From a5e458ecb33ae87e46b2237174a194f6252a97cf Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 10 Oct 2019 08:53:30 +0200 Subject: Finish documentation of set_nd and test it --- docs/reference/index.html | 15 +++ docs/reference/set_nd.html | 247 +++++++++++++++++++++++++++++++++++++++++++++ docs/sitemap.xml | 3 + 3 files changed, 265 insertions(+) create mode 100644 docs/reference/set_nd.html (limited to 'docs') diff --git a/docs/reference/index.html b/docs/reference/index.html index e1acfc1..a704ad0 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -167,6 +167,21 @@

FOMC_actual_twa()

Actual and maximum moving window time average concentrations for FOMC kinetics

+ + + +

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.

diff --git a/docs/reference/set_nd.html b/docs/reference/set_nd.html new file mode 100644 index 0000000..32ac155 --- /dev/null +++ b/docs/reference/set_nd.html @@ -0,0 +1,247 @@ + + + + + + + + +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 +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 +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(r, lod, loq = NA, time_zero = TRUE, time_zero_nd_value = NA,
+  stop_after_first_nondetect = FALSE)
+
+set_nd_focus(r, lod, loq = NA, time_zero = TRUE)
+ +

Arguments

+ + + + + + + + + + + + + + + + + + + + + + + + + + +
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 at time zero?

stop_after_first_nondetect

Should we really stop after the first non-detection?

+ +

Functions

+ + +
    +

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

    • +
+ +

References

+ +

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

+ + +

Examples

+ 
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
+
+ +
+ + +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 1.4.1.

+
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+ + + + + + + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 6eff936..79d9b14 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -99,6 +99,9 @@ https://pkgdown.jrwb.de/pfm/reference/sawtooth.html + + https://pkgdown.jrwb.de/pfm/reference/set_nd.html + https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html -- cgit v1.2.1