Release for Journal of Ecology

- include exported data
- add tex file

.gitignore

@@ -10,14 +10,11 @@ talk.md
 talk.pdf
 output/*
 figure/*
-ms/Accessory/Wenk-Accessory-SI.tex
+#ms/Accessory/Wenk-Accessory-SI.tex
 ms/Accessory/Wenk-Accessory-SI.pdf
 ms/Accessory/figures/
 ms/Accessory/output/
 ms/plant_maps/full
-ms/RA/figures/
-ms/RA/Wenk-RA-SI.tex
-ms/RA/Wenk-RA-SI.pdf
 ~*.doc*
 *.whisker
 ./bootstrap

README.md

@@ -1,8 +1,6 @@
 # Studies on Reproductive Allocation for 14 plant species in Kuringgai National Park, Australia
 
-This repository contains code needed to reproduce the articles:
-
-**Wenk EH, Abramowicz K, Westoby M, & Falster DS** Coordinated shifts in allocation among reproductive tissues across 14 coexisting plant species. bioRxiv: 141473. doi: 10.1101/141473 
+This repository contains code needed to reproduce the article:
 
 **Wenk EH, Abramowicz K, Westoby M, & Falster DS** (2018) Investment in reproduction for 14 iteroparous perennials is large and associated with other life-history and functional traits. Journal of Ecology (in press).
 
@@ -46,23 +44,7 @@ which will save a combined set of variables and metadata into the folder `export
 
 Those wishing to reuse our data should start with these summary files, before delving into the raw-data.
 
-**First paper**:
-
-To build the figures and rerun analyses reported in the main text open a fresh R session and run:
-
-```r
-remake::make("ms-Accessory")
-```
-
-Figures will appear in the directory `ms/Accessory/figures/`.
-
-To build the supplementary materials run:
-
-```r
-remake::make("ms/Accessory/Wenk-Accessory-SI.pdf")
-```
-
-**Second paper**:
+**Results from the paper**:
 
 To build the figures reported in the main text open a fresh R session and run:
 

