Analyze outliers in results file for all parameters
Source:R/anlzMWRoutlierall.R
anlzMWRoutlierall.Rd
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", "zip"),
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,
bssize = 11,
runchk = TRUE,
warn = TRUE
)
Arguments
- res
character string of path to the results file or
data.frame
for results returned byreadMWRresults
- acc
character string of path to the data quality objectives file for accuracy or
data.frame
returned byreadMWRacc
- fset
optional list of inputs with elements named
res
,acc
,frecom
,sit
, orwqx
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, as separate png files, or as a zipped file of 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
- bssize
numeric for overall plot text scaling, passed to
theme_minimal
- runchk
logical to run data checks with
checkMWRresults
orcheckMWRacc
, applies only ifres
oracc
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/RtmpRCuadE/outlierall.docx
# create png output
anlzMWRoutlierall(resdat, accdat, group = 'month', format = 'png', output_dir = tempdir())
#> PNG files created successfully! Files located at /tmp/RtmpRCuadE
# create zipped png output
anlzMWRoutlierall(resdat, accdat, group = 'month', format = 'zip', output_dir = tempdir())
#> PNG files created successfully! Zipped files located at /tmp/RtmpRCuadE
# }