.POSIXct(max(Licor_time, na.rm=TRUE))
# # ));
# # };
# #
# # if ( window_start >= window_end ) {
# # p_o <- paste("ERROR -- ERROR -- Time Window start time is after end time \n"); write_out(p_o);
# # return (NULL);
# # }
# #
# # # indices of first and last in overlap window
# # TDL_time_ind_first <- min(seq(1,TDL_n)[!is.na(TDL_time)][TDL_time[!is.na(TDL_time)] >= window_start]);
# # TDL_time_ind_last <- max(seq(1,TDL_n)[!is.na(TDL_time)][TDL_time[!is.na(TDL_time)] <= window_end ]);
# # Licor_time_ind_first <- min(seq(1,Licor_n)[!is.na(Licor_time)][Licor_time[!is.na(Licor_time)] >= window_start]);
# # Licor_time_ind_last <- max(seq(1,Licor_n)[!is.na(Licor_time)][Licor_time[!is.na(Licor_time)] <= window_end ]);
# #
# # p_o <- paste(" Time window used for analysis is: ", window_start, " to ", window_end, ".", "\n"); write_out(p_o);
#
# } # if TDL & Licor
#
# # if (sw$use_TDL & (sw$use_Licor==0)) { # TDL data only
# # TDL_time_ind_first <- 1;
# # TDL_time_ind_last <- TDL_n;
# # Licor_time_ind_first <- NA;
# # Licor_time_ind_last <- NA;
# # };
# # if ((sw$use_TDL==0) & sw$use_Licor) { # Licor data only
# # TDL_time_ind_first <- NA;
# # TDL_time_ind_last <- NA;
# # Licor_time_ind_first <- 1;
# # Licor_time_ind_last <- Licor_n;
# # };
#
# # 10/2/2011 1:59PM
# # When sites are specified in TDL file that are not in the template file (because more than 4 sites are used),
# # then there are NAs for times for used sites. In this case, the matching times above may be different
# # from the min/max times below. In this case, we should use the matching times (that is, always use the matching times)
# # otherwise errors result from NA times in time_window_TDL_Licor_interp().
# # The logic is: use the widest matching times within the timewindow.
#
# # Time overlap 9/8/2011
# # use timewindow start time
# window_start <-
# max(c(
# if(sw$use_TDL ) {as.POSIXct(min(TDL_time , na.rm=TRUE))} else {NA}
# , if(sw$use_Licor) {as.POSIXct(min(Licor_time, na.rm=TRUE))} else {NA}
# , if(!is.na(val_timewindow$start_time)) {if((val_timewindow$start_time > 0)) {as.POSIXct(val_timewindow$start_time)} else {NA}} else {NA}
# ), na.rm=TRUE);
# window_end <-
# min(c(
# if(sw$use_TDL ) {as.POSIXct(max(TDL_time , na.rm=TRUE))} else {NA}
# , if(sw$use_Licor) {as.POSIXct(max(Licor_time, na.rm=TRUE))} else {NA}
# , if(!is.na(val_timewindow$end_time)) {if((val_timewindow$end_time > 0)) {as.POSIXct(val_timewindow$end_time)} else {NA}} else {NA}
# ), na.rm=TRUE);
#
# if ( window_start >= window_end ) {
# p_o <- paste("ERROR -- ERROR -- Time Window start time is after end time \n"); write_out(p_o);
# return (NULL);
# }
#
# p_o <- paste(" Time window used for analysis is: ", window_start, " to ", window_end, ".", "\n"); write_out(p_o);
#
# # indices of first and last in overlap window
# if (sw$use_TDL) { # TDL
# TDL_time_ind_first <- min(seq(1,TDL_n)[!is.na(TDL_time)][TDL_time[!is.na(TDL_time)] >= window_start]);
# TDL_time_ind_last <- max(seq(1,TDL_n)[!is.na(TDL_time)][TDL_time[!is.na(TDL_time)] <= window_end ]);
# } else {
# TDL_time_ind_first <- NA;
# TDL_time_ind_last <- NA;
# };
# if (sw$use_Licor) { # Licor
# Licor_time_ind_first <- min(seq(1,Licor_n)[!is.na(Licor_time)][Licor_time[!is.na(Licor_time)] >= window_start]);
# Licor_time_ind_last <- max(seq(1,Licor_n)[!is.na(Licor_time)][Licor_time[!is.na(Licor_time)] <= window_end ]);
# } else {
# Licor_time_ind_first <- NA;
# Licor_time_ind_last <- NA;
# };
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#' Find the overlapping time window of the TDL and Licor files and return the start/end indices of each file
#'
#' Unused sites (comment):
#' When sites are specified in TDL file that are not in the template file (because more than 4 sites are used),
#' then there are NAs for times for used sites. In this case, the matching times above may be different
#' from the min/max times below. In this case, we should use the matching times (that is, always use the matching times)
#' otherwise errors result from NA times in \code{\link{time_window_TDL_Licor_interp}}.