analysis.R

@@ -0,0 +1,238 @@
+library("stats")
+library("stringr")
+library("smatr")
+library("plyr")
+library("tidyr")
+library("dplyr")
+library("xtable")
+library("igraph")
+library("rmarkdown")
+library("broom")
+library("ggtern")
+library("ggmap")
+library("yaml")
+library("mgcv")
+library("knitr")
+source("R/figures.R")
+source("R/FlowerParts.R")
+source("R/GraphRepresentation.R")
+source("R/Growth.R")
+source("R/Investment.R")
+source("R/ms-accessory.R")
+source("R/ms-RA.R")
+source("R/ms-SuppMatt.R")
+source("R/ReproductionTissues.R")
+source("R/Species.R")
+source("R/Summaries.R")
+source("R/Utils.R")
+source("R/WeightCalculations.R")
+dir.create("ms/RA/figures", FALSE, TRUE)
+dir.create("ms", FALSE, TRUE)
+dir.create("export", FALSE, TRUE)
+pdf("ms/RA/figures/schematic.pdf", height = 2.5, width = 7.5)
+plotRASexamples()
+dev.off()
+library("remake")
+make_script(file = "analysis.R")
+BAER_PartsList <- make_OrderedListsOfParts_BAER()
+BOLE_PartsList <- make_OrderedListsOfParts_BOLE()
+COER_PartsList <- make_OrderedListsOfParts_COER()
+EPMI_PartsList <- make_OrderedListsOfParts_EPMI()
+GRBU_PartsList <- make_OrderedListsOfParts_GRBU()
+GRSP_PartsList <- make_OrderedListsOfParts_GRSP()
+HATE_PartsList <- make_OrderedListsOfParts_HATE()
+HEPU_PartsList <- make_OrderedListsOfParts_HEPU()
+LEES_PartsList <- make_OrderedListsOfParts_LEES()
+PELA_PartsList <- make_OrderedListsOfParts_PELA()
+PEPU_PartsList <- make_OrderedListsOfParts_PEPU()
+PHPH_PartsList <- make_OrderedListsOfParts_PHPH()
+PILI_PartsList <- make_OrderedListsOfParts_PILI()
+PUTU_PartsList <- make_OrderedListsOfParts_PUTU()
+pdf("ms/map.pdf", width = 4L, height = 4L)
+figure_site_map("data/sites.csv")
+dev.off()
+IndividualsList <- read_csv("data/individuals.csv")
+FlowerPartsData <- read_csv("data/flowerParts.csv")
+Reproduction_raw <- read_csv("data/reproduction.csv")
+ReproductionData <- filterForAllocation(Reproduction_raw, IndividualsList)
+HarvestData_raw <- read_csv("data/harvest.csv")
+HarvestData <- preprocessHarvest(HarvestData_raw, IndividualsList)
+FloweringCategories <- read_csv("data/flowerCategories.csv")
+MultiplierTable <- read_csv("data/multiplierTable.csv")
+InvestmentCategories <- yaml.load_file("data/accessoryParts.yml")
+LMA_1 <- read_csv("data/LMA.csv")
+LMA <- process_LMA(LMA_1)
+wood_density_spp1 <- read_csv("data/woodDensity.csv")
+wood_density_spp <- process_wood_density(wood_density_spp1)
+seedsize <- read_csv("data/seedsize.csv")
+leavesPerLength_1 <- read_csv("data/leaves_per_length.csv")
+leavesPerLength <- process_leaves_per_length(leavesPerLength_1)
+leafLoss_1 <- read_csv("data/leaderGrowthLL.csv")
+leafLoss <- process_leaf_loss(leafLoss_1, leavesPerLength)
+variable_list <- read_csv("data/variable_metadata.csv")
+write.csv(variable_list, "export/Variable_metadata.csv", row.names = FALSE)
+BAER_IndividualsList <- filterToBAER(IndividualsList)
+BAER_FlowerPartsData <- filterToBAER(FlowerPartsData)
+BAER_HarvestData <- filterToBAER(HarvestData)
+BAER_ReproductionData <- filterToBAER(ReproductionData)
+BAER_PartsSummary <- make_PartsSummary(BAER_FlowerPartsData, BAER_PartsList)
+BAER_GraphMaps <- make_BAER_GraphMaps(BAER_PartsSummary, MultiplierTable)
