diff --git a/NAMESPACE b/NAMESPACE index 35c790e..7efa390 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,13 +1,15 @@ # Generated by roxygen2 (4.1.0): do not edit by hand +S3method(aggregate_metab,swmpr) S3method(comb,swmpr) S3method(ecometab,swmpr) -S3method(plot_met,swmpr) +S3method(plot_metab,swmpr) S3method(setstep,swmpr) export(aggregate.swmpr) +export(aggregate_metab) export(all_params) export(all_params_dtrng) -export(calcKL) +export(calckl) export(comb) export(decomp) export(decomp.swmpr) @@ -18,12 +20,12 @@ export(hist.swmpr) export(import_local) export(lines.swmpr) export(map_reserve) -export(met_day) +export(metab_day) export(na.approx.swmpr) export(param_names) export(parser) export(plot.swmpr) -export(plot_met) +export(plot_metab) export(plot_summary) export(plot_summary.swmpr) export(qaqc) diff --git a/R/swmpr_analyze.R b/R/swmpr_analyze.R index 95883ea..cfa1a87 100644 --- a/R/swmpr_analyze.R +++ b/R/swmpr_analyze.R @@ -119,6 +119,103 @@ aggregate.swmpr <- function(x, by, FUN = function(x) mean(x, na.rm = TRUE), para } +#' Aggregate metabolism data +#' +#' Aggregate a metabolism attribute from swmpr data by a specified time period and method +#' +#' @param swmpr_in input swmpr object +#' @param by chr string of time period for aggregation one of \code{'years'}, \code{'quarters'}, \code{'months'}, \code{'weeks'}, \code{'days'}, or \code{'hours'} +#' @param na.action function for treating missing data, default \code{na.pass} +#' @param alpha numeric indicating alpha level of confidence interval for aggregated data +#' @param ... additional arguments passed to other methods +#' +#' @import data.table +#' +#' @export +#' +#' @details The function summarizes metabolism data by averaging across set periods of observation. Confidence intervals are also returned based on the specified alpha level. It is used within \code{\link{plot_metab}} function to view summarized metabolism results. Data can be aggregated by \code{'years'}, \code{'quarters'}, \code{'months'}, or \code{'weeks'} for the supplied function, which defaults to the \code{\link[base]{mean}}. The method of treating NA values for the user-supplied function should be noted since this may greatly affect the quantity of data that are returned. +#' +#' @return Returns an aggregated metabolism \code{\link[base]{data.frame}} if the \code{metabolism} attribute of the swmpr object is not \code{NULL}. +#' +#' @seealso \code{\link[stats]{aggregate}}, \code{\link{aggregate.swmpr}}, \code{\link{ecometab}}, \code{\link{plot_metab}} +#' +#' @examples +#' ## import water quality and weather data +#' data(apadbwq) +#' data(apaebmet) +#' +#' ## qaqc, combine +#' wq <- qaqc(apadbwq) +#' met <- qaqc(apaebmet) +#' dat <- comb(wq, met) +#' +#' ## estimate metabolism +#' res <- ecometab(dat, trace = TRUE) +#' +#' ## aggregate metabolism +#' aggregate_metab(res, by = 'weeks') +#' +#' ## change aggregatin period and alpha +#' aggregate_metab(res, by = 'months', alpha = 0.1) +aggregate_metab <- function(swmpr_in, ...) UseMethod('aggregate_metab') + +#' @rdname aggregate_metab +#' +#' @export +#' +#' @method aggregate_metab swmpr +aggregate_metab.swmpr <- function(swmpr_in, by = 'weeks', na.action = na.pass, alpha = 0.05, ...){ + + # attributes + timezone <- attr(swmpr_in, 'timezone') + metabolism <- attr(swmpr_in, 'metabolism') + + # sanity checks + if(is.null(metabolism)) + stop('No metabolism data, use the ecometab function') + if(!by %in% c('years', 'quarters', 'months', 'weeks', 'days')) + stop('Unknown value for by, see help documentation') + + # data + to_agg <- metabolism + to_agg <- to_agg[, names(to_agg) %in% c('date', 'Pg', 'Rt', 'NEM')] + + # create agg values from date + if(by != 'days'){ + to_agg$date <- round( + data.table::as.IDate(to_agg$date, tz = timezone), + digits = by + ) + to_agg$date <- base::as.Date(to_agg$date, tz = timezone) + } + + # long-form + to_agg <- tidyr::gather(to_agg, Estimate, Value, -date) + to_agg$Estimate <- as.character(to_agg$Estimate) + + # aggregate + sum_fun <- function(x, alpha_in = alpha, out){ + x <- na.omit(x) + means <- mean(x) + margs <- suppressWarnings( + qt(1 - alpha_in/2, length(x) - 1) * sd(x)/sqrt(length(x)) + ) + upper <- means + margs + lower <- means - margs + return(get(out)) + } + aggs <- dplyr::group_by(to_agg, date, Estimate) + aggs <- dplyr::summarize(aggs, + means = sum_fun(Value, out = 'means'), + lower = sum_fun(Value, out = 'lower'), + upper = sum_fun(Value, out = 'upper') + ) + + # return output + return(aggs) + +} + #' Smooth swmpr data #' #' Smooth swmpr data with a moving window average @@ -542,7 +639,7 @@ plot.swmpr <- function(x, type = 'l', ...) { if(attr(swmpr_in, 'qaqc_cols')) swmpr_in <- qaqc(swmpr_in, qaqc_keep = NULL) - if(ncol(swmpr_in) > 2) stop('Only one parameter can be plotted') + if(ncol(swmpr_in) > 2) stop('Specify the parameter to plot') parameters <- attr(swmpr_in, 'parameters') @@ -860,24 +957,20 @@ plot_summary.swmpr <- function(swmpr_in, param, years = NULL, ...){ #' #' @param swmpr_in Input swmpr object which must include time series of dissolved oxygen, #' @param depth_val numeric value for station depth if time series is not available -#' @param met_units chr indicating units of output for oxygen, either as mmol or grams +#' @param metab_units chr indicating units of output for oxygen, either as mmol or grams #' @param trace logical indicating if progress is shown in the console #' @param ... arguments passed to other methods #' #' @return The original \code{\link{swmpr}} object is returned that includes a metabolism attribute as a \code{\link[base]{data.frame}} of daily integrated metabolism estimates. See the examples for retrieval. #' \describe{ #' \item{\code{date}}{The metabolic day for each estimate, defined as the approximate 24 hour period between sunsets on adjacent calendar days.} -#' \item{\code{ddo}}{Mean hourly rate of change for DO, mmol/m3/hr} -#' \item{\code{D}}{Mean air-sea gas exchange of DO, mmol/m2/hr} #' \item{\code{DOF_d}}{Mean DO flux during day hours, mmol/m2/hr} #' \item{\code{D_d}}{Mean air-sea gas exchange of DO during day hours, mmol/m2/hr} #' \item{\code{DOF_n}}{Mean DO flux during night hours, mmol/m2/hr} #' \item{\code{D_n}}{Mean air-sea gas exchange of DO during night hours, mmol/m2/hr} -#' \item{\code{Pg}}{Gross production, O2 mmol/m2/d} -#' \item{\code{Rt}}{Total respiration, O2 mmol/m2/d} -#' \item{\code{NEM}}{Net ecosytem metabolism, O2 mmol/m2/d} -#' \item{\code{Pg_vol}}{Volumetric gross production, O2 mmol/m3/d} -#' \item{\code{Rt_vol}}{Volumetric total respiration, O2 mmold/m3/d} +#' \item{\code{Pg}}{Gross production, O2 mmol/m2/d, calculated as ((DOF_d - D_d) - (DOF_n - D_n)) * day hours} +#' \item{\code{Rt}}{Total respiration, O2 mmol/m2/d, calculated as (DOF_n - D_n) * 24} +#' \item{\code{NEM}}{Net ecosytem metabolism, O2 mmol/m2/d, calculated as Pg + Rt} #' } #' #' @import oce reshape2 wq @@ -887,15 +980,15 @@ plot_summary.swmpr <- function(swmpr_in, param, years = NULL, ...){ #' @details #' Input data must be combined water quality and weather datasets. This is typically done using the \code{\link{comb}} function after creating separate swmpr objects. #' -#' The open-water method is a common approach to quantify net ecosystem metabolism using a mass balance equation that describes the change in dissolved oxygen over time from the balance between