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accounting for various forms of compression
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,147 @@ | ||
| --- | ||
| title: "Missing Data" | ||
| output: rmarkdown::html_vignette | ||
| vignette: > | ||
| %\VignetteIndexEntry{Missing Data} | ||
| %\VignetteEngine{knitr::rmarkdown} | ||
| %\VignetteEncoding{UTF-8} | ||
| --- | ||
|
|
||
| ```{r setup, echo=FALSE, results='hide', warning=FALSE} | ||
| knitr::opts_chunk$set( | ||
| message = FALSE, | ||
| warning = FALSE, | ||
| background = '#F7F7F7', | ||
| fig.align = 'center', | ||
| dev = 'png', | ||
| comment = "#>" | ||
| ) | ||
| # keep examples from using more than 2 cores | ||
| data.table::setDTthreads(Sys.getenv("OMP_THREAD_LIMIT", unset = 2)) | ||
| options(width = 100, stringsAsFactors = FALSE, timeout = 600) | ||
| ``` | ||
|
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||
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| ```{r} | ||
| library(aqp) | ||
| library(soilDB) | ||
| ``` | ||
|
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| ```{r} | ||
| # example data | ||
| data("jacobs2000") | ||
| # fully populated | ||
| plotSPC(jacobs2000, name.style = 'center-center', | ||
| cex.names = 0.8, color = 'time_saturated') | ||
| # missing some data | ||
| plotSPC(jacobs2000, name.style = 'center-center', | ||
| cex.names = 0.8, color = 'concentration_color') | ||
| # very nearly complete | ||
| plotSPC(jacobs2000, name.style = 'center-center', | ||
| cex.names = 0.8, color = 'matrix_color') | ||
| # variables to consider | ||
| v <- c('time_saturated', 'concentration_color', 'matrix_color') | ||
| # compute data completeness by profile | ||
| # ignore 2C horizons | ||
| jacobs2000$data.complete <- evalMissingData( | ||
| jacobs2000, | ||
| vars = v, | ||
| method = 'relative', | ||
| p = '2C' | ||
| ) | ||
| jacobs2000$data.complete.abs <- evalMissingData( | ||
| jacobs2000, | ||
| vars = v, | ||
| method = 'absolute', | ||
| p = '2C' | ||
| ) | ||
| # compute data completeness by horizon | ||
| # ignore 2C horizons | ||
| jacobs2000$hz.data.complete <- evalMissingData( | ||
| jacobs2000, | ||
| vars = v, | ||
| method = 'horizon', | ||
| p = '2C' | ||
| ) | ||
| # "fraction complete" by horizon | ||
| plotSPC( | ||
| jacobs2000, name.style = 'center-center', | ||
| cex.names = 0.8, color = 'hz.data.complete' | ||
| ) | ||
| # rank on profile completeness | ||
| new.order <- order(jacobs2000$data.complete) | ||
| # plot along data completeness ranking | ||
| plotSPC( | ||
| jacobs2000, name.style = 'center-center', | ||
| cex.names = 0.8, color = 'hz.data.complete', | ||
| plot.order = new.order | ||
| ) | ||
| # add relative completeness axis | ||
| # note re-ordering of axis labels | ||
| axis( | ||
| side = 1, at = 1:length(jacobs2000), | ||
| labels = round(jacobs2000$data.complete[new.order], 2), | ||
| line = 0, cex.axis = 0.75 | ||
| ) | ||
| # add absolute completeness (cm) | ||
| axis( | ||
| side = 1, at = 1:length(jacobs2000), | ||
| labels = jacobs2000$data.complete.abs[new.order], | ||
| line = 2.5, cex.axis=0.75 | ||
| ) | ||
| ``` | ||
|
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||
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| ```{r} | ||
| x <- fetchKSSL(series = 'pierre') | ||
| par(mar = c(0, 0, 3, 2)) | ||
| plotSPC(x, color = 'clay', width = 0.3, name.style = 'center-center', label = 'pedon_completeness_index') | ||
| plotSPC(x, color = 'cec7', width = 0.3, name.style = 'center-center', label = 'pedon_completeness_index') | ||
| plotSPC(x, color = 'estimated_oc', width = 0.3, name.style = 'center-center', label = 'pedon_completeness_index') | ||
| plotSPC(x, color = 'ph_h2o', width = 0.3, name.style = 'center-center', label = 'pedon_completeness_index') | ||
| plotSPC(x, color = 'db_13b', width = 0.3, name.style = 'center-center', label = 'pedon_completeness_index') | ||
| par(mar = c(1, 0, 3, 2)) | ||
| plotSPC(x, color = 'ph_h2o', width = 0.3, name.style = 'center-center', label = 'pedon_completeness_index') | ||
| .b <- x[, , .LAST, .BOTTOM] | ||
| text(x = 1:length(x), y = .b, labels = x$pi, cex = 0.85, pos = 1) | ||
| mtext('Profile Information Index (bytes)', side = 1, line = -0.5) | ||
| v <- c('clay', 'db_13b', 'cec7', 'ph_h2o') | ||
| x$rel.not.missing <- evalMissingData(x, vars = v, method = 'relative') | ||
| x$abs.not.missing <- evalMissingData(x, vars = v, method = 'absolute') | ||
| x$hz.not.missing <- evalMissingData(x, vars = v, method = 'horizon') | ||
| o <- order(x$rel.not.missing) | ||
| plotSPC(x, color = 'hz.not.missing', width = 0.33, name.style = 'center-center', label = 'pedon_completeness_index', plot.order = o) | ||
| text(x = 1:length(x), y = .b[o], labels = round(x$rel.not.missing[o], 2), cex = 0.85, pos = 1) | ||
| mtext('Relative Non-Missing Fraction', side = 1, line = -0.5) | ||
| o <- order(x$abs.not.missing) | ||
| plotSPC(x, color = 'hz.not.missing', width = 0.33, name.style = 'center-center', label = 'pedon_completeness_index', plot.order = o) | ||
| text(x = 1:length(x), y = .b[o], labels = x$abs.not.missing[o], cex = 0.85, pos = 1) | ||
| mtext('Absolute Non-Missing (cm)', side = 1, line = -0.5) | ||
| ``` |