+BAER_Investment <- CalculateInvestmentForBAER(BAER_ReproductionData, FloweringCategories, MultiplierTable, BAER_GraphMaps, BAER_PartsSummary)
+BAER_ReproductiveCosts <- CalculateReproductiveCostsForBAER(BAER_IndividualsList, InvestmentCategories, BAER_Investment, BAER_PartsSummary)
+BAER_Growth <- CalculateGrowthForBAER(BAER_HarvestData, BAER_IndividualsList)
+BOLE_IndividualsList <- filterToBOLE(IndividualsList)
+BOLE_FlowerPartsData <- filterToBOLE(FlowerPartsData)
+BOLE_HarvestData <- filterToBOLE(HarvestData)
+BOLE_ReproductionData <- filterToBOLE(ReproductionData)
+BOLE_PartsSummary <- make_PartsSummary(BOLE_FlowerPartsData, BOLE_PartsList)
+BOLE_GraphMaps <- make_BOLE_GraphMaps(BOLE_PartsSummary, MultiplierTable)
+BOLE_Investment <- CalculateInvestmentForBOLE(BOLE_ReproductionData, FloweringCategories, MultiplierTable, BOLE_GraphMaps, BOLE_PartsSummary)
+BOLE_ReproductiveCosts <- CalculateReproductiveCostsForBOLE(BOLE_IndividualsList, InvestmentCategories, BOLE_Investment, BOLE_PartsSummary)
+BOLE_Growth <- CalculateGrowthForBOLE(BOLE_HarvestData, BOLE_IndividualsList)
+COER_IndividualsList <- filterToCOER(IndividualsList)
+COER_FlowerPartsData <- filterToCOER(FlowerPartsData)
+COER_HarvestData <- filterToCOER(HarvestData)
+COER_ReproductionData <- filterToCOER(ReproductionData)
+COER_PartsSummary <- make_PartsSummary(COER_FlowerPartsData, COER_PartsList)
+COER_GraphMaps <- make_COER_GraphMaps(COER_PartsSummary, MultiplierTable)
+COER_Investment <- CalculateInvestmentForCOER(COER_ReproductionData, FloweringCategories, MultiplierTable, COER_GraphMaps, COER_PartsSummary)
+COER_ReproductiveCosts <- CalculateReproductiveCostsForCOER(COER_IndividualsList, InvestmentCategories, COER_Investment, COER_PartsSummary)
+COER_Growth <- CalculateGrowthForCOER(COER_HarvestData, COER_IndividualsList)
+EPMI_IndividualsList <- filterToEPMI(IndividualsList)
+EPMI_FlowerPartsData <- filterToEPMI(FlowerPartsData)
+EPMI_HarvestData <- filterToEPMI(HarvestData)
+EPMI_ReproductionData <- filterToEPMI(ReproductionData)
+EPMI_PartsSummary <- make_PartsSummary(EPMI_FlowerPartsData, EPMI_PartsList)
+EPMI_GraphMaps <- make_EPMI_GraphMaps(EPMI_PartsSummary, MultiplierTable)
+EPMI_Investment <- CalculateInvestmentForEPMI(EPMI_ReproductionData, FloweringCategories, MultiplierTable, EPMI_GraphMaps, EPMI_PartsSummary)
+EPMI_ReproductiveCosts <- CalculateReproductiveCostsForEPMI(EPMI_IndividualsList, InvestmentCategories, EPMI_Investment, EPMI_PartsSummary)
+EPMI_Growth <- CalculateGrowthForEPMI(EPMI_HarvestData, EPMI_IndividualsList)
+GRBU_IndividualsList <- filterToGRBU(IndividualsList)
+GRBU_FlowerPartsData <- filterToGRBU(FlowerPartsData)
+GRBU_HarvestData <- filterToGRBU(HarvestData)
+GRBU_ReproductionData <- filterToGRBU(ReproductionData)
+GRBU_PartsSummary <- make_PartsSummary(GRBU_FlowerPartsData, GRBU_PartsList)
+GRBU_GraphMaps <- make_GRBU_GraphMaps(GRBU_PartsSummary, MultiplierTable)
+GRBU_Investment <- CalculateInvestmentForGRBU(GRBU_ReproductionData, FloweringCategories, MultiplierTable, GRBU_GraphMaps, GRBU_PartsSummary)
+GRBU_ReproductiveCosts <- CalculateReproductiveCostsForGRBU(GRBU_IndividualsList, InvestmentCategories, GRBU_Investment, GRBU_PartsSummary)