photosynthetic and respiration rates, corrected for air-sea gas diffusion at the surface. The air-sea gas exchange is estimated as the difference between the DO saturation concentration and observed DO concentration, multiplied by a volumetric reaeration coefficient (see the appendix in Thebault et al. 2008). The diffusion-corrected DO flux estimates are averaged during day and night for each 24 hour period in the time series, where flux is an hourly rate of DO change. DO flux is averaged during night hours for respiration and averaged during day hours for net production. Respiration rates are assumed constant during day and night such that total daily rates are calculated as hourly respiration multiplied by 24. The metabolic day is considered the approximate 24 hour period between sunsets on two adjacent calendar days. Respiration is subtracted from daily net production estimates to yield gross production. +#' The open-water method is a common approach to quantify net ecosystem metabolism using a mass balance equation that describes the change in dissolved oxygen over time from the balance between photosynthetic and respiration rates, corrected for air-sea gas diffusion at the surface. The air-sea gas exchange is estimated as the difference between the DO saturation concentration and observed DO concentration, multiplied by a volumetric reaeration coefficient (see the appendix in Thebault et al. 2008). The diffusion-corrected DO flux estimates are averaged during day and night for each 24 hour period in the time series, where flux is an hourly rate of DO change. DO flux is averaged during night hours for respiration and averaged during day hours for net production. Respiration rates are assumed constant during day and night such that total daily rates are calculated as hourly respiration multiplied by 24. The metabolic day is considered the 24 hour period between sunsets on two adjacent calendar days. Respiration is subtracted from daily net production estimates to yield gross production. #' -#' Volumetric rates for gross production and total respiration are based on total depth of the water column, which is assumed to be mixed. Water column depth is based on mean value for the depth variable across the time series in the \code{\link{swmpr}} object and is floored at 1 meter for very shallow stations. Additionally, the volumetric reaeration coefficient requires an estimate of the anemometer height of the weather station, which is set as 10 meters by default. The metadata should be consulted for exact height. The value can be changed manually using a \code{height} argument, which is passed to \code{\link{calcKL}}. +#' Aereal rates for gross production and total respiration are based on volumetric rates corrected for total depth of the water column, which is assumed to be mixed. Water column depth is based on mean value for the depth variable across the time series in the \code{\link{swmpr}} object and is floored at 1 meter for very shallow stations. Additionally, the volumetric reaeration coefficient requires an estimate of the anemometer height of the weather station, which is set as 10 meters by default. The metadata should be consulted for exact height. The value can be changed manually using a \code{height} argument, which is passed to \code{\link{calckl}}. #' #' Metabolism estimates are not returned for dates with less than three hourly records during either day or night periods. Missing values for air temperature, barometric pressure, and wind speed are replaced with the climatological means for the period of record. Climatological means are based on hourly average values by month. #' -#' All estimates are in mmol of oxygen but can be converted to grams by changing the default arguments (i.e., 1mmol O2 = 32 mg O2, 1000 mg = 1g, multiply all estimates by 32/1000). +#' All estimates are in mmol of oxygen but can be converted to grams by setting \code{metab_units = 'grams'} (i.e., 1mmol O2 = 32 mg O2, 1000 mg = 1g, multiply all estimates by 32/1000). #' -#' The specific approach for estimating metabolism is described in more detail in Caffrey et al. 2013. +#' The specific approach for estimating metabolism with the open-water method is described in more detail in Caffrey et al. 2013. #' #' @references #' Caffrey JM, Murrell MC, Amacker KS, Harper J, Phipps S, Woodrey M. 2013. Seasonal and inter-annual patterns in primary production, respiration and net ecosystem metabolism in 3 estuaries in the northeast Gulf of Mexico. Estuaries and Coasts. 37(1):222-241. @@ -905,7 +998,7 @@ plot_summary.swmpr <- function(swmpr_in, param, years = NULL, ...){ #' Thebault J, Schraga TS, Cloern JE, Dunlavey EG. 2008. Primary production and carrying capacity of former salt ponds after reconnection to San Francisco Bay. Wetlands. 28(3):841-851. #' #' @seealso -#' \code{\link{comb}}, \code{\link{plot_met}} +#' \code{\link{comb}}, \code{\link{plot_metab}} #' #' @examples #' ## import water quality and weather data @@ -925,7 +1018,7 @@ plot_summary.swmpr <- function(swmpr_in, param, years = NULL, ...){ #' res <- attr(res, 'metabolism') #' #' ## output units in grams of oxygen -#' res <- ecometab(dat, trace = TRUE, met_units = 'grams') +#' res <- ecometab(dat, trace = TRUE, metab_units = 'grams') #' res <- attr(res, 'metabolism') ecometab <- function(swmpr_in, ...) UseMethod('ecometab') @@ -934,12 +1027,12 @@ ecometab <- function(swmpr_in, ...) UseMethod('ecometab') #' @export #' #' @method ecometab swmpr -ecometab.swmpr <- function(swmpr_in, depth_val = NULL, met_units = 'mmol', trace = FALSE, ...){ +ecometab.swmpr <- function(swmpr_in, depth_val = NULL, metab_units = 'mmol', trace = FALSE, ...){ stat <- attr(swmpr_in, 'station') # stop if units not mmol or grams - if(any(!(grepl('mmol|grams', met_units)))) + if(any(!(grepl('mmol|grams', metab_units)))) stop('Units must be mmol or grams') # stop if input data does not include wq and met @@ -1026,11 +1119,11 @@ ecometab.swmpr <- function(swmpr_in, depth_val = NULL, met_units = 'mmol', trace H <- rep(mean(pmax(1, dat$depth), na.rm = T), nrow(dat)) else H <- rep(depth.val, nrow(dat)) - #use met_day to add columns indicating light/day, date, and hours of sunlight - dat <- met_day(dat, stat) + #use metab_day to add columns indicating light/day, date, and hours of sunlight + dat <- metab_day(dat, stat) #get air sea gas-exchange using wx data with climate means - KL <- with(dat, calcKL(temp, sal, atemp_mix, wspd_mix, bp_mix, ...)) + KL <- with(dat, calckl(temp, sal, atemp_mix, wspd_mix, bp_mix, ...)) rm(list = c('atemp_mix', 'wspd_mix', 'bp_mix')) #get volumetric reaeration coefficient from KL @@ -1040,12 +1133,12 @@ ecometab.swmpr <- function(swmpr_in, depth_val = NULL, met_units = 'mmol', trace D = Ka * (do / dosat - do) #combine all data for processing - proc_dat <- dat[, names(dat) %in% c('met_date', 'solar_period', 'day_hrs')] + proc_dat <- dat[, names(dat) %in% c('metab_date', 'solar_period', 'day_hrs')] proc_dat <- data.frame(proc_dat, ddo, H, D) #get daily/nightly flux estimates for Pg, Rt, NEM estimates out <- lapply( - split(proc_dat, proc_dat$met_date), + split(proc_dat, proc_dat$metab_date), function(x){ #filter for minimum no. of records @@ -1073,14 +1166,9 @@ ecometab.swmpr <- function(swmpr_in, depth_val = NULL, met_units = 'mmol', trace Pg_vol <- Pg / mean(x$H, na.rm = T) Rt_vol <- Rt / mean(x$H, na.rm = T) - #dep vars to take mean - var_out <- x[!names(x) %in% c('solar_period', 'solar_time', 'met_date', - 'day_hrs', 'H')] - var_out <- data.frame(rbind(apply(var_out, 2, function(x) mean(x, na.rm = T)))) - - data.frame(date = unique(x$met_date), - var_out, DOF_d, D_d, DOF_n, D_n, Pg, Rt, NEM, - Pg_vol, Rt_vol + # output + data.frame(date = unique(x$metab_date), + DOF_d, D_d, DOF_n, D_n, Pg, Rt, NEM ) } @@ -1090,7 +1178,7 @@ ecometab.swmpr <- function(swmpr_in, depth_val = NULL, met_units = 'mmol', trace row.names(out) <- 1:nrow(out) # change units to grams - if('grams' %in% met_units){ + if('grams' %in% metab_units){ # convert metab data to g m^-2 d^-1 # 1mmolO2 = 32 mg O2, 1000mg = 1g, multiply by 32/1000 @@ -1101,7 +1189,7 @@ ecometab.swmpr <- function(swmpr_in, depth_val = NULL, met_units = 'mmol', trace # append to metabolism attribute attr(swmpr_in, 'metabolism') <- out - attr(swmpr_in, 'met_units') <- met_units + attr(swmpr_in, 'metab_units') <- metab_units if(trace) tictoc::toc() @@ -1115,23 +1203,26 @@ ecometab.swmpr <- function(swmpr_in, depth_val = NULL, met_units = 'mmol', trace #' Plot gross production, total respiration, and net ecosystem metabolism for a swmpr object. #' #' @param swmpr_in input swmpr object +#' @param by chr string describing aggregation period, passed to \code{\link{aggregate_metab}}. See details for accepted values. +#' @param alpha numeric indicating alpha level for confidence intervals in aggregated data. Use \code{NULL} to remove from the plot. +#' @param width numeric indicating width of top and bottom segments on error bars #' @param pretty logical indicating use of predefined plot aesthetics -#' @param ... +#' @param ... arguments passed to or from other methods #' #' @export #' #' @import ggplot2 #' #' @details -#' A plot will only be returned if the \code{metabolism} attribute for the \code{\link{swmpr}} object is not \code{NULL}. The \code{\link{ecometab}} function is used to create metabolism estimates. See the examples. +#' A plot will only be returned if the \code{metabolism} attribute for the \code{\link{swmpr}} object is not \code{NULL}. Daily metabolism estimates are also aggregated into weekly averages. Accepted aggregation periods are \code{'years'}, \code{'quarters'}, \code{'months'}, \code{'weeks'}, and \code{'days'} (if no aggregation is preferred). #' -#' By default, \code{pretty = TRUE} will return a \code{\link[ggplot2]{ggplot}} object with predefined aesthetics. Setting \code{pretty = FALSE} will return the plot with minimal modifications to the \code{\link[ggplot2]{object}}. Use the latter approach for easier customization of the plot. +#' By default, \code{pretty = TRUE} will return a \code{\link[ggplot2]{ggplot}} object with predefined aesthetics. Setting \code{pretty = FALSE} will return the plot with minimal modifications to the \code{\link[ggplot2]{ggplot}} object. Use the latter approach for easier customization of the plot. #' #' @return #' A \code{\link[ggplot2]{ggplot}} object which can be further modified. #' #' @seealso -#' \code\link{ecometab} +#' \code{\link{aggregate_metab}}, \code{\link{ecometab}} #' #' @examples #' ## import water quality and weather data @@ -1147,47 +1238,63 @@ ecometab.swmpr <- function(swmpr_in, depth_val = NULL, met_units = 'mmol', trace #' res <- ecometab(dat, trace = TRUE) #' #' ## plot -#' plot_met(res) -plot_met <- function(swmpr_in, ...) UseMethod('plot_met') +#' plot_metab(res) +#' +#' ## change alpha, aggregation period, widths +#' plot_metab(res, by = 'quarters', alpha = 0.1, widths = 0) +#' +#' ## plot daily raw, no aesthetics +#' plot_metab(res, by = 'days', pretty = FALSE) +plot_metab <- function(swmpr_in, ...) UseMethod('plot_metab') -#' @rdname plot_met +#' @rdname plot_metab #' #' @export #' -#' @method plot_met swmpr -plot_met.swmpr <- function(swmpr_in, pretty = TRUE, ...){ +#' @method plot_metab swmpr +plot_metab.swmpr <- function(swmpr_in, by = 'months', alpha = 0.05, width = 10, pretty = TRUE, ...){ # get metabolism estimates metabolism <- attr(swmpr_in, 'metabolism') - met_units <- attr(swmpr_in, 'met_units') + metab_units <- attr(swmpr_in, 'metab_units') if(is.null(metabolism)) stop('No metabolism data, use the ecometab function') - # format for plotting - to_plo <- metabolism[, c('date', 'Pg', 'Rt', 'NEM')] - to_plo <- tidyr::gather(to_plo, Estimate, Value, -date) + # aggregate metab results by time period + to_plo <- aggregate_metab(swmpr_in, by = by, alpha = alpha) - # plot - p <- ggplot(to_plo, aes(x = date, y = Value, group = Estimate)) + + ## base plot + p <- ggplot(to_plo, aes(x = date, y = means, group = Estimate)) + geom_line() + # add bars if not days and alpha not null + if(by != 'days' & !is.null(alpha)) + p <- p + + geom_errorbar(aes(ymin = lower, ymax = upper, group = Estimate), + width = width) + + # return blank if(!pretty) return(p) # ylabs - ylab <- expression(paste('mmol ', O [2], ' ', m^-2, d^-1)) - if(met_units == 'grams') - ylab <- expression(paste('g ', O [2], ' ', m^-2, d^-1)) + ylabs <- expression(paste('mmol ', O [2], ' ', m^-2, d^-1)) + if(metab_units == 'grams') + ylabs <- expression(paste('g ', O [2], ' ', m^-2, d^-1)) p <- p + geom_line(aes(colour = Estimate)) + geom_point(aes(colour = Estimate)) + theme_bw() + - theme(axis.title.x = element_blank()) - scale_y_continuous(ylab) + theme(axis.title.x = element_blank()) + + scale_y_continuous(ylabs) + if(by != 'days' & !is.null(alpha)) + p <- p + + geom_errorbar(aes(ymin = lower, ymax = upper, + colour = Estimate, group = Estimate), width = width) + return(p) - } \ No newline at end of file diff --git a/R/swmpr_misc.R b/R/swmpr_misc.R index d7d21a6..0899b0a 100644 --- a/R/swmpr_misc.R +++ b/R/swmpr_misc.R @@ -11,7 +11,7 @@ #' @return Returns a swmpr object to be used with S3 methods #' #' @details -#' This function is a simple wrapper to \code{\link[base]{structure}} that is used internally within other functions to create a swmpr object. The function does not have to be used explicitly. Attributes of a swmpr object include \code{names}, \code{row.names}, \code{class}, \code{station}, \code{parameters}, \code{qaqc_cols}, \code{date_rng}, \code{timezone}, \code{stamp_class}, \code{metabolism} (if present), and \code{met_units} (if present). +#' This function is a simple wrapper to \code{\link[base]{structure}} that is used internally within other functions to create a swmpr object. The function does not have to be used explicitly. Attributes of a swmpr object include \code{names}, \code{row.names}, \code{class}, \code{station}, \code{parameters}, \code{qaqc_cols}, \code{date_rng}, \code{timezone}, \code{stamp_class}, \code{metabolism} (if present), and \code{metab_units} (if present). #' swmpr <- function(stat_in, meta_in){ @@ -45,7 +45,7 @@ swmpr <- function(stat_in, meta_in){ timezone = timezone, stamp_class = class(stat_in$datetimestamp), metabolism = NULL, - met_units = NULL + metab_units = NULL ) } @@ -490,7 +490,7 @@ map_reserve <- function(nerr_site_id, zoom = 11, text_sz = 6, text_col = 'black' #' @seealso #' \code{\link{ecometab}} #' -met_day <- function(dat_in, stat_in){ +metab_day <- function(dat_in, stat_in){ stat_meta <- stat_locs[grep(gsub('wq$', '', stat_in), stat_locs$station_code),] @@ -531,14 +531,14 @@ met_day <- function(dat_in, stat_in){ ss_dat <- ss_dat[!duplicated(strftime(ss_dat[, 1], format = '%Y-%m_%d')), ] ss_dat <- data.frame( ss_dat, - met_date = as.Date(ss_dat$sunrise, tz = tz) + metab_date = as.Date(ss_dat$sunrise, tz = tz) ) - ss_dat <- melt(ss_dat, id.vars = 'met_date') + ss_dat <- melt(ss_dat, id.vars = 'metab_date') if(!"POSIXct" %in% class(ss_dat$value)) ss_dat$value <- as.POSIXct(ss_dat$value, origin='1970-01-01',tz=tz) ss_dat <- ss_dat[order(ss_dat$value),] ss_dat$day_hrs <- unlist(lapply( - split(ss_dat, ss_dat$met_date), + split(ss_dat, ss_dat$metab_date), function(x) rep(as.numeric(x[2, 'value'] - x[1, 'value']), 2) )) names(ss_dat)[names(ss_dat) %in% c('variable', 'value')] <- c('solar_period', 'solar_time') @@ -577,7 +577,7 @@ met_day <- function(dat_in, stat_in){ #' @seealso #' \code{\link{ecometab}} #' -calcKL <- function(temp, sal, atemp, wspd, bp, height = 10){ +calckl <- function(temp, sal, atemp, wspd, bp, height = 10){ #celsius to kelvin conversion CtoK <- function(val) val + 273.15 diff --git a/README.Rmd b/README.Rmd index 25ead1a..f096078 100644 --- a/README.Rmd +++ b/README.Rmd @@ -353,14 +353,14 @@ dat <- qaqc(apacpnut) plot_summary(dat, param = 'chla_n') ``` -Estimates of ecosystem metabolism provide a useful measure of overall system productivity. These estimates are commonly used to evaluate whether an ecosystem is a net source or sink of organic material. The open-water method is a common approach to quantify net ecosystem metabolism using a mass balance equation that describes the change in dissolved oxygen over time from the balance between photosynthetic and respiration rates, corrected for air-sea gas diffusion at the surface. The diffusion-corrected DO flux estimates are averaged during day and night for each 24 hour period in the time series, where flux is an hourly rate of DO change. DO flux is averaged during night hours for respiration and averaged during day hours for net production. Respiration rates are assumed constant during day and night such that total daily rates are calculated as hourly respiration multiplied by 24. The metabolic day is considered the approximate 24 hour period between sunsets on two adjacent calendar days. Respiration is subtracted from daily net production estimates to yield gross production. +Estimates of ecosystem metabolism provide a useful measure of overall system productivity. These estimates are commonly used to evaluate whether an ecosystem is a net source or sink of organic material. The open-water method is a common approach to quantify net ecosystem metabolism using a mass balance equation that describes the change in dissolved oxygen over time from the balance between photosynthetic and respiration rates, corrected for air-sea gas diffusion at the surface. The diffusion-corrected DO flux estimates are averaged during day and night for each 24 hour period in the time series, where flux is an hourly rate of DO change. DO flux is averaged during night hours for respiration and averaged during day hours for net production. Respiration rates are assumed constant during day and night such that total daily rates are calculated as hourly respiration multiplied by 24. The metabolic day is considered the 24 hour period between sunsets on two adjacent calendar days. Respiration is subtracted from daily net production estimates to yield gross production. The `ecometab` function is used to implement an adaptation of the open-water method. Several assumptions must be met for a valid interpretation of the results. In general, the dissolved oxygen time series is assumed to represent the same water mass over time. Tidal advection may have a significant influence on the time series, which can contribute to a significant amount of noise in metabolic estimates. The extent to which tidal advection influences the dissolved oxygen signal depends on various site-level characteristics and an intimate knowledge of the site may be required. Volumetric rates for gross production and total respiration are also based on total depth of the water column, which is assumed to be mixed. Water column depth is based on mean value for the depth variable across the time series and is floored at 1 meter for very shallow stations. Additionally, the volumetric reaeration coefficient requires an estimate of the anemometer height of the weather station, which is set as 10 meters by default. The metadata should be consulted for exact height. Other assumptions may apply and the user should consult the relevant literature (see the references in the help file). All estimates are in mmol of oxygen but can be converted to grams by changing the default arguments (i.e., 1mmol O2 = 32 mg O2, 1000 mg = 1g, multiply all estimates by 32/1000). -The following is an example that shows how to use the function from a combined water quality and weather data set. +The following is an example that shows how to use the function from a combined water quality and weather data set. The results can be plotted using `plot_metab`. -```{r eval = FALSE} +```{r eval = TRUE, cache = TRUE, fig.height = 4, fig.width = 8, warning = FALSE} ## import water quality and weather data data(apadbwq) data(apaebmet) @@ -371,7 +371,8 @@ met <- qaqc(apaebmet) dat <- comb(wq, met) ## estimate metabolism -res <- ecometab(dat, trace = TRUE) +res <- ecometab(dat, trace = FALSE) +plot_metab(res) ``` #Function list @@ -406,6 +407,8 @@ See help documentation for more details on each function (e.g., `?all_params`). `aggregate.swmpr` Aggregate swmpr objects for different time periods - years, quarters, months, weeks, days, or hours. Aggregation function is user-supplied but defaults to mean. +`aggregate_metab` Aggregate metabolism data from a swmpr object. This is primarly used within `plot_metab` but may be useful for simple summaries of raw daily data. + `ecometab.swmpr` Estimate ecosystem metabolism for a combined water quality and weatehr dataset using the open-water method. `decomp.swmpr` Decompose a swmpr time series into trend, seasonal, and residual components. This is a simple wrapper to `decompose`. Decomposition of monthly or daily trends is possible. @@ -420,6 +423,8 @@ See help documentation for more details on each function (e.g., `?all_params`). `plot.swmpr` Plot a univariate time series for a swmpr object. The parameter name must be specified. +`plot_metab` Plot ecosystem metabolism estimates after running `ecometab` on a swmpr object. + `plot_summary` Create summary plots of seasonal/annual trends and anomalies for a water quality or weather parameter. `smoother.swmpr` Smooth swmpr objects with a moving window average. Window size and sides can be specified, passed to `filter`. @@ -430,7 +435,7 @@ See help documentation for more details on each function (e.g., `?all_params`). `map_reserve` Create a map of all stations in a reserve using the ggmap package. -`met_day` Identify the metabolic day for each approximate 24 period in an hourly time series. This is only used within the `ecometab` function. +`metab_day` Identify the metabolic day for each approximate 24 period in an hourly time series. This is only used within the `ecometab` function. `param_names` Returns column names as a list for the parameter type(s) (nutrients, weather, or water quality). Includes QAQC columns with 'f_' prefix. Used internally in other functions. diff --git a/README.html b/README.html index 652cfd4..8414542 100644 --- a/README.html +++ b/README.html @@ -340,9 +340,9 @@

