diff --git a/vignettes/TADAR5.Rmd b/vignettes/TADAR5.Rmd index e1fd16d4..783d8eb8 100644 --- a/vignettes/TADAR5.Rmd +++ b/vignettes/TADAR5.Rmd @@ -191,7 +191,9 @@ table or pie chart of the counts of unique values in a user-specified field with ```{r fieldValues_actmedia, fig.width=8, fig.height=6, fig.fullwidth=TRUE} # Create pie chart for ActivityMediaName -TADA_FieldValuesPie(R5Profile, field = "ActivityMediaName") +ActMedName_Pie <- TADA_FieldValuesPie(R5Profile, field = "ActivityMediaName") + +ActMedName_Pie # Create table with count for each ActivityMediaName FieldValues_ActMedia <- TADA_FieldValuesTable(R5Profile, field = "ActivityMediaName") @@ -240,11 +242,11 @@ We can use **TADA_FieldValuesTable** and **TADA_FieldValuesPie** again to review R5Profile <- TADA_AnalysisDataFilter(R5Profile, clean = FALSE) # Create pie chart for TADA.UseForAnalysis.Flag -TADA_FieldValuesPie(R5Profile, field = "TADA.UseForAnalysis.Flag") - -FieldValues_AnalysisFlag <- TADA_FieldValuesTable(R5Profile, field = "TADA.UseForAnalysis.Flag") +FieldVal_Pie <- TADA_FieldValuesPie(R5Profile, field = "TADA.UseForAnalysis.Flag") +FieldVal_Pie +FieldValues_AnalysisFlag <- TADA_FieldValuesTable(R5Profile, field = "TADA.UseForAnalysis.Flag") ``` `r rmarkdown::paged_table(FieldValues_AnalysisFlag)` @@ -300,7 +302,6 @@ specify what the special characters are. ``` {r TADA_AutoClean} # run TADA_AutoClean on filtered dataset to convert special characters, result units, and depth units and identify censored data. R5Profile <- TADA_AutoClean(R5Profile) - ``` ## Monitoring Location Review @@ -308,7 +309,9 @@ R5Profile <- TADA_AutoClean(R5Profile) Now let's take a look at a breakdown of these monitoring location types. The previous function removed non-surface water results. Depending upon your program's goals and methods, you might want to further filter the monitoring location types in the data set.. ```{r MonitoringLocations, fig.width=8, fig.height=6, fig.fullwidth=TRUE} -TADA_FieldValuesPie(R5Profile, field = "MonitoringLocationTypeName") +MonLocTypNam_Pie <- TADA_FieldValuesPie(R5Profile, field = "MonitoringLocationTypeName") + +MonLocTypNam_Pie ``` **Question 4: How many unique Monitoring Location Types (MonitoringLocationTypeName) are present? Which is the most common?** @@ -343,7 +346,9 @@ characteristics collected at the site. Users may click on a site to view a pop-up with this summary information. This can be a good first step in identifying incorrect coordinates that are outside of the desired state(s) of interest or outside of the US. ```{r Map, fig.width=8, fig.height=6, fig.fullwidth=TRUE} -TADA_OverviewMap(R5Profile) +OvwMap <- TADA_OverviewMap(R5Profile) + +OvwMap ``` @@ -710,7 +715,9 @@ R5ProfileClean5 <- TADA_FindQCActivities(R5ProfileClean4, ) # Generate pie chart for ActivityTypeCode -TADA_FieldValuesPie(R5ProfileClean5, "ActivityTypeCode") +ActTypCod_Pie <- TADA_FieldValuesPie(R5ProfileClean5, "ActivityTypeCode") + +ActTypCod_Pie ``` **Question 10: How many ActivityTypeCodes are present after removing QC samples? Which ActivityTypeCode is the most common?** @@ -732,7 +739,9 @@ that we want to remove. In this next example, there are multiple MeasureQualifie review. ```{r MeasureQualifierCodeReview, fig.width=8, fig.height=6, fig.fullwidth=TRUE} -TADA_FieldValuesPie(R5ProfileClean5, "MeasureQualifierCode") +MQC_Pie <- TADA_FieldValuesPie(R5ProfileClean5, "MeasureQualifierCode") + +MQC_Pie ``` MeasureQualifierCode definitions are available @@ -959,7 +968,9 @@ To start, review the list of parameters in the dataframe using the ```{r TADA_FieldValuesTable_chars} -FieldValuesTable_Chars <- TADA_FieldValuesTable(R5ProfileClean8, field = "TADA.CharacteristicName") +Char_Pie <- FieldValuesTable_Chars <- TADA_FieldValuesTable(R5ProfileClean8, field = "TADA.CharacteristicName") + +Char_Pie ``` `r rmarkdown::paged_table(FieldValuesTable_Chars)` @@ -1048,25 +1059,27 @@ characteristic-level to review a column of interest. In this example we review v ```{r DO_Method, fig.width=8, fig.height=6, fig.fullwidth=TRUE} #C Create pie chart for SampleCollectionMethod.MethodName for Dissolved Oxygen (DO results) -TADA_FieldValuesPie(R5ProfileClean8, field = "SampleCollectionMethod.MethodName", characteristicName = "DISSOLVED OXYGEN (DO)") +DO_SCM_Pie <- TADA_FieldValuesPie(R5ProfileClean8, field = "SampleCollectionMethod.MethodName", characteristicName = "DISSOLVED OXYGEN (DO)") + +DO_SCM_Pie # Create table for SampleCollectionMethod.MethodName for Dissolved Oxygen (DO results) FieldValuesTable_DO_scm <- TADA_FieldValuesTable(R5ProfileClean8, field = "SampleCollectionMethod.MethodName", characteristicName = "DISSOLVED OXYGEN (DO)") - - ``` `r rmarkdown::paged_table(FieldValuesTable_DO_scm)` Generate a scatterplot with two characteristics. -```{r review_identifiers, fig.width=8, fig.height=6, fig.fullwidth=TRUE} +```{r review_identifiers} # review unique identifiers unique(R5ProfileClean8$TADA.ComparableDataIdentifier) ``` ```{r TADA_TwoCharacteristicScatterplot, echo=TRUE, fig.fullwidth=TRUE, fig.height=6, fig.width=8} # choose two and generate scatterplot -TADA_TwoCharacteristicScatterplot(R5ProfileClean8, id_cols = "TADA.ComparableDataIdentifier", groups = c("TEMPERATURE_NA_NA_DEG C", "DISSOLVED OXYGEN (DO)_NA_NA_MG/L")) +DO_Temp_Scatter <- TADA_TwoCharacteristicScatterplot(R5ProfileClean8, id_cols = "TADA.ComparableDataIdentifier", groups = c("TEMPERATURE_NA_NA_DEG C", "DISSOLVED OXYGEN (DO)_NA_NA_MG/L")) + +DO_Temp_Scatter ``` @@ -1074,14 +1087,16 @@ Now we will summarize results for a single comparable data group using the TADA.ComparableDataIdentifier (i.e., comparable characteristic, unit, speciation, and fraction combination) using **TADA_Histogram** and **TADA_Boxplot**. Note that users may generate a list output of multiple plots if their input dataset has more than one unique comparable data group. -```{r filter_dataframe, echo=TRUE, fig.fullwidth=TRUE, fig.height=6, fig.width=8} +```{r filter_dataframe, echo=TRUE} # filter dataframe to only "DISSOLVED OXYGEN (DO)_NA_NA_MG/L" R5ProfileCleanDO <- dplyr::filter(R5ProfileClean8, TADA.ComparableDataIdentifier == "DISSOLVED OXYGEN (DO)_NA_NA_MG/L") ``` ```{r Histogram, echo=TRUE, fig.fullwidth=TRUE, fig.height=6, fig.width=8} # generate a histogram -TADA_Histogram(R5ProfileCleanDO, id_cols = "TADA.ComparableDataIdentifier") +DO_Hist <- TADA_Histogram(R5ProfileCleanDO, id_cols = "TADA.ComparableDataIdentifier") + +DO_Hist # generate stats table R5ProfileCleanDO_stats <- TADA_Stats(R5ProfileCleanDO) @@ -1092,7 +1107,9 @@ R5ProfileCleanDO_stats <- TADA_Stats(R5ProfileCleanDO) Generate interactive box plot. ```{r boxplot, echo=TRUE, fig.fullwidth=TRUE, fig.height=6, fig.width=8} -TADA_Boxplot(R5ProfileCleanDO, id_cols = "TADA.ComparableDataIdentifier") +DO_Box <- TADA_Boxplot(R5ProfileCleanDO, id_cols = "TADA.ComparableDataIdentifier") + +DO_Box ``` Generate interactive scatterplot. @@ -1105,7 +1122,9 @@ R5ProfileCleanDO_dailymax <- TADA_AggregateMeasurements(R5ProfileCleanDO, ``` ```{r scatterplot, echo=TRUE, fig.fullwidth=TRUE, fig.height=6, fig.width=8} -TADA_Scatterplot(R5ProfileCleanDO_dailymax, id_cols = "TADA.ComparableDataIdentifier") +DO_Scatter <- TADA_Scatterplot(R5ProfileCleanDO_dailymax, id_cols = "TADA.ComparableDataIdentifier") + +DO_Scatter ``` **Question 15: Which figure generating functions can be used to visualize more than one characteristic? Which can be used to visualize only one characteristic?**