+GRBU_Growth <- CalculateGrowthForGRBU(GRBU_HarvestData, GRBU_IndividualsList)
+GRSP_IndividualsList <- filterToGRSP(IndividualsList)
+GRSP_FlowerPartsData <- filterToGRSP(FlowerPartsData)
+GRSP_HarvestData <- filterToGRSP(HarvestData)
+GRSP_ReproductionData <- filterToGRSP(ReproductionData)
+GRSP_PartsSummary <- make_PartsSummary(GRSP_FlowerPartsData, GRSP_PartsList)
+GRSP_GraphMaps <- make_GRSP_GraphMaps(GRSP_PartsSummary, MultiplierTable)
+GRSP_Investment <- CalculateInvestmentForGRSP(GRSP_ReproductionData, FloweringCategories, MultiplierTable, GRSP_GraphMaps, GRSP_PartsSummary)
+GRSP_ReproductiveCosts <- CalculateReproductiveCostsForGRSP(GRSP_IndividualsList, InvestmentCategories, GRSP_Investment, GRSP_PartsSummary)
+GRSP_Growth <- CalculateGrowthForGRSP(GRSP_HarvestData, GRSP_IndividualsList)
+HATE_IndividualsList <- filterToHATE(IndividualsList)
+HATE_FlowerPartsData <- filterToHATE(FlowerPartsData)
+HATE_HarvestData <- filterToHATE(HarvestData)
+HATE_ReproductionData <- filterToHATE(ReproductionData)
+HATE_PartsSummary <- make_PartsSummary(HATE_FlowerPartsData, HATE_PartsList)
+HATE_GraphMaps <- make_HATE_GraphMaps(HATE_PartsSummary, MultiplierTable)
+HATE_Investment <- CalculateInvestmentForHATE(HATE_ReproductionData, FloweringCategories, MultiplierTable, HATE_GraphMaps, HATE_PartsSummary)
+HATE_ReproductiveCosts <- CalculateReproductiveCostsForHATE(HATE_IndividualsList, InvestmentCategories, HATE_Investment, HATE_PartsSummary)
+HATE_Growth <- CalculateGrowthForHATE(HATE_HarvestData, HATE_IndividualsList)
+HEPU_IndividualsList <- filterToHEPU(IndividualsList)
+HEPU_FlowerPartsData <- filterToHEPU(FlowerPartsData)
+HEPU_HarvestData <- filterToHEPU(HarvestData)
+HEPU_ReproductionData <- filterToHEPU(ReproductionData)
+HEPU_PartsSummary <- make_PartsSummary(HEPU_FlowerPartsData, HEPU_PartsList)
+HEPU_GraphMaps <- make_HEPU_GraphMaps(HEPU_PartsSummary, MultiplierTable)
+HEPU_Investment <- CalculateInvestmentForHEPU(HEPU_ReproductionData, FloweringCategories, MultiplierTable, HEPU_GraphMaps, HEPU_PartsSummary)
+HEPU_ReproductiveCosts <- CalculateReproductiveCostsForHEPU(HEPU_IndividualsList, InvestmentCategories, HEPU_Investment, HEPU_PartsSummary)
+HEPU_Growth <- CalculateGrowthForHEPU(HEPU_HarvestData, HEPU_IndividualsList)
+LEES_IndividualsList <- filterToLEES(IndividualsList)
+LEES_FlowerPartsData <- filterToLEES(FlowerPartsData)
+LEES_HarvestData <- filterToLEES(HarvestData)
+LEES_ReproductionData <- filterToLEES(ReproductionData)
+LEES_PartsSummary <- make_PartsSummary(LEES_FlowerPartsData, LEES_PartsList)
+LEES_GraphMaps <- make_LEES_GraphMaps(LEES_PartsSummary, MultiplierTable)
+LEES_Investment <- CalculateInvestmentForLEES(LEES_ReproductionData, FloweringCategories, MultiplierTable, LEES_GraphMaps, LEES_PartsSummary)
+LEES_ReproductiveCosts <- CalculateReproductiveCostsForLEES(LEES_IndividualsList, InvestmentCategories, LEES_Investment, LEES_PartsSummary)
+LEES_Growth <- CalculateGrowthForLEES(LEES_HarvestData, LEES_IndividualsList)
+PELA_IndividualsList <- filterToPELA(IndividualsList)
+PELA_FlowerPartsData <- filterToPELA(FlowerPartsData)
+PELA_HarvestData <- filterToPELA(HarvestData)
