Submission

- added README
- improved supplements

.gitignore

@@ -284,6 +284,7 @@ TSWLatexianTemp*
 
 ## Own:
 templates/
-unused/
+archive/
 organizational/
+publications/
 feedback/

README.md

@@ -1 +1,102 @@
-# Agricultural Plastic Covers—Source of Plastic Debris in Soil?
+# Agricultural Plastic Covers—Source of Plastic Debris in Soil?
+
+Submitted dissertation thesis for the partial fulfillment of the requirements
+for a Doctor of Natural Sciences
+
+*By Zacharias Steinmetz*
+
+## Summary
+
+The use of agricultural plastic covers has become common practice for
+its agronomic benefits such as improving yields and crop quality,
+managing harvest times better, and increasing pesticide and water use
+efficiency. However, plastic covers are suspected of partially breaking
+down into smaller debris and thereby contributing to soil pollution with
+microplastics. A better understanding of the sources and fate of plastic
+debris in terrestrial systems has so far been hindered by the lack of
+adequate analytical techniques for the mass-based and polymer-selective
+quantification of plastic debris in soil. The aim of this dissertation
+was thus to assess, develop, and validate thermoanalytical methods for
+the mass-based quantification of relevant polymers in and around
+agricultural fields previously covered with fleeces, perforated foils,
+and plastic mulches. Thermogravimetry/mass spectrometry (TGA/MS) enabled
+direct plastic analyses of 50 mg of soil without any sample preparation.
+With polyethylene terephthalate (PET) as a preliminary model, the method
+limit of detection (LOD) was 0.7 g kg<sup>−1</sup>. But the missing
+chromatographic separation complicated the quantification of polymer mixtures.
+Therefore, a pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) method
+was developed that additionally exploited the selective solubility of
+polymers in specific solvents prior to analysis. By dissolving polyethylene
+(PE), polypropylene (PP), and polystyrene (PS) in a mixture of
+1,2,4-trichlorobenzene and *p*-xylene after density separation,
+up to 50 g soil became amenable to routine plastic analysis. Method
+LODs were 0.3–2.2 mg kg<sup>−1</sup>, and the recovery of 20 mg kg<sup>−1</sup>
+PE, PP, and PS from a reference loamy sand was 86–105%. In the reference
+silty clay, however, poor PS recoveries, potentially induced by the additional
+separation step, suggested a semi-quantitative evaluation of PS. Yet, the
+new solvent-based Py-GC/MS method enabled a first exploratory screening of
+plastic-covered soil. It revealed PE, PP, and PS contents above LOD in
+six fields (6% of all samples). In three fields, PE levels of
+3–35 mg kg<sup>−1</sup> were associated with the use of 40 μm thin perforated
+foils. By contrast, 50 μm PE films were not shown to induce plastic
+levels above LOD. PP and PS contents of 5–19 mg kg<sup>−1</sup>
+were restricted to single observations on four sites and potentially
+originated from littering. The results suggest that the short-term use
+of thicker and more durable plastic covers should be preferred to limit
+plastic emissions and accumulation in soil. By providing mass-based
+information on the distribution of the three most common plastics in
+agricultural soil, this work may facilitate comparisons with modeling
+and effect data and thus contribute to a better risk assessment and
+regulation of plastics. However, the fate of plastic debris in the
+terrestrial environment remains incompletely understood and needs to be
+scrutinized in future, more systematic research. This should include the
+study of aging processes, the interaction of plastics with other organic
+and inorganic compounds, and the environmental impact of biodegradable
+plastics and nanoplastics.
+
+## Included Files and Folders
+
+<dl>
+  <code>README.md</code>
+  <dd>
+    Readme file
+  </dd>
+  <code>thesis.pdf</code>
+  <dd>
+    Dissertation as PDF file
+  </dd>
+  <code>thesis.tex</code>
+  <dd>
+    Dissertation as editable LaTeX source file including all thesis contents
+    from the following subdirectories: <code>frontbackmatter/</code>,
+    <code>chapters/</code>, <code>appendices/</code>
+  </dd>
+  <code>proposal.pdf</code>
+  <dd>
+    Thesis proposal as PDF file
+  </dd>
+  <code>proposal.tex</code>
+  <dd>
+    Thesis proposal as editable LaTeX source file
+  </dd>
+  <code>references.bib</code>
+  <dd>
+    Complete bibliographical data of the references cited
+  </dd>
+  <code>figures/</code>
+  <dd>
+    Figures
+  </dd>
+    <code>tables/</code>
+  <dd>
+    Tables
+  </dd>
+    <code>supplements/</code>
+  <dd>
+    Supplemental (raw) data and code
+  </dd>
+    <code>cv/</code>
+  <dd>
+    Curriculum vitae
+  </dd>
+</dl>

