fix formatting of itemized lists in documentation

R/checkMWRacc.R

@@ -7,19 +7,19 @@
 #' 
 #' The following checks are made: 
 #' \itemize{
-#'  \item{Column name spelling: }{Should be the following: Parameter, uom, MDL, UQL, Value Range, Field Duplicate, Lab Duplicate, Field Blank, Lab Blank, Spike/Check Accuracy}
-#'  \item{Columns present: }{All columns from the previous check should be present}
-#'  \item{Column types: }{All columns should be characters/text, except for MDL and UQL}
-#'  \item{\code{Value Range} column na check: }{The character string \code{"na"} should not be in the \code{Value Range} column, \code{"all"} should be used if the entire range applies}
-#'  \item{Unrecognized characters: }{Fields describing accuracy checks should not include symbols or text other than \eqn{<=}, \eqn{\leq}, \eqn{<}, \eqn{>=}, \eqn{\geq}, \eqn{>}, \eqn{\pm}, \code{"\%"}, \code{"BDL"}, \code{"AQL"}, \code{"log"}, or \code{"all"}}
-#'  \item{Number of rows per parameter in \code{Value Range}: }{Should not exceed two}
-#'  \item{Overlap in \code{Value Range} column: }{Entries in \code{Value Range} should not overlap for a parameter}
-#'  \item{Gap in \code{Value Range} column: }{Entries in \code{Value Range} should not include a gap for a parameter, warning only}
-#'  \item{Parameter: }{Should match parameter names in the \code{Simple Parameter} or \code{WQX Parameter} columns of the \code{\link{paramsMWR}} data}
-#'  \item{Units: }{No missing entries in units (\code{uom}), except pH which can be blank}
-#'  \item{Single unit: }{Each unique \code{Parameter} should have only one type for the units (\code{uom})}
-#'  \item{Correct units: }{Each unique \code{Parameter} should have an entry in the units (\code{uom}) that matches one of the acceptable values in the \code{Units of measure} column of the \code{\link{paramsMWR}} data}
-#'  \item{Empty columns: }{Columns with all missing or NA values will return a warning}
+#'  \item Column name spelling: Should be the following: Parameter, uom, MDL, UQL, Value Range, Field Duplicate, Lab Duplicate, Field Blank, Lab Blank, Spike/Check Accuracy
+#'  \item Columns present: All columns from the previous check should be present
+#'  \item Column types: All columns should be characters/text, except for MDL and UQL
+#'  \item \code{Value Range} column na check: The character string \code{"na"} should not be in the \code{Value Range} column, \code{"all"} should be used if the entire range applies
+#'  \item Unrecognized characters: Fields describing accuracy checks should not include symbols or text other than \eqn{<=}, \eqn{\leq}, \eqn{<}, \eqn{>=}, \eqn{\geq}, \eqn{>}, \eqn{\pm}, \code{"\%"}, \code{"BDL"}, \code{"AQL"}, \code{"log"}, or \code{"all"}
+#'  \item Number of rows per parameter in \code{Value Range}: Should not exceed two
+#'  \item Overlap in \code{Value Range} column: Entries in \code{Value Range} should not overlap for a parameter
+#'  \item Gap in \code{Value Range} column: Entries in \code{Value Range} should not include a gap for a parameter, warning only
+#'  \item Parameter: Should match parameter names in the \code{Simple Parameter} or \code{WQX Parameter} columns of the \code{\link{paramsMWR}} data
+#'  \item Units: No missing entries in units (\code{uom}), except pH which can be blank
+#'  \item Single unit: Each unique \code{Parameter} should have only one type for the units (\code{uom})
+#'  \item Correct units: Each unique \code{Parameter} should have an entry in the units (\code{uom}) that matches one of the acceptable values in the \code{Units of measure} column of the \code{\link{paramsMWR}} data
+#'  \item Empty columns: Columns with all missing or NA values will return a warning
 #' }
 #'
 #' @return \code{accdat} is returned as is if no errors are found, otherwise an informative error message is returned prompting the user to make the required correction to the raw data before proceeding. 