An overview of methods for swmpr objects

## plot plot_summary(dat, param = 'chla_n')

plot of chunk unnamed-chunk-21

-

Estimates of ecosystem metabolism provide a useful measure of overall system productivity. Such estimates are commonly used to evaluate whether an ecosystem is a net source or sink of organic material. The open-water method is used to infer net ecosystem metabolism using a mass balance equation that describes the change in dissolved oxygen over time as a function of photosynthetic rate, minus respiration rate, corrected for air-sea gas diffusion at the surface. The diffusion-corrected DO flux estimates are averaged during day and night for each 24 hour period in the time series, where flux is an hourly rate of DO change. DO flux is averaged during night hours for respiration and averaged during day hours for net production. Respiration rates are assumed constant during day and night such that total daily rates are calculated as hourly respiration multiplied by 24. The metabolic day is considered the approximate 24 hour period between sunsets on two adjacent calendar days. Respiration is subtracted from daily net production estimates to yield gross production.

+

Estimates of ecosystem metabolism provide a useful measure of overall system productivity. These estimates are commonly used to evaluate whether an ecosystem is a net source or sink of organic material. The open-water method is a common approach to quantify net ecosystem metabolism using a mass balance equation that describes the change in dissolved oxygen over time from the balance between photosynthetic and respiration rates, corrected for air-sea gas diffusion at the surface. The diffusion-corrected DO flux estimates are averaged during day and night for each 24 hour period in the time series, where flux is an hourly rate of DO change. DO flux is averaged during night hours for respiration and averaged during day hours for net production. Respiration rates are assumed constant during day and night such that total daily rates are calculated as hourly respiration multiplied by 24. The metabolic day is considered the 24 hour period between sunsets on two adjacent calendar days. Respiration is subtracted from daily net production estimates to yield gross production.

The ecometab function is used to implement an adaptation of the open-water method.
Several assumptions must be met for a valid interpretation of the results. In general, the dissolved oxygen time series is assumed to represent the same water mass over time. Tidal advection may have a significant influence on the time series, which can contribute to a significant amount of noise in metabolic estimates. The extent to which tidal advection influences the dissolved oxygen signal depends on various site-level characteristics and an intimate knowledge of the site may be required. Volumetric rates for gross production and total respiration are also based on total depth of the water column, which is assumed to be mixed. Water column depth is based on mean value for the depth variable across the time series and is floored at 1 meter for very shallow stations. Additionally, the volumetric reaeration coefficient requires an estimate of the anemometer height of the weather station, which is set as 10 meters by default. The metadata should be consulted for exact height. Other assumptions may apply and the user should consult the relevant literature (see the references in the help file). All estimates are in mmol of oxygen but can be converted to grams by changing the default arguments (i.e., 1mmol O2 = 32 mg O2, 1000 mg = 1g, multiply all estimates by 32/1000).

-

The following is an example that shows how to use wihte function from a combined water quality and weather data set.

+

The following is an example that shows how to use the function from a combined water quality and weather data set. The results can be plotted using plot_metab.

## import water quality and weather data
 data(apadbwq)
 data(apaebmet)
@@ -353,7 +353,9 @@ 
An overview of methods for swmpr objects

 dat <- comb(wq, met)
 
 ## estimate metabolism
-res <- ecometab(dat, trace = TRUE)
+res <- ecometab(dat, trace = FALSE) +plot_metab(res) +

plot of chunk unnamed-chunk-22

Function list

@@ -377,6 +379,7 @@

Organize

Analyze

aggregate.swmpr Aggregate swmpr objects for different time periods - years, quarters, months, weeks, days, or hours. Aggregation function is user-supplied but defaults to mean.

+

aggregate_metab Aggregate metabolism data from a swmpr object. This is primarly used within plot_metab but may be useful for simple summaries of raw daily data.

ecometab.swmpr Estimate ecosystem metabolism for a combined water quality and weatehr dataset using the open-water method.

decomp.swmpr Decompose a swmpr time series into trend, seasonal, and residual components. This is a simple wrapper to decompose. Decomposition of monthly or daily trends is possible.

decomp_cj.swmpr Decompose a swmpr time series into grandmean, annual, seasonal, and events components. This is a simple wrapper to decompTs in the wq package. Only monthly decomposition is possible.

@@ -384,6 +387,7 @@

Analyze

lines.swmpr Add lines to an existing swmpr plot.

na.approx.swmpr Linearly interpolate missing data (NA values) in a swmpr object. The maximum gap size that is interpolated is defined as a maximum number of records with missing data.

plot.swmpr Plot a univariate time series for a swmpr object. The parameter name must be specified.

+

plot_metab Plot ecosystem metabolism estimates after running ecometab on a swmpr object.

plot_summary Create summary plots of seasonal/annual trends and anomalies for a water quality or weather parameter.

smoother.swmpr Smooth swmpr objects with a moving window average. Window size and sides can be specified, passed to filter.

@@ -391,7 +395,7 @@

Analyze

Miscellaneous

calcKL Estimate the reaeration coefficient for air-sea gas exchange. This is only used within the ecometab function.

map_reserve Create a map of all stations in a reserve using the ggmap package.

-

met_day Identify the metabolic day for each approximate 24 period in an hourly time series. This is only used within the ecometab function.

+

metab_day Identify the metabolic day for each approximate 24 period in an hourly time series. This is only used within the ecometab function.

param_names Returns column names as a list for the parameter type(s) (nutrients, weather, or water quality). Includes QAQC columns with ‘f_’ prefix. Used internally in other functions.

parser Parses html returned from CDMO web services, used internally in retrieval functions.

site_codes Metadata for all stations, wrapper to exportStationCodesXMLNew function on web services.