supplements/esm1/README

@@ -0,0 +1,97 @@
+Data from: Quantitative Analysis of Poly(ethylene terephthalate) Microplastics
+in Soil via Thermogravimetry–Mass Spectrometry
+
+Jan David (a), Zacharias Steinmetz (a), Jiří Kučerík (b), and
+Gabriele E. Schaumann (a)
+
+(a) Group of Environmental and Soil Chemistry, Institute for Environmental
+    Sciences, University of Koblenz-Landau, Fortstraße 7, 76829 Landau,
+    Germany
+(b) Institute of Chemistry and Technology of Environmental Protection, Faculty
+    of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno,
+    Czech Republic
+
+Corresponding author: Gabriele E. Schaumann (E-mail: schaumann@uni-landau.de)
+
+
+Note
+====
+
+This collection contains data and R code to reproduce the findings published in
+the following article:
+
+David, J., Steinmetz, Z., Kučerík, J., and Schaumann, G. E.: Quantitative
+Analysis of Poly(ethylene terephthalate) Microplastics in Soil via
+Thermogravimetry–Mass Spectrometry, Analytical Chemistry, 2018
+
+
+Files
+=====
+
+data             TGA and DSC data
+src              R source files
+src/func         loading R packages, global variables, and functions
+
+
+Getting started
+===============
+
+Please make sure that you use up-to-date software (see below). To reproduce data
+processing and analysis, execute src/func/init.R before running the R scripts in
+src.
+
+
+System information
+==================
+
+R version 4.1.0 (2021-05-18)
+Platform: x86_64-pc-linux-gnu (64-bit)
+Running under: Manjaro Linux
+
+Matrix products: default
+BLAS:   /usr/lib/libblas.so.3.9.1
+LAPACK: /usr/lib/liblapack.so.3.9.1
+
+locale:
+ [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8
+ [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
+ [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C
+[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
+
+attached base packages:
+[1] stats     graphics  grDevices utils     datasets  methods   base
+
+other attached packages:
+ [1] OpenSpecy_0.9.2   viridis_0.6.1     viridisLite_0.4.0 patchwork_1.1.1
+ [5] ggrepel_0.9.1     ggsignif_0.6.2    ggplot2_3.3.4     xtable_1.8-4
+ [9] multcomp_1.4-17   TH.data_1.0-10    MASS_7.3-54       survival_3.2-11
+[13] mvtnorm_1.1-2     readxl_1.3.1      envalysis_0.5.1   data.table_1.14.0
+[17] magrittr_2.0.1
+
+loaded via a namespace (and not attached):
+ [1] httr_1.4.2              jsonlite_1.7.2          splines_4.1.0
+ [4] carData_3.0-4           osfr_0.2.8              gtools_3.9.2
+ [7] shiny_1.6.0             assertthat_0.2.1        latticeExtra_0.6-29
+[10] cellranger_1.1.0        pillar_1.6.1            lattice_0.20-44
+[13] glue_1.4.2              digest_0.6.27           promises_1.2.0.1
+[16] RColorBrewer_1.1-2      colorspace_2.0-1        sandwich_3.0-1
+[19] httpuv_1.6.1            htmltools_0.5.1.1       Matrix_1.3-3
+[22] pkgconfig_2.0.3         httpcode_0.3.0          haven_2.4.1
+[25] purrr_0.3.4             scales_1.1.1            later_1.2.0
+[28] jpeg_0.1-8.1            openxlsx_4.2.4          rio_0.5.26
+[31] tibble_3.1.2            generics_0.1.0          car_3.0-10
+[34] ellipsis_0.3.2          cachem_1.0.5            withr_2.4.2
+[37] hyperSpec_0.99-20201127 lazyeval_0.2.2          mime_0.10
+[40] crayon_1.4.1            memoise_2.0.0           fs_1.5.0
+[43] fansi_0.5.0             forcats_0.5.1           xml2_1.3.2
+[46] foreign_0.8-81          tools_4.1.0             hms_1.1.0
+[49] lifecycle_1.0.0         munsell_0.5.0           plotrix_3.8-1
+[52] zip_2.2.0               signal_0.7-7            compiler_4.1.0
+[55] hexView_0.3-4           rlang_0.4.11            grid_4.1.0
+[58] drc_3.0-1               testthat_3.0.3          gtable_0.3.0
+[61] codetools_0.2-18        abind_1.4-5             DBI_1.1.1
+[64] curl_4.3.1              R6_2.5.0                gridExtra_2.3
+[67] zoo_1.8-9               dplyr_1.0.7             fastmap_1.1.0
+[70] utf8_1.2.1              stringi_1.6.2           crul_1.1.0
+[73] Rcpp_1.0.6              vctrs_0.3.8             png_0.1-7
+[76] tidyselect_1.1.1        lmtest_0.9-38

supplements/esm1/src.R → supplements/esm1/src/src.R

@@ -1,12 +1,10 @@
 #### Load packages and functions ####
-
-setwd("~/Documents/PhD/Thesis/supplements/")
-source("R/init.R")
+source("func/init.R")
 
