From a5503d3e26408f7308a7bf4da617205b93d17422 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 10 Oct 2019 09:21:46 +0200 Subject: Fix documentation for set_nd --- R/set_nd.R | 10 +++++++--- docs/reference/index.html | 11 +---------- docs/reference/set_nd.html | 47 +++++++++++----------------------------------- man/set_nd.Rd | 19 +++++++------------ 4 files changed, 26 insertions(+), 61 deletions(-) diff --git a/R/set_nd.R b/R/set_nd.R index 5d98940..10c5cba 100644 --- a/R/set_nd.R +++ b/R/set_nd.R @@ -1,5 +1,5 @@ #' Set non-detects in residue series without replicates - +#' #' Sets non-detects directly before or directly after detects to NA. Values between #' lod and loq are set to their mean value if an loq is specified. #' If 'time_zero' is set to TRUE, the residue series is assumed to start with time @@ -9,7 +9,7 @@ #' If stopping after the first non-detection is requested, as in in the FOCUS #' variant of the function, an loq has to be specified in order to decide #' if any later detections are above the loq. - +#' #' @param r A character vector of sequential residues without replicates, with #' non-detects specified as 'nd' and unquantified values above the limit of #' detection specified as 'nq', otherwise coercible to numeric @@ -19,9 +19,13 @@ #' @param time_zero Is the first value in the series a time zero value? #' @param time_zero_nd_value Which value should we use for non-detects at time zero? #' @param stop_after_first_nondetect Should we really stop after the first non-detection? -#' @references FOCUS (2014) p. 75, 76, 131, 132 +#' @references FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation +#' Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, +#' 18 December 2014, p. 251 +#' @describeIn set_nd Set non-detects in residues series #' @export #' @examples +#' # FOCUS (2014) p. 75/76 and 131/132 #' parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd") #' set_nd(parent_1, 0.02) #' parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd") diff --git a/docs/reference/index.html b/docs/reference/index.html index a704ad0..455ee07 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -172,16 +172,7 @@

set_nd() set_nd_focus()

-

Set non-detects in residue series without replicates -Sets non-detects directly before or directly after detects to NA. Values between -lod and loq are set to their mean value if an loq is specified. -If 'time_zero' is set to TRUE, the residue series is assumed to start with time -zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the -set_nd_focus variant, this is zero, otherwise this argument has NA as default -value. -If stopping after the first non-detection is requested, as in in the FOCUS -variant of the function, an loq has to be specified in order to decide -if any later detections are above the loq.

+

Set non-detects in residue series without replicates

diff --git a/docs/reference/set_nd.html b/docs/reference/set_nd.html index 32ac155..75a8fb1 100644 --- a/docs/reference/set_nd.html +++ b/docs/reference/set_nd.html @@ -6,16 +6,7 @@ -Set non-detects in residue series without replicates -Sets non-detects directly before or directly after detects to NA. Values between -lod and loq are set to their mean value if an loq is specified. -If 'time_zero' is set to TRUE, the residue series is assumed to start with time -zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the -set_nd_focus variant, this is zero, otherwise this argument has NA as default -value. -If stopping after the first non-detection is requested, as in in the FOCUS -variant of the function, an loq has to be specified in order to decide -if any later detections are above the loq. — set_nd • pfm +Set non-detects in residue series without replicates — set_nd • pfm @@ -41,19 +32,9 @@ if any later detections are above the loq. — set_nd • pfm - + -
-

Set non-detects in residue series without replicates -Sets non-detects directly before or directly after detects to NA. Values between -lod and loq are set to their mean value if an loq is specified. -If 'time_zero' is set to TRUE, the residue series is assumed to start with time -zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the -set_nd_focus variant, this is zero, otherwise this argument has NA as default -value. -If stopping after the first non-detection is requested, as in in the FOCUS -variant of the function, an loq has to be specified in order to decide -if any later detections are above the loq.

+

Set non-detects in residue series without replicates

-

Set non-detects in residue series without replicates -Sets non-detects directly before or directly after detects to NA. Values between +

Sets non-detects directly before or directly after detects to NA. Values between lod and loq are set to their mean value if an loq is specified. If 'time_zero' is set to TRUE, the residue series is assumed to start with time zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the @@ -195,16 +166,20 @@ stop after the first non-detection is to be applied

    +

  • set_nd: Set non-detects in residues series

  • set_nd_focus: Set non-detects in residues series according to FOCUS rules

References

-

FOCUS (2014) p. 75, 76, 131, 132

+

FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation + Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, + 18 December 2014, p. 251

Examples

- 
parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
+    
# FOCUS (2014) p. 75/76 and 131/132
+parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
 set_nd(parent_1, 0.02)
#>  [1] 0.12 0.09 0.05 0.03 0.01   NA   NA   NA   NA   NA
parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
 set_nd(parent_2, 0.02)
#>  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01   NA   NA
set_nd_focus(parent_2, 0.02, loq = 0.05)
#>  [1] 0.12 0.09 0.05 0.03 0.01   NA   NA   NA   NA   NA
parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
 set_nd(parent_3, 0.02)
#>  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01   NA   NA
set_nd_focus(parent_3, 0.02, loq = 0.05)
#>  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01   NA   NA
metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
diff --git a/man/set_nd.Rd b/man/set_nd.Rd
index 8c6003c..bdbc6d2 100644
--- a/man/set_nd.Rd
+++ b/man/set_nd.Rd
@@ -3,16 +3,7 @@
 \name{set_nd}
 \alias{set_nd}
 \alias{set_nd_focus}
-\title{Set non-detects in residue series without replicates
-Sets non-detects directly before or directly after detects to NA. Values between
-lod and loq are set to their mean value if an loq is specified.
-If 'time_zero' is set to TRUE, the residue series is assumed to start with time
-zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
-set_nd_focus variant, this is zero, otherwise this argument has NA as default
-value.
-If stopping after the first non-detection is requested, as in in the FOCUS
-variant of the function, an loq has to be specified in order to decide
-if any later detections are above the loq.}
+\title{Set non-detects in residue series without replicates}
 \usage{
 set_nd(r, lod, loq = NA, time_zero = TRUE, time_zero_nd_value = NA,
   stop_after_first_nondetect = FALSE)
@@ -36,7 +27,6 @@ stop after the first non-detection is to be applied}
 \item{stop_after_first_nondetect}{Should we really stop after the first non-detection?}
 }
 \description{
-Set non-detects in residue series without replicates
 Sets non-detects directly before or directly after detects to NA. Values between
 lod and loq are set to their mean value if an loq is specified.
 If 'time_zero' is set to TRUE, the residue series is assumed to start with time
@@ -49,10 +39,13 @@ if any later detections are above the loq.
 }
 \section{Functions}{
 \itemize{
+\item \code{set_nd}: Set non-detects in residues series
+
 \item \code{set_nd_focus}: Set non-detects in residues series according to FOCUS rules
 }}
 
 \examples{
+# FOCUS (2014) p. 75/76 and 131/132
 parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
 set_nd(parent_1, 0.02)
 parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
@@ -65,5 +58,7 @@ metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03
 set_nd(metabolite, 0.02)
 }
 \references{
-FOCUS (2014) p. 75, 76, 131, 132
+FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
+  Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 
+  18 December 2014, p. 251
 }
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