#' The logic is: use the widest matching times within the timewindow.
#'
#' Indicate first and last times for TDL and Licor.
#'
#' Report first and last times.
#'
#' Indicate the time window specified.
#'
#' Set TDL and Licor times to NA outside the time window.
#'
#' Indicate the first and last matching TDL and Licor times in time window.
#'
#' Check that TDL and Licor first and last times are identical.
#'
#' Indices for first and last times in TDL and Licor files.
#'
#' Use narrower timewindow start and end times, if specified.
#'
#' @param TDL_time xxxPARAMxxx
#' @param TDL_n xxxPARAMxxx
#' @param Licor_time xxxPARAMxxx
#' @param Licor_n xxxPARAMxxx
#' @param val_timewindow xxxPARAMxxx
#' @param sw xxxPARAMxxx
#'
#' @return TDL_Licor_times xxxRETURNxxx
#'
align_TDL_Licor_times <-
function# find the overlapping time window of the TDL and Licor files and return the start/end indices of each file
###
(TDL_time
###
, TDL_n
###
, Licor_time
###
, Licor_n
###
, val_timewindow
###
, sw
###
)
{
# DEBUGGING
# TDL_time <- TDL$time ;
# TDL_n <- TDL$n ;
# Licor_time <- Licor$time ;
# Licor_n <- Licor$n ;
# val_timewindow <- val$timewindow ;
# 10/2/2011 1:59PM
##details<<
## Unused sites (comment):
## When sites are specified in TDL file that are not in the template file (because more than 4 sites are used),
## then there are NAs for times for used sites. In this case, the matching times above may be different
## from the min/max times below. In this case, we should use the matching times (that is, always use the matching times)
## otherwise errors result from NA times in \code{\link{time_window_TDL_Licor_interp}}.
## The logic is: use the widest matching times within the timewindow.
##details<<
## Indicate first and last times for TDL and Licor.
TDL_run_time_first <- if(sw$use_TDL ) {as.POSIXct(min(TDL_time , na.rm=TRUE))} else {NA}
TDL_run_time_last <- if(sw$use_TDL ) {as.POSIXct(max(TDL_time , na.rm=TRUE))} else {NA}
Licor_run_time_first <- if(sw$use_Licor) {as.POSIXct(min(Licor_time, na.rm=TRUE))} else {NA}
Licor_run_time_last <- if(sw$use_Licor) {as.POSIXct(max(Licor_time, na.rm=TRUE))} else {NA}
##details<<
## Report first and last times.
if(sw$use_TDL ) {
p_o <- paste(" TDL first and last run times are ",
TDL_run_time_first,
" to ",
TDL_run_time_last,
"\n"); write_out(p_o);
}
if(sw$use_Licor) {
p_o <- paste(" Licor first and last run times are ",
Licor_run_time_first,
" to ",
Licor_run_time_last,
"\n"); write_out(p_o);