R/checkMWRfrecom.R

@@ -7,12 +7,12 @@
 #' 
 #' The following checks are made: 
 #' \itemize{
-#'  \item{Column name spelling: }{Should be the following: Parameter, Field Duplicate, Lab Duplicate, Field Blank, Lab Blank, Spike/Check Accuracy, % Completeness}
-#'  \item{Columns present: }{All columns from the previous check should be present}
-#'  \item{Non-numeric values: }{Values entered in columns other than the first should be numeric}
-#'  \item{Values outside of 0 - 100: }{Values entered in columns other than the first should not be outside of 0 and 100}
-#'  \item{Parameter: }{Should match parameter names in the \code{Simple Parameter} or \code{WQX Parameter} columns of the \code{\link{paramsMWR}} data}
-#'  \item{Empty columns: }{Columns with all missing or NA values will return a warning}
+#'  \item Column name spelling: Should be the following: Parameter, Field Duplicate, Lab Duplicate, Field Blank, Lab Blank, Spike/Check Accuracy, % Completeness
+#'  \item Columns present: All columns from the previous check should be present
+#'  \item Non-numeric values: Values entered in columns other than the first should be numeric
+#'  \item Values outside of 0 - 100: Values entered in columns other than the first should not be outside of 0 and 100
+#'  \item Parameter: Should match parameter names in the \code{Simple Parameter} or \code{WQX Parameter} columns of the \code{\link{paramsMWR}} data
+#'  \item Empty columns: Columns with all missing or NA values will return a warning
 #' }
 #' 
 #' @return \code{frecomdat} is returned as is if no errors are found, otherwise an informative error message is returned prompting the user to make the required correction to the raw data before proceeding. 

R/checkMWRresults.R

@@ -7,21 +7,21 @@
 #' 
 #' The following checks are made: 
 #' \itemize{
-#'  \item{Column name spelling: }{Should be the following: Monitoring Location ID, Activity Type, Activity Start Date, Activity Start Time, Activity Depth/Height Measure, Activity Depth/Height Unit, Activity Relative Depth Name, Characteristic Name, Result Value, Result Unit, Quantitation Limit, QC Reference Value, Result Measure Qualifier, Result Attribute, Sample Collection Method ID, Project ID, Local Record ID, Result Comment}
-#'  \item{Columns present: }{All columns from the previous check should be present}
-#'  \item{Activity Type: }{Should be one of Field Msr/Obs, Sample-Routine, Quality Control Sample-Field Blank, Quality Control Sample-Lab Blank, Quality Control Sample-Lab Duplicate, Quality Control Sample-Lab Spike, Quality Control-Calibration Check, Quality Control-Meter Lab Duplicate, Quality Control-Meter Lab Blank}
-#'  \item{Date formats: }{Should be mm/dd/yyyy and parsed correctly on import}
-#'  \item{Depth data present: }{Depth data should be included in Activity Depth/Height Measure or Activity Relative Depth Name for all rows where Activity Type is Field Msr/Obs or Sample-Routine}
-#'  \item{Non-numeric Activity Depth/Height Measure: }{All depth values should be numbers, excluding missing values}
-#'  \item{Activity Depth/Height Unit: }{All entries should be \code{ft}, \code{m}, or blank}
-#'  \item{Activity Relative Depth Name: }{Should be either Surface, Bottom, Midwater, Near Bottom, or blank (warning only)}
-#'  \item{Activity Depth/Height Measure out of range: }{All depth values should be less than or equal to 1 meter / 3.3 feet or entered as Surface in the Activity Relative Depth Name column (warning only)}
-#'  \item{Characteristic Name: }{Should match parameter names in the \code{Simple Parameter} or \code{WQX Parameter} columns of the \code{\link{paramsMWR}} data (warning only)}
-#'  \item{Result Value: }{Should be a numeric value or a text value as AQL or BDL}
-#'  \item{QC Reference Value: }{Should be a numeric value or a text value as AQL or BDL}
-#'  \item{Result Unit: }{No missing entries in \code{Result Unit}, except pH which can be blank}
-#'  \item{Single Result Unit: }{Each unique parameter in \code{Characteristic Name} should have only one entry in \code{Result Unit} (excludes entries for lab spikes reported as \code{\%} or \code{\% recovery})}
-#'  \item{Correct Result Unit: }{Each unique parameter in \code{Characteristic Name} should have an entry in \code{Result Unit} that matches one of the acceptable values in the \code{Units of measure} column of the \code{\link{paramsMWR}} data (excludes entries for lab spikes reported as \code{\%} or \code{\% recovery})}
+#'  \item Column name spelling: Should be the following: Monitoring Location ID, Activity Type, Activity Start Date, Activity Start Time, Activity Depth/Height Measure, Activity Depth/Height Unit, Activity Relative Depth Name, Characteristic Name, Result Value, Result Unit, Quantitation Limit, QC Reference Value, Result Measure Qualifier, Result Attribute, Sample Collection Method ID, Project ID, Local Record ID, Result Comment
+#'  \item Columns present: All columns from the previous check should be present
+#'  \item Activity Type: Should be one of Field Msr/Obs, Sample-Routine, Quality Control Sample-Field Blank, Quality Control Sample-Lab Blank, Quality Control Sample-Lab Duplicate, Quality Control Sample-Lab Spike, Quality Control-Calibration Check, Quality Control-Meter Lab Duplicate, Quality Control-Meter Lab Blank
+#'  \item Date formats: Should be mm/dd/yyyy and parsed correctly on import
+#'  \item Depth data present: Depth data should be included in Activity Depth/Height Measure or Activity Relative Depth Name for all rows where Activity Type is Field Msr/Obs or Sample-Routine
+#'  \item Non-numeric Activity Depth/Height Measure: All depth values should be numbers, excluding missing values
+#'  \item Activity Depth/Height Unit: All entries should be \code{ft}, \code{m}, or blank
+#'  \item Activity Relative Depth Name: Should be either Surface, Bottom, Midwater, Near Bottom, or blank (warning only)
+#'  \item Activity Depth/Height Measure out of range: All depth values should be less than or equal to 1 meter / 3.3 feet or entered as Surface in the Activity Relative Depth Name column (warning only)
+#'  \item Characteristic Name: Should match parameter names in the \code{Simple Parameter} or \code{WQX Parameter} columns of the \code{\link{paramsMWR}} data (warning only)
+#'  \item Result Value: Should be a numeric value or a text value as AQL or BDL
+#'  \item QC Reference Value: Should be a numeric value or a text value as AQL or BDL
+#'  \item Result Unit: No missing entries in \code{Result Unit}, except pH which can be blank
+#'  \item Single Result Unit: Each unique parameter in \code{Characteristic Name} should have only one entry in \code{Result Unit} (excludes entries for lab spikes reported as \code{\%} or \code{\% recovery})
+#'  \item Correct Result Unit: Each unique parameter in \code{Characteristic Name} should have an entry in \code{Result Unit} that matches one of the acceptable values in the \code{Units of measure} column of the \code{\link{paramsMWR}} data (excludes entries for lab spikes reported as \code{\%} or \code{\% recovery})
 #' }
 #' 
 #' @return \code{resdat} is returned as is if no errors are found, otherwise an informative error message is returned prompting the user to make the required correction to the raw data before proceeding. Checks with warnings can be fixed at the discretion of the user before proceeding.

