Analyze outliers in results file for all parameters

Usage

anlzMWRoutlierall(
  res = NULL,
  acc = NULL,
  fset = NULL,
  fig_height = 4,
  fig_width = 8,
  format = c("word", "png"),
  output_dir,
  output_file = NULL,
  type = c("box", "jitterbox", "jitter"),
  group,
  dtrng = NULL,
  repel = TRUE,
  outliers = FALSE,
  labsize = 3,
  fill = "lightgrey",
  alpha = 0.8,
  width = 0.8,
  yscl = "auto",
  ttlsize = 1.2,
  runchk = TRUE,
  warn = TRUE
)

Arguments

res: character string of path to the results file or data.frame for results returned by readMWRresults
acc: character string of path to the data quality objectives file for accuracy or data.frame returned by readMWRacc
fset: optional list of inputs with elements named res, acc, frecom, sit, or wqx overrides the other arguments
fig_height: numeric for plot heights in inches
fig_width: numeric for plot width in inches
format: character string indicating if results are placed in a word file or as separate png files in output_dir
output_dir: character string of the output directory for the results
output_file: optional character string for the file name if format = "word"
type: character indicating "box", "jitterbox", or "jitter", see details
group: character indicating whether the summaries are grouped by month, site, or week of year
dtrng: character string of length two for the date ranges as YYYY-MM-DD, optional
repel: logical indicating if overlapping outlier labels are offset
outliers: logical indicating if outliers are returned to the console instead of plotting
labsize: numeric indicating font size for the outlier labels
fill: numeric indicating fill color for boxplots
alpha: numeric from 0 to 1 indicating transparency of fill color
width: numeric for width of boxplots
yscl: character indicating one of "auto" (default), "log", or "linear", see details
ttlsize: numeric value indicating font size of the title relative to other text in the plot
runchk: logical to run data checks with checkMWRresults or checkMWRacc, applies only if res or acc are file paths
warn: logical to return warnings to the console (default)

Value

A word document named outlierall.docx (or name passed to output_file) if format = "word" or separate png files for each parameter if format = "png" will be saved in the directory specified by output_dir

Details

This function is a wrapper to anlzMWRoutlier to create plots for all parameters with appropriate data in the water quality monitoring results

Examples

# results data path
respth <- system.file('extdata/ExampleResults.xlsx', package = 'MassWateR')

# results data
resdat <- readMWRresults(respth)
#> Running checks on results data...
#> 	Checking column names... OK
#> 	Checking all required columns are present... OK
#> 	Checking valid Activity Types... OK
#> 	Checking Activity Start Date formats... OK
#> 	Checking depth data present... OK
#> 	Checking for non-numeric values in Activity Depth/Height Measure... OK
#> 	Checking Activity Depth/Height Unit... OK
#> 	Checking Activity Relative Depth Name formats... OK
#> 	Checking values in Activity Depth/Height Measure > 1 m / 3.3 ft... OK
#> 	Checking Characteristic Name formats... OK
#> 	Checking Result Values... OK
#> 	Checking for non-numeric values in Quantitation Limit... OK
#> 	Checking QC Reference Values... OK
#> 	Checking for missing entries for Result Unit... OK
#> 	Checking if more than one unit per Characteristic Name... OK
#> 	Checking acceptable units for each entry in Characteristic Name... OK
#> 
#> All checks passed!

# accuracy path
accpth <- system.file('extdata/ExampleDQOAccuracy.xlsx', 
     package = 'MassWateR')

# accuracy data
accdat <- readMWRacc(accpth)
#> Running checks on data quality objectives for accuracy...
#> 	Checking column names... OK
#> 	Checking all required columns are present... OK
#> 	Checking column types... OK
#> 	Checking no "na" in Value Range... OK
#> 	Checking for text other than <=, ≤, <, >=, ≥, >, ±, %, AQL, BQL, log, or all... OK
#> 	Checking overlaps in Value Range... OK
#> 	Checking gaps in Value Range... OK
#> 	Checking Parameter formats... OK
#> 	Checking for missing entries for unit (uom)... OK
#> 	Checking if more than one unit (uom) per Parameter... OK
#> 	Checking acceptable units (uom) for each entry in Parameter... OK
#> 	Checking empty columns... OK
#> 
#> All checks passed!

# \donttest{
# create word output
anlzMWRoutlierall(resdat, accdat, group = 'month', format = 'word', output_dir = tempdir())
#> Word document created successfully! File located at /tmp/Rtmp1xXRSs/outlierall.docx

# create png output
anlzMWRoutlierall(resdat, accdat, group = 'month', format = 'png', output_dir = tempdir())
#> PNG files created successfully! Files located at /tmp/Rtmp1xXRSs
# }