}
##details<<
## Indicate the time window specified.
time_window_first <-
if(!is.na(val_timewindow$start_time)) {if((val_timewindow$start_time > 0)) {as.POSIXct(val_timewindow$start_time)} else {NA}} else {NA};
time_window_last <-
if(!is.na(val_timewindow$end_time)) {if((val_timewindow$end_time > 0)) {as.POSIXct(val_timewindow$end_time)} else {NA}} else {NA};
p_o <- paste(" Specified time window times are ",
if(!is.na(time_window_first)) {time_window_first} else {"_BEGIN_"} ,
" to ",
if(!is.na(time_window_last)) {time_window_last} else {"_END_"} ,
"\n"); write_out(p_o);
if (!is.na(time_window_first) & !is.na(time_window_last)) {
if ( time_window_first >= time_window_last ) {
p_o <- paste("ERROR -- ERROR -- Time Window start time is after end time \n"); write_out(p_o);
return (NULL);
}
}
##details<<
## Set TDL and Licor times to NA outside the time window.
TDL_time_window <- TDL_time;
TDL_time_window [(TDL_time_window < time_window_first)] <- NA;
TDL_time_window [(TDL_time_window > time_window_last )] <- NA;
Licor_time_window <- Licor_time;
Licor_time_window[(Licor_time_window < time_window_first)] <- NA;
Licor_time_window[(Licor_time_window > time_window_last )] <- NA;
##details<<
## Indicate the first and last matching TDL and Licor times in time window.
if (sw$use_TDL & sw$use_Licor) {
# clumbsy: running these min/max lines repeatedly matches them up
for (ii in 1:20) {
# Set TDL and Licor times to NA outside the other (Licor and TDL) times
Licor_time_window[(Licor_time_window < min(TDL_time_window,na.rm=TRUE) )] <- NA;
Licor_time_window[(Licor_time_window > max(TDL_time_window,na.rm=TRUE) )] <- NA;
TDL_time_window [(TDL_time_window < min(Licor_time_window,na.rm=TRUE))] <- NA;
TDL_time_window [(TDL_time_window > max(Licor_time_window,na.rm=TRUE))] <- NA;
}
## The above code works (looping over min/max), but something like below would be better.
## Want to match the lowest common time and the highest common time
# TinL <- TDL_time_window %in% Licor_time_window; # indices in TDL also in Licor
# LinT <- Licor_time_window %in% TDL_time_window;
#
# # indices of first and last in overlap window
# temp_TDL_time_ind_first <- min(seq(1,TDL_n)[TinL]) ;
# temp_TDL_time_ind_last <- max(seq(1,TDL_n)[TinL]) ;
# temp_Licor_time_ind_first <- min(seq(1,Licor_n)[LinT]);
# temp_Licor_time_ind_last <- max(seq(1,Licor_n)[LinT]);
#
# # report first and last matching times
# p_o <- paste(" First matching time TDL=",
# TDL_time[temp_TDL_time_ind_first],
# ", Licor=",
# Licor_time[temp_Licor_time_ind_first], "\n"); write_out(p_o);
# p_o <- paste(" Last matching time TDL=",
# TDL_time[temp_TDL_time_ind_last],
# ", Licor=",
# Licor_time[temp_Licor_time_ind_last], "\n"); write_out(p_o);
}
if (sw$use_TDL) {
if (sum(!is.na(TDL_time_window))==0) {
p_o <- paste("ERROR -- ERROR -- no TDL times overlapping with Licor and time window \n"); write_out(p_o);
return (NULL);
} else {
TDL_time_window_first <- min(TDL_time_window,na.rm=TRUE);
TDL_time_window_last <- max(TDL_time_window,na.rm=TRUE);
}
}
if (sw$use_Licor) {
if (sum(!is.na(Licor_time_window))==0) {
p_o <- paste("ERROR -- ERROR -- no Licor times overlapping with TDL and time window \n"); write_out(p_o);
return (NULL);
} else {
Licor_time_window_first <- min(Licor_time_window,na.rm=TRUE);
Licor_time_window_last <- max(Licor_time_window,na.rm=TRUE);
