From 020bce41dd821b5949f824eaa3a2998584a14585 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 15 Oct 2019 11:27:59 +0200 Subject: Residue processing for depth profiles over time --- docs/reference/set_nd.html | 222 --------------------------------------------- 1 file changed, 222 deletions(-) delete mode 100644 docs/reference/set_nd.html (limited to 'docs/reference/set_nd.html') diff --git a/docs/reference/set_nd.html b/docs/reference/set_nd.html deleted file mode 100644 index 7b0e779..0000000 --- a/docs/reference/set_nd.html +++ /dev/null @@ -1,222 +0,0 @@ - - - - - - - - -Set non-detects in residue series without replicates — set_nd • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Set non-detects in residue series without replicates

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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.

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set_nd(r, lod, loq = NA, time_zero = TRUE, time_zero_nd_value = NA,
-  stop_after_first_nondetect = FALSE)
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-set_nd_focus(r, lod, loq = NA, time_zero = TRUE)
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Arguments

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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

lod

Limit of detection (numeric)

loq

Limit of quantification(numeric). Must be specified if the FOCUS rule to -stop after the first non-detection is to be applied

time_zero

Is the first value in the series a time zero value?

time_zero_nd_value

Which value should we use for non-detects or zero values at time zero?

stop_after_first_nondetect

Should we really stop after the first non-detection?

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Functions

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  • set_nd: Set non-detects in residues series

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

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References

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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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Examples

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# 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")
-set_nd(metabolite, 0.02)
#>  [1]   NA   NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01   NA
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