+PELA_ReproductionData <- filterToPELA(ReproductionData)
+PELA_PartsSummary <- make_PartsSummary(PELA_FlowerPartsData, PELA_PartsList)
+PELA_GraphMaps <- make_PELA_GraphMaps(PELA_PartsSummary, MultiplierTable)
+PELA_Investment <- CalculateInvestmentForPELA(PELA_ReproductionData, FloweringCategories, MultiplierTable, PELA_GraphMaps, PELA_PartsSummary)
+PELA_ReproductiveCosts <- CalculateReproductiveCostsForPELA(PELA_IndividualsList, InvestmentCategories, PELA_Investment, PELA_PartsSummary)
+PELA_Growth <- CalculateGrowthForPELA(PELA_HarvestData, PELA_IndividualsList)
+PEPU_IndividualsList <- filterToPEPU(IndividualsList)
+PEPU_FlowerPartsData <- filterToPEPU(FlowerPartsData)
+PEPU_HarvestData <- filterToPEPU(HarvestData)
+PEPU_ReproductionData <- filterToPEPU(ReproductionData)
+PEPU_PartsSummary <- make_PartsSummary(PEPU_FlowerPartsData, PEPU_PartsList)
+PEPU_GraphMaps <- make_PEPU_GraphMaps(PEPU_PartsSummary, MultiplierTable)
+PEPU_Investment <- CalculateInvestmentForPEPU(PEPU_ReproductionData, FloweringCategories, MultiplierTable, PEPU_GraphMaps, PEPU_PartsSummary)
+PEPU_ReproductiveCosts <- CalculateReproductiveCostsForPEPU(PEPU_IndividualsList, InvestmentCategories, PEPU_Investment, PEPU_PartsSummary)
+PEPU_Growth <- CalculateGrowthForPEPU(PEPU_HarvestData, PEPU_IndividualsList)
+PHPH_IndividualsList <- filterToPHPH(IndividualsList)
+PHPH_FlowerPartsData <- filterToPHPH(FlowerPartsData)
+PHPH_HarvestData <- filterToPHPH(HarvestData)
+PHPH_ReproductionData <- filterToPHPH(ReproductionData)
+PHPH_PartsSummary <- make_PartsSummary(PHPH_FlowerPartsData, PHPH_PartsList)
+PHPH_GraphMaps <- make_PHPH_GraphMaps(PHPH_PartsSummary, MultiplierTable)
+PHPH_Investment <- CalculateInvestmentForPHPH(PHPH_ReproductionData, FloweringCategories, MultiplierTable, PHPH_GraphMaps, PHPH_PartsSummary)
+PHPH_ReproductiveCosts <- CalculateReproductiveCostsForPHPH(PHPH_IndividualsList, InvestmentCategories, PHPH_Investment, PHPH_PartsSummary)
+PHPH_Growth <- CalculateGrowthForPHPH(PHPH_HarvestData, PHPH_IndividualsList)
+PILI_IndividualsList <- filterToPILI(IndividualsList)
+PILI_FlowerPartsData <- filterToPILI(FlowerPartsData)
+PILI_HarvestData <- filterToPILI(HarvestData)
+PILI_ReproductionData <- filterToPILI(ReproductionData)
+PILI_PartsSummary <- make_PartsSummary(PILI_FlowerPartsData, PILI_PartsList)
+PILI_GraphMaps <- make_PILI_GraphMaps(PILI_PartsSummary, MultiplierTable)
+PILI_Investment <- CalculateInvestmentForPILI(PILI_ReproductionData, FloweringCategories, MultiplierTable, PILI_GraphMaps, PILI_PartsSummary)
+PILI_ReproductiveCosts <- CalculateReproductiveCostsForPILI(PILI_IndividualsList, InvestmentCategories, PILI_Investment, PILI_PartsSummary)
+PILI_Growth <- CalculateGrowthForPILI(PILI_HarvestData, PILI_IndividualsList)
+PUTU_IndividualsList <- filterToPUTU(IndividualsList)
+PUTU_FlowerPartsData <- filterToPUTU(FlowerPartsData)
+PUTU_HarvestData <- filterToPUTU(HarvestData)
+PUTU_ReproductionData <- filterToPUTU(ReproductionData)
+PUTU_PartsSummary <- make_PartsSummary(PUTU_FlowerPartsData, PUTU_PartsList)
+PUTU_GraphMaps <- make_PUTU_GraphMaps(PUTU_PartsSummary, MultiplierTable)