diff --git a/README.md b/README.md index 653b238..8a2e651 100644 --- a/README.md +++ b/README.md @@ -403,12 +403,12 @@ plot_summary(dat, param = 'chla_n') ![plot of chunk unnamed-chunk-21](README_files/figure-html/unnamed-chunk-21.png) -Estimates of ecosystem metabolism provide a useful measure of overall system productivity. Such estimates are commonly used to evaluate whether an ecosystem is a net source or sink of organic material. The open-water method is used to infer net ecosystem metabolism using a mass balance equation that describes the change in dissolved oxygen over time as a function of photosynthetic rate, minus respiration rate, corrected for air-sea gas diffusion at the surface. The diffusion-corrected DO flux estimates are averaged during day and night for each 24 hour period in the time series, where flux is an hourly rate of DO change. DO flux is averaged during night hours for respiration and averaged during day hours for net production. Respiration rates are assumed constant during day and night such that total daily rates are calculated as hourly respiration multiplied by 24. The metabolic day is considered the approximate 24 hour period between sunsets on two adjacent calendar days. Respiration is subtracted from daily net production estimates to yield gross production. +Estimates of ecosystem metabolism provide a useful measure of overall system productivity. These estimates are commonly used to evaluate whether an ecosystem is a net source or sink of organic material. The open-water method is a common approach to quantify net ecosystem metabolism using a mass balance equation that describes the change in dissolved oxygen over time from the balance between photosynthetic and respiration rates, corrected for air-sea gas diffusion at the surface. The diffusion-corrected DO flux estimates are averaged during day and night for each 24 hour period in the time series, where flux is an hourly rate of DO change. DO flux is averaged during night hours for respiration and averaged during day hours for net production. Respiration rates are assumed constant during day and night such that total daily rates are calculated as hourly respiration multiplied by 24. The metabolic day is considered the 24 hour period between sunsets on two adjacent calendar days. Respiration is subtracted from daily net production estimates to yield gross production. The `ecometab` function is used to implement an adaptation of the open-water method. Several assumptions must be met for a valid interpretation of the results. In general, the dissolved oxygen time series is assumed to represent the same water mass over time. Tidal advection may have a significant influence on the time series, which can contribute to a significant amount of noise in metabolic estimates. The extent to which tidal advection influences the dissolved oxygen signal depends on various site-level characteristics and an intimate knowledge of the site may be required. Volumetric rates for gross production and total respiration are also based on total depth of the water column, which is assumed to be mixed. Water column depth is based on mean value for the depth variable across the time series and is floored at 1 meter for very shallow stations. Additionally, the volumetric reaeration coefficient requires an estimate of the anemometer height of the weather station, which is set as 10 meters by default. The metadata should be consulted for exact height. Other assumptions may apply and the user should consult the relevant literature (see the references in the help file). All estimates are in mmol of oxygen but can be converted to grams by changing the default arguments (i.e., 1mmol O2 = 32 mg O2, 1000 mg = 1g, multiply all estimates by 32/1000). -The following is an example that shows how to use wihte function from a combined water quality and weather data set. +The following is an example that shows how to use the function from a combined water quality and weather data set. The results can be plotted using `plot_metab`. ```r @@ -422,9 +422,12 @@ met <- qaqc(apaebmet) dat <- comb(wq, met) ## estimate metabolism -res <- ecometab(dat, trace = TRUE) +res <- ecometab(dat, trace = FALSE) +plot_metab(res) ``` +![plot of chunk unnamed-chunk-22](README_files/figure-html/unnamed-chunk-22.png) + #Function list See help documentation for more details on each function (e.g., `?all_params`). @@ -457,6 +460,8 @@ See help documentation for more details on each function (e.g., `?all_params`). `aggregate.swmpr` Aggregate swmpr objects for different time periods - years, quarters, months, weeks, days, or hours. Aggregation function is user-supplied but defaults to mean. +`aggregate_metab` Aggregate metabolism data from a swmpr object. This is primarly used within `plot_metab` but may be useful for simple summaries of raw daily data. + `ecometab.swmpr` Estimate ecosystem metabolism for a combined water quality and weatehr dataset using the open-water method. `decomp.swmpr` Decompose a swmpr time series into trend, seasonal, and residual components. This is a simple wrapper to `decompose`. Decomposition of monthly or daily trends is possible. @@ -471,6 +476,8 @@ See help documentation for more details on each function (e.g., `?all_params`). `plot.swmpr` Plot a univariate time series for a swmpr object. The parameter name must be specified. +`plot_metab` Plot ecosystem metabolism estimates after running `ecometab` on a swmpr object. + `plot_summary` Create summary plots of seasonal/annual trends and anomalies for a water quality or weather parameter. `smoother.swmpr` Smooth swmpr objects with a moving window average. Window size and sides can be specified, passed to `filter`. @@ -481,7 +488,7 @@ See help documentation for more details on each function (e.g., `?all_params`). `map_reserve` Create a map of all stations in a reserve using the ggmap package. -`met_day` Identify the metabolic day for each approximate 24 period in an hourly time series. This is only used within the `ecometab` function. +`metab_day` Identify the metabolic day for each approximate 24 period in an hourly time series. This is only used within the `ecometab` function. `param_names` Returns column names as a list for the parameter type(s) (nutrients, weather, or water quality). Includes QAQC columns with 'f_' prefix. Used internally in other functions. diff --git a/README_cache/html/unnamed-chunk-22_af537b6b99482fdaf74e62660a19ed60.RData b/README_cache/html/unnamed-chunk-22_af537b6b99482fdaf74e62660a19ed60.RData new file mode 100644 index 0000000..4f5ae37 Binary files /dev/null and b/README_cache/html/unnamed-chunk-22_af537b6b99482fdaf74e62660a19ed60.RData differ diff --git a/README_cache/html/unnamed-chunk-22_af537b6b99482fdaf74e62660a19ed60.rdb b/README_cache/html/unnamed-chunk-22_af537b6b99482fdaf74e62660a19ed60.rdb new file mode 100644 index 0000000..e181a83 Binary files /dev/null and b/README_cache/html/unnamed-chunk-22_af537b6b99482fdaf74e62660a19ed60.rdb differ diff --git a/README_cache/html/unnamed-chunk-22_af537b6b99482fdaf74e62660a19ed60.rdx b/README_cache/html/unnamed-chunk-22_af537b6b99482fdaf74e62660a19ed60.rdx new file mode 100644 index 0000000..0d930f0 Binary files /dev/null and b/README_cache/html/unnamed-chunk-22_af537b6b99482fdaf74e62660a19ed60.rdx differ diff --git a/README_files/figure-html/unnamed-chunk-22.png b/README_files/figure-html/unnamed-chunk-22.png new file mode 100644 index 0000000..bad3c21 Binary files /dev/null and b/README_files/figure-html/unnamed-chunk-22.png differ diff --git a/ggmapTemp.png b/ggmapTemp.png index 5f13204..d77a4af 100644 Binary files a/ggmapTemp.png and b/ggmapTemp.png differ diff --git a/man/aggregate_metab.Rd b/man/aggregate_metab.Rd new file mode 100644 index 0000000..2cf1b80 --- /dev/null +++ b/man/aggregate_metab.Rd @@ -0,0 +1,55 @@ +% Generated by roxygen2 (4.1.0): do not edit by hand +% Please edit documentation in R/swmpr_analyze.R +\name{aggregate_metab} +\alias{aggregate_metab} +\alias{aggregate_metab.swmpr} +\title{Aggregate metabolism data} +\usage{ +aggregate_metab(swmpr_in, ...) + +\method{aggregate_metab}{swmpr}(swmpr_in, by = "weeks", na.action = na.pass, + alpha = 0.05, ...) +} +\arguments{ +\item{swmpr_in}{input swmpr object} + +\item{...