 #### Examplary TGA/DTG curve ####
 
 example <- list()
-example$data <- fread("esm1/data/tga-dtg-sample.csv")
+example$data <- fread("../data/tga-dtg-sample.csv")
 example$data[, Sample := factor(Sample, c("LUFA soil", "PET in soil", "PET dust"))]
 
 lty <- c("solid", "dashed", "solid")
@@ -35,13 +33,13 @@ example$mass <-
                                  "Pure PET")) +
   theme_publish(base_family = font) + theme(legend.direction = "vertical")
 example$tga / example$dtg / example$mass + plot_annotation(theme = theme(plot.margin = margin()))
-ggsave('../figures/tga-dtg-sample.pdf', scale = 1.5, width = marginwidth,
+ggsave('../../../figures/tga-dtg-sample.pdf', scale = 1.5, width = marginwidth,
        height = 3.5, unit = 'in', device = cairo_pdf)
 
 #### TGA/MS curves ####
 
 tga <- list()
-tga$data <- fread("esm1/data/tga-ms.csv")
+tga$data <- fread("../data/tga-ms.csv")
 
 tga$data[, Label := paste0(toupper(substring(IS, 1, 1)), substring(IS, 2), " internal standard")]
 
@@ -70,13 +68,13 @@ tga$mz154 <-
   guides(color = guide_colorbar(title.vjust = 1),
          shape = guide_legend(title.vjust = 1))
 tga$tga / tga$mz105 / tga$mz154 + plot_annotation(theme = theme(plot.margin = margin()))
-ggsave('../figures/tga-ms.pdf', scale = 1.5, width = pagewidth,
+ggsave('../../../figures/tga-ms.pdf', scale = 1.5, width = pagewidth,
        height = 4, unit = 'in', device = cairo_pdf)
 
 #### Calibration ####
 
 cal <- list()
-cal$data <- fread("esm1/data/tga-calibration.csv")
+cal$data <- fread("../data/tga-calibration.csv")
 
 cal$data[, Label := paste0(toupper(substring(IS, 1, 1)), substring(IS, 2), " internal standard")]
 
@@ -109,13 +107,13 @@ cal$plot154 <-
   scale_y_continuous(label=scientific_10) +
   theme_publish(base_family = font) + theme(strip.text.x = element_text(size=0))
 cal$plot105 / cal$plot154 + plot_annotation(theme = theme(plot.margin = margin()))
-ggsave('../figures/tga-calibration.pdf', scale = 1.5, width = pagewidth,
+ggsave('../../../figures/tga-calibration.pdf', scale = 1.5, width = pagewidth,
        height = 3, unit = 'in', device = cairo_pdf)
 
 #### Capillary checks ####
 
 cap <- list()
-cap$data <- fread("esm1/data/tga-capillary-checks.csv")
+cap$data <- fread("../data/tga-capillary-checks.csv")
 
 cap$data[, Label := paste0(toupper(substring(IS, 1, 1)), substring(IS, 2), " internal standard")]
 cap$data[PET > 30, Case := "40–50"]
@@ -133,12 +131,12 @@ ggplot(cap$data, aes(Temp, mz105*10^9, group = interaction(PET, Case, Type))) +
   theme_publish(base_family = font) +
   guides(color = guide_colorbar(title.vjust = 1),
          shape = guide_legend(title.vjust = 1))
-ggsave('../figures/tga-capillary-checks.pdf', scale = 1.5, width = pagewidth,
+ggsave('../../../figures/tga-capillary-checks.pdf', scale = 1.5, width = pagewidth,
        height = 2.2, unit = 'in', device = cairo_pdf)
 
 #### Capillary pressure ####
 
-cap$pressure <- fread("esm1/data/tga-capillary-pressure.csv")
+cap$pressure <- fread("../data/tga-capillary-pressure.csv")
 cap$pressure[, Date := as.Date(Date)]
 
 ggplot(cap$pressure, aes(x = Date, y = Pressure * 10^6)) +
@@ -153,13 +151,13 @@ ggplot(cap$pressure, aes(x = Date, y = Pressure * 10^6)) +
   ylab(expression("Pressure [10"^-9~"bar]")) +
   scale_y_continuous(limits = c(7, 21)) +
   theme_publish(base_family = font)
-ggsave('../figures/tga-capillary-pressure.pdf', scale = 1.5, width = textwidth,
-       height = 2, unit = 'in', device = cairo_pdf)
+ggsave('../../../figures/tga-capillary-pressure.pdf', scale = 1.5,
+       width = textwidth, height = 2, unit = 'in', device = cairo_pdf)
 