}
}
if (sw$use_TDL & sw$use_Licor) {
##details<<
## Check that TDL and Licor first and last times are identical.
if (!(TDL_time_window_first == Licor_time_window_first)) {
p_o <- paste("WARNING: first time window times don't match, are - ",
"TDL:", TDL_time_window_first,
", Licor:", Licor_time_window_first,
"\n"); write_out(p_o);
}
if (!(TDL_time_window_last == Licor_time_window_last)) {
p_o <- paste("WARNING: last time window times don't match, are - ",
"TDL:", TDL_time_window_last,
", Licor:", Licor_time_window_last,
"\n"); write_out(p_o);
}
}
##details<<
## Indices for first and last times in TDL and Licor files.
if (sw$use_TDL) {
TDL_time_ind_first <- seq(1,TDL_n )[(!is.na(TDL_time ) & (TDL_time == TDL_time_window_first ))];
TDL_time_ind_last <- seq(1,TDL_n )[(!is.na(TDL_time ) & (TDL_time == TDL_time_window_last ))];
p_o <- paste(" TDL first and last times used are ",
"index ", TDL_time_ind_first, " time ", TDL_time_window_first,
" to ",
"index ", TDL_time_ind_last, " time ", TDL_time_window_last,
"\n"); write_out(p_o);
} else {
TDL_time_ind_first <- NA;
TDL_time_ind_last <- NA;
}
if (sw$use_Licor) {
Licor_time_ind_first <- seq(1,Licor_n)[(!is.na(Licor_time) & (Licor_time == Licor_time_window_first))];
Licor_time_ind_last <- seq(1,Licor_n)[(!is.na(Licor_time) & (Licor_time == Licor_time_window_last ))];
p_o <- paste(" Licor first and last times used are ",
"index ", Licor_time_ind_first, " time ", Licor_time_window_first,
" to ",
"index ", Licor_time_ind_last, " time ", Licor_time_window_last,
"\n"); write_out(p_o);
} else {
Licor_time_ind_first <- NA;
Licor_time_ind_last <- NA;
}
if (sw$use_TDL & sw$use_Licor) {
TDL_time_points <- TDL_time_ind_last - TDL_time_ind_first ;
Licor_time_points <- Licor_time_ind_last - Licor_time_ind_first;
p_o <- paste(" On average there are roughly", format(TDL_time_points/Licor_time_points, digits=4), "TDL timepoints per Licor timepoint.", "\n"); write_out(p_o);
