Kennedy and El-Sabaawi - Decay patterns of invasive plants and plastic trash in urban streams - R code and Data

Appendix Supplement A2 - R Code and Data from: Kennedy KTM & El-Sabaawi RW. 2018 Decay patterns of invasive plants and plastic trash in urban streams -Urban Ecosystems. This data was collected in urban streams in Victoria, BC, Canada and analysed using R version 3.2.5 (2016-04-14) -- "Very, Very Secure Dishes". The following details the Excel workbook contents for each tab and heading descriptions for the data in each tab. Read Me tab - the description of the data. ### Section 1: Tabs for Leaf Decay Comparisons by Stream and Type data and R code. R Code for Leaf decay k kdd tab - The R code used to compare leaf decay k and kdd by stream and by lead type, and draw plots of Leaf toughness by type and Leaf LMA by type - (copy into a new R script for use).kkcalcdd tab - the kkcalcdd dataset (save as .csv for use with R code). kkcalcddnov042015GRAPH tab - the kkcalcddnov042015GRAPH dataset (save as .csv for use with R code). kkcalcddnov042015 tab - the kkcalcddnov042015 dataset (save as .csv for use with R code). kkcalcnov52015noT0notrash tab - the kkcalcnov52015noT0notrash dataset (save as .csv for use with R code). The kkcalcdd tab, kkcalcddnov042015GRAPH tab, kkcalcddnov042015 tab, and kkcalcnov52015noT0notrash tab all have the same column headings:entry - database entry number; stream - Stream site; subsite - subsite at stream; week - week code; timeelapsed - time elapsed in days; type - litter type; pack - pack number; inmass - initial mass in grams; finmass - final mass in grams; inif - (initial mass - final mass); neglnmr - the negative ln of inif; time - time elapsed in days; dd - degree days elapsed; k - the decay rate k; kdd - the decay rate in kdd.### Section 2: Tabs for Leaf Toughness and Leaf LMA Comparisons data and R code: R Code for Leaf Toughness LMA tab - The R code used to compare leaf toughness and leaf mass per area, and draw plots of Leaf toughness by type and Leaf LMA by type - (copy into a new R script for use). LeafToughKW tab - the LeafToughKW dataset (save as .csv for use with R code). The LeafToughKW tab column headings: id - the sample id number; type - the type of leaf; tough - the leaf samples' toughness in g/mm2 as measured with a penetrometer. LeafLMAKW tab - the LeafLMAKW dataset (save as .csv for use with R code). The LeafLMAKW tab column headings: id - the sample id number; type - the type of leaf; LMA - the leaf samples' Leaf Mass per Area (LMA) in mg/cm2. ### Section 3: Tabs for Invertebrate DCA Ordination, Bayesian Clustering, and Ordination Plot data and R code. R Code for Invert ordination tab - The R code used for the invertebrate DCA Ordination, Bayesian Clustering, and ordination plot and by litter type - (copy into a new R script for use). sy2 tab - the sy2 dataset (save as .csv for use with R code). sy2 tab - column headings: id - pack identifier; Chironomidae - Hellinger transformed counts of Chironomidae; Dugesiidae - Hellinger transformed counts of Dugesiidae; Hirudinea - Hellinger transformed counts of Hirudinea; Psychodidae - Hellinger transformed counts of Psychodidae; Crangonyx - Hellinger transformed counts of Crangonyx; Nemetoda - Hellinger transformed counts of Nemetoda; Lepidostomatidae - Hellinger transformed counts of Lepidostomatidae; Nemouridae - Hellinger transformed counts of Nemouridae; Chloroperlidae - Hellinger transformed counts of Chloroperlidae; Copepoda - Hellinger transformed counts of Copepoda; Dixidae - Hellinger transformed counts of Dixidae; Physidae - Hellinger transformed counts of Physidae. dcasy2scores tab - the dcasy2scores dataset (save as .csv for use with R code). dcasy2scores tab - column headings: pack - pack identifier; DCA1 - DCA 1st axis coordinate; DCA2 - DCA 2nd axis coordinate; marker - pack marker ( first letter = stream, second letter = type). dcasy2invertvectors tab - the dcasy2invert vectors dataset (save as .csv for use with R code). dcasy2invertvectors tab - column headings: species - invertebrate species; DCA1 - DCA 1st axis coordinate; DCA2 - DCA 2nd axis coordinate; DCA3 - DCA 3rd axis coordinate; DCA4 - DCA 4th axis coordinate; totals - DCA totals; marker - invertebrate species marker; ### Section 4: Tabs for invertebrate diversity Comparisons by Stream and Type data and R code. R Code for Invert alpha Shannon tab - The R code used to compare invertebrate alpha diversity and Shannon diversity by stream and by litter type, and draw plots of invertebrate alpha and Shannon diversity by stream and litter type - (copy into a new R script for use). Fall bug Diversity FINAL tab - the Fall bug Diversity FINAL dataset (save as .csv for use with R code). The Fall bug Diversity FINAL tab column headings: id - invertebrate sample ID number; pack - pack number; sdiv - Shannon diversity; fisha - Fisher's alpha; adiv - alpha diversity; indiv - number of individuals; stream – stream; type - litter type; lnindiv1 - ln(indiv +1); lnadiv1 - ln(adiv +1); lnsdiv1 - ln(sdiv +1). Fall bug Diversity tab - the Fall bug Diversity dataset (save as .csv for use with R code). The Fall bug Diversity tab column headings: id - invertebrate sample ID number; pack - pack number; sdiv - Shannon diversity; fisha - Fisher's alpha; adiv - alpha diversity; indiv - number of individuals; stream – stream; type - litter type; ### Section 5: Raw invertebrate count data tab - Our complete week 2 invertebrate count dataset prior to constraint for ordination. Raw invertebrate count data tab column headings: Entry #- data entry number; Pack – pack number; Id - pack identifier; stream – stream identifier, Type – pack type; fraction – fraction of pack identified; Counts of individuals: Chironomidae; Dugesiidae; Oligochaeta; Hirudinea; Psychodidae; Crangonyx; Nemetoda; Lepidostomatidae; Nemouridae; Chloroperlidae; Limnephilidae; Copepoda; Hydridae; Dixidae; Elmidae; Heptageniidae; Simuliidae; Physidae; Planorbidae; Ancylidae; Sphaeriidae; Hydrobiidae; Valvatidae; Lymnaeidae; Rhyacophilidae; Daphniidae; Athericidae; Ceratopogonidae; Astacidae; Tipulidae; Ptychopteridae; Dolichopodidae; Empididae; Stratiomyidae; Tabanidae; Phryganeidae; Coenagrionidae; Aeshnidae; Malacostraca; Sialidae; All individuals – sum of all individuals in the pack (sum formula); # of groups – sum of groups in the pack; All individuals - sum of all individuals in the pack (absolute value); individuals/groups (number of individuals divided by number of groups).