+PUTU_Investment <- CalculateInvestmentForPUTU(PUTU_ReproductionData, FloweringCategories, MultiplierTable, PUTU_GraphMaps, PUTU_PartsSummary)
+PUTU_ReproductiveCosts <- CalculateReproductiveCostsForPUTU(PUTU_IndividualsList, InvestmentCategories, PUTU_Investment, PUTU_PartsSummary)
+PUTU_Growth <- CalculateGrowthForPUTU(PUTU_HarvestData, PUTU_IndividualsList)
+Growth_all <- combine_Growth(BAER_Growth, BOLE_Growth, COER_Growth, EPMI_Growth, GRBU_Growth, GRSP_Growth, HATE_Growth, HEPU_Growth, LEES_Growth, PELA_Growth, PEPU_Growth, PHPH_Growth, PILI_Growth, PUTU_Growth, NULL)
+pdf("ms/RA/figures/leaf_weight.pdf", width = 16L, height = 9L)
+figure_leaf_weight(Growth_all)
+dev.off()
+pdf("ms/RA/figures/height.pdf", width = 16L, height = 9L)
+figure_height(Growth_all)
+dev.off()
+ReproductiveCosts_all <- combine_data_frames(BAER_ReproductiveCosts, BOLE_ReproductiveCosts, COER_ReproductiveCosts, EPMI_ReproductiveCosts, GRBU_ReproductiveCosts, GRSP_ReproductiveCosts, HATE_ReproductiveCosts, HEPU_ReproductiveCosts, LEES_ReproductiveCosts, PELA_ReproductiveCosts, PEPU_ReproductiveCosts, PHPH_ReproductiveCosts, PILI_ReproductiveCosts, PUTU_ReproductiveCosts, NULL)
+SummaryInd_1 <- combine_by_individual(IndividualsList, Growth_all, ReproductiveCosts_all, LMA, leafLoss, wood_density_spp, seedsize)
+SummaryInd <- sort_by_variable(SummaryInd_1, variable_list)
+fits_figure_allocation_all_a <- fit_allocation_model(SummaryInd)
+pdf("ms/RA/figures/RA_all_a.pdf", width = 16L, height = 9L)
+figure_allocation_all_a(fits_figure_allocation_all_a)
+dev.off()
+pdf("ms/RA/figures/investment.pdf", width = 16L, height = 9L)
+figure_investment_weight(SummaryInd)
+dev.off()
+SummarySppAge <- get_species_values(SummaryInd, groups = c("species", "age"))
+pdf("ms/RA/figures/RA_demo.pdf", width = 16L, height = 4L)
+figure_allocation_demo_single(SummarySppAge)
+dev.off()
+pdf("ms/RA/figures/RA_demo_all.pdf", width = 16L, height = 32L)
+figure_allocation_demo_all(SummarySppAge)
+dev.off()
+pdf("ms/RA/figures/abstract.pdf", width = 8L, height = 4L)
+figure_graphical_abstract(SummarySppAge)
+dev.off()
+SummarySpp <- get_species_values(SummaryInd, groups = "species")
+pdf("ms/RA/figures/life_history.pdf", width = 8L, height = 4L)
+figure_life_history(SummarySpp, SummarySppAge, fits_figure_allocation_all_a)
+dev.off()
+pdf("ms/RA/figures/leaf_loss.pdf", width = 4L, height = 4L)
+figure_LMA_leafloss(SummarySpp)
+dev.off()
+write.csv(SummaryInd, "export/SummaryInd.csv", row.names = FALSE)
+PartsSummary_all <- combine_list_elements(BAER_PartsSummary, BOLE_PartsSummary, COER_PartsSummary, EPMI_PartsSummary, GRBU_PartsSummary, GRSP_PartsSummary, HATE_PartsSummary, HEPU_PartsSummary, LEES_PartsSummary, PELA_PartsSummary, PEPU_PartsSummary, PHPH_PartsSummary, PILI_PartsSummary, PUTU_PartsSummary, element = "AvWeightPerUnit")
+Investment_FD_all <- combine_list_elements(BAER_Investment, BOLE_Investment, COER_Investment, EPMI_Investment, GRBU_Investment, GRSP_Investment, HATE_Investment, HEPU_Investment, LEES_Investment, PELA_Investment, PEPU_Investment, PHPH_Investment, PILI_Investment, PUTU_Investment, element = "FD")
+knitr::knit("ms/RA/Wenk-RA-SI.Rnw", "ms/RA/Wenk-RA-SI.tex")
+latex_build("ms/RA/Wenk-RA-SI.tex", clean = TRUE)