R/checkMWRsites.R

@@ -6,13 +6,13 @@
 #' 
 #' The following checks are made: 
 #' \itemize{
-#'  \item{Column name spelling: }{Should be the following: Monitoring Location ID, Monitoring Location Name, Monitoring Location Latitude, Monitoring Location Longitude, Location Group}
-#'  \item{Columns present: }{All columns from the previous check should be present}
-#'  \item{Missing longitude or latitude: }{No missing entries in Monitoring Location Latitude or Monitoring Location Longitude}
-#'  \item{Non-numeric latitude values: }{Values entered in Monitoring Location Latitude must be numeric}
-#'  \item{Non-numeric longitude values: }{Values entered in Monitoring Location Longitude must be numeric}
-#'  \item{Positive longitude values: }{Values in Monitoring Location Longitude must be negative}
-#'  \item{Missing Location ID: }{No missing entries for Monitoring Location ID}
+#'  \item Column name spelling: Should be the following: Monitoring Location ID, Monitoring Location Name, Monitoring Location Latitude, Monitoring Location Longitude, Location Group
+#'  \item Columns present: All columns from the previous check should be present
+#'  \item Missing longitude or latitude: No missing entries in Monitoring Location Latitude or Monitoring Location Longitude
+#'  \item Non-numeric latitude values: Values entered in Monitoring Location Latitude must be numeric
+#'  \item Non-numeric longitude values: Values entered in Monitoring Location Longitude must be numeric
+#'  \item Positive longitude values: Values in Monitoring Location Longitude must be negative
+#'  \item Missing Location ID: No missing entries for Monitoring Location ID
 #' }
 #' 
 #' @return \code{sitdat} is returned as is if no errors are found, otherwise an informative error message is returned prompting the user to make the required correction to the raw data before proceeding. 

R/checkMWRwqx.R

@@ -7,10 +7,10 @@
 #' 
 #' The following checks are made: 
 #' \itemize{
-#'  \item{Column name spelling: }{Should be the following: Parameter, Sampling Method Context, Method Speciation, Result Sample Fraction, Analytical Method, Analytical Method Context}
-#'  \item{Columns present: }{All columns from the previous check should be present}
-#'  \item{Unique parameters: }{Values in \code{Parameter} should be unique (no duplicates)}
-#'  \item{Parameter: }{Should match parameter names in the \code{Simple Parameter} or \code{WQX Parameter} columns of the \code{\link{paramsMWR}} data (warning only)}
+#'  \item Column name spelling: Should be the following: Parameter, Sampling Method Context, Method Speciation, Result Sample Fraction, Analytical Method, Analytical Method Context
+#'  \item Columns present: All columns from the previous check should be present
+#'  \item Unique parameters: Values in \code{Parameter} should be unique (no duplicates)
+#'  \item Parameter: Should match parameter names in the \code{Simple Parameter} or \code{WQX Parameter} columns of the \code{\link{paramsMWR}} data (warning only)
 #' }
 #' 
 #' @return \code{wqxdat} is returned as is if no errors are found, otherwise an informative error message is returned prompting the user to make the required correction to the raw data before proceeding. Checks with warnings can be fixed at the discretion of the user before proceeding.