 #### Polymer DSC ####
 
 dsc <- list()
-dsc$data <- fread("esm1/data/dsc.csv")
+dsc$data <- fread("../data/dsc.csv")
 
 ggplot(dsc$data, aes(Temp, AvgHF)) +
   geom_line(aes(color = Sample)) +
@@ -170,13 +168,13 @@ ggplot(dsc$data, aes(Temp, AvgHF)) +
                                  "Dust (PETKA CZ)",
                                  "Reference (PlasticsEurope)")) +
   theme_publish(base_family = font)
-ggsave('../figures/dsc.pdf', scale = 1.5, width = textwidth,
+ggsave('../../../figures/dsc.pdf', scale = 1.5, width = textwidth,
        height = 2, unit = 'in', device = cairo_pdf)
 
 #### Cysteine comparison ####
 
 cys <- list()
-cys$comp <- fread("esm1/data/cysteine-comparison.csv")
+cys$comp <- fread("../data/cysteine-comparison.csv")
 cys$comp[, Cys := as.factor(Cys)]
 
 cys$comptga <-
@@ -194,13 +192,13 @@ cys$compmz33 <-
   theme_publish(base_family = font) + theme(strip.text.x = element_text(size=0))
 cys$comptga / cys$compmz33 +
   plot_annotation(theme = theme(plot.margin = margin()))
-ggsave('../figures/cysteine-comparison.pdf', scale = 1.5, width = textwidth,
-       height = 3, unit = 'in', device = cairo_pdf)
+ggsave('../../../figures/cysteine-comparison.pdf', scale = 1.5,
+       width = textwidth, height = 3, unit = 'in', device = cairo_pdf)
 
 #### Cysteine tests ####
 
-cys$lin <- fread("esm1/data/cysteine-linearity.csv")
-cys$deg <- fread("esm1/data/cysteine-degradation.csv")
+cys$lin <- fread("../data/cysteine-linearity.csv")
+cys$deg <- fread("../data/cysteine-degradation.csv")
 
 cys$cal <- calibration(mz33 ~ Cys, data = cys$lin)
 cys$conc <- cys$cal$model$model[,2]
@@ -241,12 +239,12 @@ cys$mz33 <-
          shape = guide_legend(title.vjust = 1))
 cys$calcurve / cys$tga / cys$mz33 +
   plot_annotation(theme = theme(plot.margin = margin()))
-ggsave('../figures/cysteine-tests.pdf', scale = 1.5, width = textwidth,
+ggsave('../../../figures/cysteine-tests.pdf', scale = 1.5, width = textwidth,
        height = 4, unit = 'in', device = cairo_pdf)
 
 #### Control measurements ####
 contr <- list()
-contr$data <- fread("esm1/data/control-measurements.csv")
+contr$data <- fread("../data/control-measurements.csv")
 contr$melt <- melt(contr$data, id = c("PET", "IS"),
                    measure = c("mz18", "mz28", "mz44", "SigRatio"),
                    variable.name = "Mass", value.name = "Signal")
@@ -274,5 +272,5 @@ contr$masses <-
   facet_wrap(~ Label)
 contr$sigratio / contr$masses +
   plot_annotation(theme = theme(plot.margin = margin()))
-ggsave('../figures/control-measurements.pdf', scale = 1.5, width = pagewidth,
-       height = 3.5, unit = 'in', device = cairo_pdf)
+ggsave('../../../figures/control-measurements.pdf', scale = 1.5,
+       width = pagewidth, height = 3.5, unit = 'in', device = cairo_pdf)

supplements/esm2/README

@@ -13,6 +13,8 @@ Gabriele E. Schaumann (a)
 
 Corresponding author: Gabriele E. Schaumann (E-mail: schaumann@uni-landau.de)
 
+See also: https://doi.org/10.6084/m9.figshare.11861664
+
 
 Note
 ====
@@ -36,7 +38,7 @@ data/reports            chromatogram reports listing all identified and
 data/targets            list of PE, PP, and PS target compounds with retention
                         times and CAS numbers
 data/samples.csv        sample list of the recovery experiment
-data/seqtable.csv		    sequence table containing all Py-GC/MS measurements
+data/seqtable.csv       sequence table containing all Py-GC/MS measurements
 
 see data/DESCRIPTION for detailed information on files types and contents
 

supplements/esm2/src/func/init.R

@@ -0,0 +1,11 @@
+wd <- getwd()
+setwd(dirname(sys.frame(1)$ofile))
+
+source("packages.R")
+source("variables.R")
+source("wrappers.R")
+source("read_openchrom.R")
+source("read_targets.R")
+
+setwd(wd)
+rm(wd)