}{additional arguments passed to other methods} + +\item{by}{chr string of time period for aggregation one of \code{'years'}, \code{'quarters'}, \code{'months'}, \code{'weeks'}, \code{'days'}, or \code{'hours'}} + +\item{na.action}{function for treating missing data, default \code{na.pass}} + +\item{alpha}{numeric indicating alpha level of confidence interval for aggregated data} +} +\value{ +Returns an aggregated metabolism \code{\link[base]{data.frame}} if the \code{metabolism} attribute of the swmpr object is not \code{NULL}. +} +\description{ +Aggregate a metabolism attribute from swmpr data by a specified time period and method +} +\details{ +The function summarizes metabolism data by averaging across set periods of observation. Confidence intervals are also returned based on the specified alpha level. It is used within \code{\link{plot_metab}} function to view summarized metabolism results. Data can be aggregated by \code{'years'}, \code{'quarters'}, \code{'months'}, or \code{'weeks'} for the supplied function, which defaults to the \code{\link[base]{mean}}. The method of treating NA values for the user-supplied function should be noted since this may greatly affect the quantity of data that are returned. +} +\examples{ +## import water quality and weather data +data(apadbwq) +data(apaebmet) + +## qaqc, combine +wq <- qaqc(apadbwq) +met <- qaqc(apaebmet) +dat <- comb(wq, met) + +## estimate metabolism +res <- ecometab(dat, trace = TRUE) + +## aggregate metabolism +aggregate_metab(res, by = 'weeks') + +## change aggregatin period and alpha +aggregate_metab(res, by = 'months', alpha = 0.1) +} +\seealso{ +\code{\link[stats]{aggregate}}, \code{\link{aggregate.swmpr}}, \code{\link{ecometab}}, \code{\link{plot_metab}} +} + diff --git a/man/calcKL.Rd b/man/calcKL.Rd index b2c4d26..f0b7e50 100644 --- a/man/calcKL.Rd +++ b/man/calcKL.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2 (4.1.0): do not edit by hand % Please edit documentation in R/swmpr_misc.R -\name{calcKL} -\alias{calcKL} +\name{calckl} +\alias{calckl} \title{Calculate oxygen mass transfer coefficient} \usage{ -calcKL(temp, sal, atemp, wspd, bp, height = 10) +calckl(temp, sal, atemp, wspd, bp, height = 10) } \arguments{ \item{temp}{numeric for water temperature (C)} diff --git a/man/ecometab.Rd b/man/ecometab.Rd index 3e83452..9da07ec 100644 --- a/man/ecometab.Rd +++ b/man/ecometab.Rd @@ -7,7 +7,7 @@ \usage{ ecometab(swmpr_in, ...) -\method{ecometab}{swmpr}(swmpr_in, depth_val = NULL, met_units = "mmol", +\method{ecometab}{swmpr}(swmpr_in, depth_val = NULL, metab_units = "mmol", trace = FALSE, ...) } \arguments{ @@ -17,7 +17,7 @@ ecometab(swmpr_in, ...) \item{depth_val}{numeric value for station depth if time series is not available} -\item{met_units}{chr indicating units of output for oxygen, either as mmol or grams} +\item{metab_units}{chr indicating units of output for oxygen, either as mmol or grams} \item{trace}{logical indicating if progress is shown in the console} } @@ -25,17 +25,13 @@ ecometab(swmpr_in, ...) The original \code{\link{swmpr}} object is returned that includes a metabolism attribute as a \code{\link[base]{data.frame}} of daily integrated metabolism estimates. See the examples for retrieval. \describe{ \item{\code{date}}{The metabolic day for each estimate, defined as the approximate 24 hour period between sunsets on adjacent calendar days.} - \item{\code{ddo}}{Mean hourly rate of change for DO, mmol/m3/hr} - \item{\code{D}}{Mean air-sea gas exchange of DO, mmol/m2/hr} \item{\code{DOF_d}}{Mean DO flux during day hours, mmol/m2/hr} \item{\code{D_d}}{Mean air-sea gas exchange of DO during day hours, mmol/m2/hr} \item{\code{DOF_n}}{Mean DO flux during night hours, mmol/m2/hr} \item{\code{D_n}}{Mean air-sea gas exchange of DO during night hours, mmol/m2/hr} - \item{\code{Pg}}{Gross production, O2 mmol/m2/d} - \item{\code{Rt}}{Total respiration, O2 mmol/m2/d} - \item{\code{NEM}}{Net ecosytem metabolism, O2 mmol/m2/d} - \item{\code{Pg_vol}}{Volumetric gross production, O2 mmol/m3/d} - \item{\code{Rt_vol}}{Volumetric total respiration, O2 mmold/m3/d} + \item{\code{Pg}}{Gross production, O2 mmol/m2/d, calculated as ((DOF_d - D_d) - (DOF_n - D_n)) * day hours} + \item{\code{Rt}}{Total respiration, O2 mmol/m2/d, calculated as (DOF_n - D_n) * 24} + \item{\code{NEM}}{Net ecosytem metabolism, O2 mmol/m2/d, calculated as Pg + Rt} } } \description{ @@ -44,15 +40,15 @@ Estimate ecosystem metabolism using the Odum open-water method. Estimates of da \details{ Input data must be combined water quality and weather datasets. This is typically done using the \code{\link{comb}} function after creating separate swmpr objects. -The open-water method is a common approach to quantify net ecosystem metabolism using a mass balance equation that describes the change in dissolved oxygen over time from the balance between photosynthetic and respiration rates, corrected for air-sea gas diffusion at the surface. The air-sea gas exchange is estimated as the difference between the DO saturation concentration and observed DO concentration, multiplied by a volumetric reaeration coefficient (see the appendix in Thebault et al. 2008). The diffusion-corrected DO flux estimates are averaged during day and night for each 24 hour period in the time series, where flux is an hourly rate of DO change. DO flux is averaged during night hours for respiration and averaged during day hours for net production. Respiration rates are assumed constant during day and night such that total daily rates are calculated as hourly respiration multiplied by 24. The metabolic day is considered the approximate 24 hour period between sunsets on two adjacent calendar days. Respiration is subtracted from daily net production estimates to yield gross production. +The open-water method is a common approach to quantify net ecosystem metabolism using a mass balance equation that describes the change in dissolved oxygen over time from the balance between photosynthetic and respiration rates, corrected for air-sea gas diffusion at the surface. The air-sea gas exchange is estimated as the difference between the DO saturation concentration and observed DO concentration, multiplied by a volumetric reaeration coefficient (see the appendix in Thebault et al. 2008). The diffusion-corrected DO flux estimates are averaged during day and night for each 24 hour period in the time series, where flux is an hourly rate of DO change. DO flux is averaged during night hours for respiration and averaged during day hours for net production. Respiration rates are assumed constant during day and night such that total daily rates are calculated as hourly respiration multiplied by 24. The metabolic day is considered the 24 hour period between sunsets on two adjacent calendar days. Respiration is subtracted from daily net production estimates to yield gross production. -Volumetric rates for gross production and total respiration are based on total depth of the water column, which is assumed to be mixed. Water column depth is based on mean value for the depth variable across the time series in the \code{\link{swmpr}} object and is floored at 1 meter for very shallow stations. Additionally, the volumetric reaeration coefficient requires an estimate of the anemometer height of the weather station, which is set as 10 meters by default. The metadata should be consulted for exact height. The value can be changed manually using a \code{height} argument, which is passed to \code{\link{calcKL}}. +Aereal rates for gross production and total respiration are based on volumetric