} # if TDL & Licor
# Time overlap 9/8/2011
##details<<
## Use narrower timewindow start and end times, if specified.
window_start <-
max(c(
if(sw$use_TDL ) {as.POSIXct(TDL_time_window_first )} else {NA}
, if(sw$use_Licor) {as.POSIXct(Licor_time_window_first)} else {NA}
), na.rm=TRUE);
window_end <-
min(c(
if(sw$use_TDL ) {as.POSIXct(TDL_time_window_last )} else {NA}
, if(sw$use_Licor) {as.POSIXct(Licor_time_window_last)} else {NA}
), na.rm=TRUE);
p_o <- paste(" Time window used for analysis is: ", window_start, " to ", window_end, ".", "\n"); write_out(p_o);
## all new code above, 10/4/2011
## commented code (at bottom) was removed from here on 10/4/2011
TDL_Licor_times <- list(); # create a list to return with data
TDL_Licor_times$TDL_time_ind_first <- TDL_time_ind_first ;
TDL_Licor_times$TDL_time_ind_last <- TDL_time_ind_last ;
TDL_Licor_times$Licor_time_ind_first <- Licor_time_ind_first ;
TDL_Licor_times$Licor_time_ind_last <- Licor_time_ind_last ;
return( TDL_Licor_times );
### TDL_Licor_times
}
## commented 10/4/2011, new code is above
# if (sw$use_TDL & sw$use_Licor) {
#
# ## pre-timewindow way of finding start/end times 9/8/2011
# # indices of overlap window for each file
# TinL <- TDL_time %in% Licor_time; # indices in TDL also in Licor
# LinT <- Licor_time %in% TDL_time;
#
# if ( (sum(TinL) == 0) || (sum(LinT) == 0) ) {
# p_o <- paste("ERROR -- ERROR -- TDL and Licor times do not overlap \n"); write_out(p_o);
# return (NULL);
# }
#
# # indices of first and last in overlap window
# temp_TDL_time_ind_first <- min(seq(1,TDL_n)[TinL]) ;
# temp_TDL_time_ind_last <- max(seq(1,TDL_n)[TinL]) ;
# temp_Licor_time_ind_first <- min(seq(1,Licor_n)[LinT]);
# temp_Licor_time_ind_last <- max(seq(1,Licor_n)[LinT]);
#
# # report first and last matching times
# p_o <- paste(" First matching time TDL=",
# TDL_time[temp_TDL_time_ind_first],
# ", Licor=",
# Licor_time[temp_Licor_time_ind_first], "\n"); write_out(p_o);
# p_o <- paste(" Last matching time TDL=",
# TDL_time[temp_TDL_time_ind_last],
# ", Licor=",
# Licor_time[temp_Licor_time_ind_last], "\n"); write_out(p_o);
#
# TDL_time_points <- temp_TDL_time_ind_last - temp_TDL_time_ind_first ;
# Licor_time_points <- temp_Licor_time_ind_last - temp_Licor_time_ind_first;
# p_o <- paste(" On average there are roughly", format(TDL_time_points/Licor_time_points, digits=4), "TDL timepoints per Licor timepoint.", "\n"); write_out(p_o);
#
# # # Time overlap 9/8/2011
# # # use timewindow start time
# # if ((val_timewindow$start_time > 0) & !is.na(val_timewindow$start_time)) {
# # window_start <-
# # max(c(
# # as.POSIXct(min(TDL_time, na.rm=TRUE))
# # , as.POSIXct(min(Licor_time, na.rm=TRUE))
# # , as.POSIXct(val_timewindow$start_time)
# # ));
# # } else {
# # window_start <-
# # max(c(
# # as.POSIXct(min(TDL_time, na.rm=TRUE))
# # , as.POSIXct(min(Licor_time, na.rm=TRUE))
# # ));
# # };
# #
# # if ((val_timewindow$end_time > 0) & !is.na(val_timewindow$end_time)) {
# # window_end <-
# # min(c(
# # as.POSIXct(max(TDL_time, na.rm=TRUE))
# # , as.POSIXct(max(Licor_time, na.rm=TRUE))
# # , as.POSIXct(val_timewindow$end_time)
# # ));
# # } else {
# # window_end <-
# # min(c(
# # as.POSIXct(max(TDL_time, na.rm=TRUE))
# # , as.POSIXct(max(Licor_time, na.rm=TRUE))
# # ));
# # };
# #
# # if ( window_start >= window_end ) {
# # p_o <- paste("ERROR -- ERROR -- Time