Create time series from water quality data

Creates a matrix time series object from an object of class "WqData", either all variables for a single site or all sites for a single variable.

Arguments

object: Object of class "WqData".
focus: Name of a site or water quality variable.
layer: Number specifying a single depth; a numeric vector of length 2 specifying top and bottom depths of layer; a list specifying multiple depths and/or layers; or just the string "max.depths".
type: ts.mon to get a monthly time series, zoo to get an object of class "zoo" with individual observation dates.
qprob: quantile probability, a number between 0 and 1.

Value

A matrix of class "mts" or "zoo".

Details

When qprob = NULL, the function averages all included depths for each day, the implicit assumption being that the layer is well-mixed and/or the samples are evenly distributed with depth in the layer. If layer = "max.depths", then only the value at the maximum depth for each time, site and variable combination will be used. If no layer is specified, all depths will be used.

The function produces a matrix time series of all variables for the specified site or all sites for the specified variable. If type = "ts.mon", available daily data are averaged to produce a monthly time series, from which a quarterly or annual series can be created if needed. If you want values for the actual dates of observation, then set type = "zoo".

When qprob is a number from 0 to 1, it is interpreted as a probability and the corresponding quantile is used to aggregate observations within the specified layer. So to get the maximum, for example, use qprob = 1. If type = "ts.mon", the same quantile is used to aggregate all the available daily values.

Note

The layer list is allowed to include negative numbers, which may have been used in the WqData object to denote variables that apply to the water column as a whole, such as, say, -1 for light attenuation coefficient. This enables focus = 's27' and layer = list(-1, c(0, 5)) to produce a time series matrix for station 27 that includes both attenuation coefficient and chlorophyll averaged over the top 5 m. Negative numbers may also have been used in the WqData object to identify qualitative depths such as “near bottom”, which is not uncommon in historical data sets. So data from such depths can be aggregated easily with other data to make these time series.

Examples


# Create new WqData object
sfb <- wqData(sfbay, c(1, 3:4), 5:12, site.order = TRUE,
  time.format = "%m/%d/%Y", type = "wide")

# Find means in the 0-10 m layer
y <- tsMake(sfb, focus = "s27", layer = c(0, 10))
plot(y, main = "Station 27")

# Or select medians in the same layer
y1 <- tsMake(sfb, focus = "s27", layer = c(0, 10), qprob = 0.5)
plot(y1, main = "Station 27")

# Compare means:medians
apply(y / y1, 2, mean, na.rm = TRUE)
#>     y.chl     y.dox     y.spm     y.ext     y.sal    y.temp     y.nox     y.nhx 
#> 1.0642680 1.0019440 1.1172737 1.0717303 0.9995585 1.0007394 1.0644137 1.0496283 

# Combine a layer with a single additional depth
y <- tsMake(sfb, focus = "chl", layer = list(c(0, 2), 5))
plot(y, main = "Chlorophyll a, ug/L")


# Use values from the deepest samples
y <- tsMake(sfb, focus = "dox", layer = "max.depths", type = "zoo")
head(y)
#>            s21 s24  s27  s30  s32  s36
#> 1993-01-05 8.9 8.9  8.9  8.9  8.9  NaN
#> 1993-02-16 NaN 8.9  9.0  9.0  8.9  8.9
#> 1993-02-24 9.0 9.0  9.1  9.0  9.1  NaN
#> 1993-03-11 NaN 9.8  9.9  9.9  9.8  9.7
#> 1993-03-18 NaN 9.6 10.4 10.5  9.6  7.9
#> 1993-03-25 9.4 9.9 11.9 11.5 11.7 11.0
plot(y, type = "h", main = "'Bottom' DO, mg/L")