rates corrected for total depth of the water column, which is assumed to be mixed. Water column depth is based on mean value for the depth variable across the time series in the \code{\link{swmpr}} object and is floored at 1 meter for very shallow stations. Additionally, the volumetric reaeration coefficient requires an estimate of the anemometer height of the weather station, which is set as 10 meters by default. The metadata should be consulted for exact height. The value can be changed manually using a \code{height} argument, which is passed to \code{\link{calckl}}. Metabolism estimates are not returned for dates with less than three hourly records during either day or night periods. Missing values for air temperature, barometric pressure, and wind speed are replaced with the climatological means for the period of record. Climatological means are based on hourly average values by month. -All estimates are in mmol of oxygen but can be converted to grams by changing the default arguments (i.e., 1mmol O2 = 32 mg O2, 1000 mg = 1g, multiply all estimates by 32/1000). +All estimates are in mmol of oxygen but can be converted to grams by setting \code{metab_units = 'grams'} (i.e., 1mmol O2 = 32 mg O2, 1000 mg = 1g, multiply all estimates by 32/1000). -The specific approach for estimating metabolism is described in more detail in Caffrey et al. 2013. +The specific approach for estimating metabolism with the open-water method is described in more detail in Caffrey et al. 2013. } \examples{ ## import water quality and weather data @@ -72,7 +68,7 @@ res <- ecometab(dat, trace = TRUE, height = 5) res <- attr(res, 'metabolism') ## output units in grams of oxygen -res <- ecometab(dat, trace = TRUE, met_units = 'grams') +res <- ecometab(dat, trace = TRUE, metab_units = 'grams') res <- attr(res, 'metabolism') } \references{ @@ -83,6 +79,6 @@ Odum HT. 1956. Primary production in flowing waters. Limnology and Oceanography. Thebault J, Schraga TS, Cloern JE, Dunlavey EG. 2008. Primary production and carrying capacity of former salt ponds after reconnection to San Francisco Bay. Wetlands. 28(3):841-851. } \seealso{ -\code{\link{comb}}, \code{\link{plot_met}} +\code{\link{comb}}, \code{\link{plot_metab}} } diff --git a/man/met_day.Rd b/man/metab_day.Rd similarity index 91% rename from man/met_day.Rd rename to man/metab_day.Rd index dce2f25..1e25479 100644 --- a/man/met_day.Rd +++ b/man/metab_day.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2 (4.1.0): do not edit by hand % Please edit documentation in R/swmpr_misc.R -\name{met_day} -\alias{met_day} +\name{metab_day} +\alias{metab_day} \title{Identify metabolic days in a swmpr time series} \usage{ -met_day(dat_in, stat_in) +metab_day(dat_in, stat_in) } \arguments{ \item{dat_in}{data.frame} diff --git a/man/plot_met.Rd b/man/plot_met.Rd deleted file mode 100644 index 59eb552..0000000 --- a/man/plot_met.Rd +++ /dev/null @@ -1,49 +0,0 @@ -% Generated by roxygen2 (4.1.0): do not edit by hand -% Please edit documentation in R/swmpr_analyze.R -\name{plot_met} -\alias{plot_met} -\alias{plot_met.swmpr} -\title{Plot ecosystem metabolism for a swmpr object} -\usage{ -plot_met(swmpr_in, ...) - -\method{plot_met}{swmpr}(swmpr_in, pretty = TRUE, ...) -} -\arguments{ -\item{swmpr_in}{input swmpr object} - -\item{...}{} - -\item{pretty}{logical indicating use of predefined plot aesthetics} -} -\value{ -A \code{\link[ggplot2]{ggplot}} object which can be further modified. -} -\description{ -Plot gross production, total respiration, and net ecosystem metabolism for a swmpr object. -} -\details{ -A plot will only be returned if the \code{metabolism} attribute for the \code{\link{swmpr}} object is not \code{NULL}. The \code{\link{ecometab}} function is used to create metabolism estimates. See the examples. - -By default, \code{pretty = TRUE} will return a \code{\link[ggplot2]{ggplot}} object with predefined aesthetics. Setting \code{pretty = FALSE} will return the plot with minimal modifications to the \code{\link[ggplot2]{object}}. Use the latter approach for easier customization of the plot. -} -\examples{ -## import water quality and weather data -data(apadbwq) -data(apaebmet) - -## qaqc, combine -wq <- qaqc(apadbwq) -met <- qaqc(apaebmet) -dat <- comb(wq, met) - -## estimate metabolism -res <- ecometab(dat, trace = TRUE) - -## plot -plot_met(res) -} -\seealso{ -\code\link{ecometab} -} - diff --git a/man/plot_metab.Rd b/man/plot_metab.Rd new file mode 100644 index 0000000..2d04c32 --- /dev/null +++ b/man/plot_metab.Rd @@ -0,0 +1,62 @@ +% Generated by roxygen2 (4.1.0): do not edit by hand +% Please edit documentation in R/swmpr_analyze.R +\name{plot_metab} +\alias{plot_metab} +\alias{plot_metab.swmpr} +\title{Plot ecosystem metabolism for a swmpr object} +\usage{ +plot_metab(swmpr_in, ...) + +\method{plot_metab}{swmpr}(swmpr_in, by = "months", alpha = 0.05, + width = 10, pretty = TRUE, ...) +} +\arguments{ +\item{swmpr_in}{input swmpr object} + +\item{...}{arguments passed to or from other methods} + +\item{by}{chr string describing aggregation period, passed to \code{\link{aggregate_metab}}. See details for accepted values.} + +\item{alpha}{numeric indicating alpha level for confidence intervals in aggregated data. Use \code{NULL} to remove from the plot.} + +\item{width}{numeric indicating width of top and bottom segments on error bars} + +\item{pretty}{logical indicating use of predefined plot aesthetics} +} +\value{ +A \code{\link[ggplot2]{ggplot}} object which can be further modified. +} +\description{ +Plot gross production, total respiration, and net ecosystem metabolism for a swmpr object. +} +\details{ +A plot will only be returned if the \code{metabolism} attribute for the \code{\link{swmpr}} object is not \code{NULL}. Daily metabolism estimates are also aggregated into weekly averages. Accepted aggregation periods are \code{'years'}, \code{'quarters'}, \code{'months'}, \code{'weeks'}, and \code{'days'} (if no aggregation is preferred). + +By default, \code{pretty = TRUE} will return a \code{\link[ggplot2]{ggplot}} object with predefined aesthetics. Setting \code{pretty = FALSE} will return the plot with minimal modifications to the \code{\link[ggplot2]{ggplot}} object. Use the latter approach for easier customization of the plot. +} +\examples{ +## import water quality and weather data +data(apadbwq) +data(apaebmet) + +## qaqc, combine +wq <- qaqc(apadbwq) +met <- qaqc(apaebmet) +dat <- comb(wq, met) + +## estimate metabolism +res <- ecometab(dat, trace = TRUE) + +## plot +plot_metab(res) + +## change alpha, aggregation period, widths +plot_metab(res, by = 'quarters', alpha = 0.1, widths = 0) + +## plot daily raw, no aesthetics +plot_metab(res, by = 'days', pretty = FALSE) +} +\seealso{ +\code{\link{aggregate_metab}}, \code{\link{ecometab}} +} + diff --git a/man/swmpr.Rd b/man/swmpr.Rd index e56c029..8c023f4 100644 --- a/man/swmpr.Rd +++ b/man/swmpr.Rd @@ -18,6 +18,6 @@ Returns a swmpr object to be used with S3 methods Wrapper for creating a swmpr object } \details{ -This function is a simple wrapper to \code{\link[base]{structure}} that is used internally within other functions to create a swmpr object. The function does not have to be used explicitly. Attributes of a swmpr object include \code{names}, \code{row.names}, \code{class}, \code{station}, \code{parameters}, \code{qaqc_cols}, \code{date_rng}, \code{timezone}, \code{stamp_class}, \code{metabolism} (if present), and \code{met_units} (if present). +This function is a simple wrapper to \code{\link[base]{structure}} that is used internally within other functions to create a swmpr object. The function does not have to be used explicitly. Attributes of a swmpr object include \code{names}, \code{row.names}, \code{class}, \code{station}, \code{parameters}, \code{qaqc_cols}, \code{date_rng}, \code{timezone}, \code{stamp_class}, \code{metabolism} (if present), and \code{metab_units} (if present). }