Window start time is after end time \n"); write_out(p_o);
# # return (NULL);
# # }
# #
# # # indices of first and last in overlap window
# # TDL_time_ind_first <- min(seq(1,TDL_n)[!is.na(TDL_time)][TDL_time[!is.na(TDL_time)] >= window_start]);
# # TDL_time_ind_last <- max(seq(1,TDL_n)[!is.na(TDL_time)][TDL_time[!is.na(TDL_time)] <= window_end ]);
# # Licor_time_ind_first <- min(seq(1,Licor_n)[!is.na(Licor_time)][Licor_time[!is.na(Licor_time)] >= window_start]);
# # Licor_time_ind_last <- max(seq(1,Licor_n)[!is.na(Licor_time)][Licor_time[!is.na(Licor_time)] <= window_end ]);
# #
# # p_o <- paste(" Time window used for analysis is: ", window_start, " to ", window_end, ".", "\n"); write_out(p_o);
#
# } # if TDL & Licor
#
# # if (sw$use_TDL & (sw$use_Licor==0)) { # TDL data only
# # TDL_time_ind_first <- 1;
# # TDL_time_ind_last <- TDL_n;
# # Licor_time_ind_first <- NA;
# # Licor_time_ind_last <- NA;
# # };
# # if ((sw$use_TDL==0) & sw$use_Licor) { # Licor data only
# # TDL_time_ind_first <- NA;
# # TDL_time_ind_last <- NA;
# # Licor_time_ind_first <- 1;
# # Licor_time_ind_last <- Licor_n;
# # };
#
# # 10/2/2011 1:59PM
# # When sites are specified in TDL file that are not in the template file (because more than 4 sites are used),
# # then there are NAs for times for used sites. In this case, the matching times above may be different
# # from the min/max times below. In this case, we should use the matching times (that is, always use the matching times)
# # otherwise errors result from NA times in time_window_TDL_Licor_interp().
# # The logic is: use the widest matching times within the timewindow.
#
# # Time overlap 9/8/2011
# # use timewindow start time
# window_start <-
# max(c(
# if(sw$use_TDL ) {as.POSIXct(min(TDL_time , na.rm=TRUE))} else {NA}
# , if(sw$use_Licor) {as.POSIXct(min(Licor_time, na.rm=TRUE))} else {NA}
# , if(!is.na(val_timewindow$start_time)) {if((val_timewindow$start_time > 0)) {as.POSIXct(val_timewindow$start_time)} else {NA}} else {NA}
# ), na.rm=TRUE);
# window_end <-
# min(c(
# if(sw$use_TDL ) {as.POSIXct(max(TDL_time , na.rm=TRUE))} else {NA}
# , if(sw$use_Licor) {as.POSIXct(max(Licor_time, na.rm=TRUE))} else {NA}
# , if(!is.na(val_timewindow$end_time)) {if((val_timewindow$end_time > 0)) {as.POSIXct(val_timewindow$end_time)} else {NA}} else {NA}
# ), na.rm=TRUE);
#
# if ( window_start >= window_end ) {
# p_o <- paste("ERROR -- ERROR -- Time Window start time is after end time \n"); write_out(p_o);
# return (NULL);
# }
#
# p_o <- paste(" Time window used for analysis is: ", window_start, " to ", window_end, ".", "\n"); write_out(p_o);
#
# # indices of first and last in overlap window
# if (sw$use_TDL) { # TDL
# TDL_time_ind_first <- min(seq(1,TDL_n)[!is.na(TDL_time)][TDL_time[!is.na(TDL_time)] >= window_start]);
# TDL_time_ind_last <- max(seq(1,TDL_n)[!is.na(TDL_time)][TDL_time[!is.na(TDL_time)] <= window_end ]);
# } else {
# TDL_time_ind_first <- NA;
# TDL_time_ind_last <- NA;
# };
# if (sw$use_Licor) { # Licor
# Licor_time_ind_first <- min(seq(1,Licor_n)[!is.na(Licor_time)][Licor_time[!is.na(Licor_time)] >= window_start]);
# Licor_time_ind_last <- max(seq(1,Licor_n)[!is.na(Licor_time)][Licor_time[!is.na(Licor_time)] <= window_end ]);
# } else {
# Licor_time_ind_first <- NA;
# Licor_time_ind_last <- NA;
# };
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