R/formMWRacc.R

@@ -5,10 +5,10 @@
 #' @details This function is used internally within \code{\link{readMWRacc}} to format the input data for downstream analysis.  The formatting includes:
 #' 
 #' \itemize{
-#'   \item{Minor formatting for units: }{For conformance to WQX, e.g., ppt is changed to ppth, s.u. is changed to NA in \code{uom}}
-#'   \item{Convert Parameter: }{All parameters are converted to \code{Simple Parameter} in \code{\link{paramsMWR}} as needed}
-#'   \item{Remove unicode: }{Remove or replace unicode characters with those that can be used in logical expressions in \code{\link{qcMWRacc}}, e.g., replace \eqn{\geq} with \eqn{>=}}
-#'   \item{Convert limits to numeric: }{Convert \code{MDL} and \code{UQL} columns to numeric}
+#'   \item Minor formatting for units: For conformance to WQX, e.g., ppt is changed to ppth, s.u. is changed to NA in \code{uom}
+#'   \item Convert Parameter: All parameters are converted to \code{Simple Parameter} in \code{\link{paramsMWR}} as needed
+#'   \item Remove unicode: Remove or replace unicode characters with those that can be used in logical expressions in \code{\link{qcMWRacc}}, e.g., replace \eqn{\geq} with \eqn{>=}
+#'   \item Convert limits to numeric: Convert \code{MDL} and \code{UQL} columns to numeric
 #' }
 #' 
 #' @return A formatted data frame of the data quality objectives file for accuracy

R/formMWRfrecom.R

@@ -5,7 +5,7 @@
 #' @details This function is used internally within \code{\link{readMWRfrecom}} to format the input data for downstream analysis.  The formatting includes:
 #' 
 #' \itemize{
-#'   \item{Convert Parameter: }{All parameters are converted to \code{Simple Parameter} in \code{\link{paramsMWR}} as needed}
+#'   \item Convert Parameter: All parameters are converted to \code{Simple Parameter} in \code{\link{paramsMWR}} as needed
 #' }
 #' 
 #' @return A formatted data frame of the data quality objectives file for frequency and completeness

R/formMWRresults.R

@@ -6,9 +6,9 @@
 #' @details This function is used internally within \code{\link{readMWRresults}} to format the input data for downstream analysis.  The formatting includes:
 #' 
 #' \itemize{
-#'   \item{Fix date and time inputs: }{Activity Start Date is converted to YYYY-MM-DD as a date object, Actvity Start Time is convered to HH:MM as a character to fix artifacts from Excel import},
-#'   \item{Minor formatting for Result Unit: }{For conformance to WQX, e.g., ppt is changed to ppth, s.u. is changed to NA}
-#'   \item{Convert characteristic names: }{All parameters in \code{Characteristic Name} are converted to \code{Simple Parameter} in \code{\link{paramsMWR}} as needed}
+#'   \item Fix date and time inputs: Activity Start Date is converted to YYYY-MM-DD as a date object, Actvity Start Time is convered to HH:MM as a character to fix artifacts from Excel import
+#'   \item Minor formatting for Result Unit: For conformance to WQX, e.g., ppt is changed to ppth, s.u. is changed to NA
+#'   \item Convert characteristic names: All parameters in \code{Characteristic Name} are converted to \code{Simple Parameter} in \code{\link{paramsMWR}} as needed
 #' }
 #' 
 #' @return A formatted data frame of the water quality monitoring results file

R/formMWRwqx.R

@@ -5,7 +5,7 @@
 #' @details This function is used internally within \code{\link{readMWRwqx}} to format the input data for downstream analysis.  The formatting includes:
 #' 
 #' \itemize{
-#'   \item{Convert characteristic names: }{All parameters in \code{Characteristic Name} are converted to \code{Simple Parameter} in \code{\link{paramsMWR}} as needed}
+#'   \item Convert characteristic names: All parameters in \code{Characteristic Name} are converted to \code{Simple Parameter} in \code{\link{paramsMWR}} as needed
 #' }
 #' 
 #' @import dplyr