| anlzMWRseason {MassWateR} | R Documentation |
Analyze seasonal trends in results file
Description
Analyze seasonal trends in results file
Usage
anlzMWRseason(
res = NULL,
param,
acc = NULL,
sit = NULL,
fset = NULL,
thresh,
group = c("month", "week"),
type = c("box", "jitterbox", "bar", "jitterbar", "jitter"),
threshlab = NULL,
threshcol = "tan",
site = NULL,
resultatt = NULL,
locgroup = NULL,
dtrng = NULL,
confint = FALSE,
fill = "lightblue",
alpha = 0.8,
width = 0.8,
yscl = "auto",
sumfun = yscl,
ttlsize = 1.2,
runchk = TRUE,
warn = TRUE
)
Arguments
res |
character string of path to the results file or |
param |
character string of the parameter to plot, must conform to entries in the |
acc |
character string of path to the data quality objectives file for accuracy or |
sit |
optional character string of path to the site metadata file or |
fset |
optional list of inputs with elements named |
thresh |
character indicating if relevant freshwater or marine threshold lines are included, one of |
group |
character indicating whether the summaries are grouped by month (default) or week of year |
type |
character indicating |
threshlab |
optional character string indicating legend label for the threshold, required only if |
threshcol |
character indicating color of threshold lines if available |
site |
character string of sites to include, default all |
resultatt |
character string of result attributes to plot, default all |
locgroup |
character string of location groups to plot from the |
dtrng |
character string of length two for the date ranges as YYYY-MM-DD, default all |
confint |
logical indicating if confidence intervals are shown, only applies if |
fill |
numeric indicating fill color for boxplots or barplots |
alpha |
numeric from 0 to 1 indicating transparency of fill color |
width |
numeric for width of boxplots or barplots |
yscl |
character indicating one of |
sumfun |
character indicating one of |
ttlsize |
numeric value indicating font size of the title relative to other text in the plot |
runchk |
logical to run data checks with |
warn |
logical to return warnings to the console (default) |
Details
Summaries of a parameter are shown as boxplots if type = "box" or as barplots if type = "bar". Points can be jittered over the boxplots by setting type = "jitterbox" or jittered over the barplots by setting type = "jitterbar". Setting type = "jitter" will show only the jittered points. For type = "bar" or type = "jitterbar", 95% confidence intervals can also be shown if confint = TRUE and they can be estimated (i.e., more than one result value per bar and sumfun is "auto", "mean", or "geomean").
Specifying group = "week" will group the samples by week of year using an integer specifying the week. Note that there can be no common month/day indicating the start of the week between years and an integer is the only way to compare summaries if the results data span multiple years.
Threshold lines applicable to marine or freshwater environments can be included in the plot by using the thresh argument. These thresholds are specific to each parameter and can be found in the thresholdMWR file. Threshold lines are plotted only for those parameters with entries in thresholdMWR and only if the value in `Result Unit` matches those in thresholdMWR. The threshold lines can be suppressed by setting thresh = 'none'. A user-supplied numeric value can also be used for the thresh argument to override the default values. An appropriate label must also be supplied to threshlab if thresh is numeric.
The y-axis scaling as arithmetic (linear) or logarithmic can be set with the yscl argument. If yscl = "auto" (default), the scaling is determined automatically from the data quality objective file for accuracy, i.e., parameters with "log" in any of the columns are plotted on log10-scale, otherwise arithmetic. Setting yscl = "linear" or yscl = "log" will set the axis as linear or log10-scale, respectively, regardless of the information in the data quality objective file for accuracy.
Similarly, the data will be summarized if type is "bar" or "jitterbar" based on the value passed to sumfun. The default if no value is provided to sumfun is to use the appropriate summary based on the value provided to yscl. If yscl = "auto" (default), then sumfun = "auto", and the mean or geometric mean is used for the summary based on information in the data quality objective file for accuracy. Using yscl = "linear" or yscl = "log" will default to the mean or geometric mean summary if no value is provided to sumfun. Any other appropriate value passed to sumfun will override the value passed to yscl. Valid summary functions for sumfun include "auto", "mean", "geomean", "median", "min", or "max").
Any entries in resdat in the "Result Value" column as "BDL" or "AQL" are replaced with appropriate values in the "Quantitation Limit" column, if present, otherwise the "MDL" or "UQL" columns from the data quality objectives file for accuracy are used. Values as "BDL" use one half of the appropriate limit.
Value
A ggplot object that can be further modified.
Examples
# results data path
respth <- system.file('extdata/ExampleResults.xlsx', package = 'MassWateR')
# results data
resdat <- readMWRresults(respth)
# accuracy path
accpth <- system.file('extdata/ExampleDQOAccuracy.xlsx',
package = 'MassWateR')
# accuracy data
accdat <- readMWRacc(accpth)
# site data path
sitpth <- system.file('extdata/ExampleSites.xlsx', package = 'MassWateR')
# site data
sitdat <- readMWRsites(sitpth)
# seasonal trends by month, boxplot
anlzMWRseason(res = resdat, param = 'DO', acc = accdat, thresh = 'fresh', group = 'month',
type = 'box')
# seasonal trends by week, boxplot
anlzMWRseason(res = resdat, param = 'DO', acc = accdat, thresh = 'fresh', group = 'week',
type = 'box')
# seasonal trends by month, May to July only
anlzMWRseason(res = resdat, param = 'DO', acc = accdat, thresh = 'fresh', group = 'month',
type = 'bar', dtrng = c('2022-05-01', '2022-07-31'))
# seasonal trends by month, barplot
anlzMWRseason(res = resdat, param = 'DO', acc = accdat, thresh = 'fresh', group = 'month',
type = 'bar')
# seasonal trends by week, barplot
anlzMWRseason(res = resdat, param = 'DO', acc = accdat, thresh = 'fresh', group = 'week',
type = 'bar')
# seasonal trends by location group, requires sitdat
anlzMWRseason(res = resdat, param = 'DO', acc = accdat, sit = sitdat, thresh = 'fresh',
group = 'month', type = 'box', locgroup = 'Assabet')