## ----global-options, include=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------- if (requireNamespace("knitr", quietly = TRUE)) { kc <- get("opts_chunk", envir = asNamespace("knitr")) kc$set( collapse = TRUE, comment = "#>", fig.retina = 2, fig.align = "center", fig.width = 6, fig.height = 3, warning = FALSE, message = FALSE ) } else { warning("Package 'knitr' not available; vignette chunk options not set.") } old_options <- options(width = 200, digits = 3) paste0 <- base::paste0 paste <- base::paste ## ----eval = TRUE, echo = FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(iSTAY) ## ----eval = FALSE, echo = TRUE------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # ## install iSTAY package from CRAN # # install.packages("iSTAY") # # ## install the latest version from github # install.packages('devtools') # library(devtools) # install_github("AnneChao/iSTAY") # # ## import packages # library(iSTAY) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # iSTAY_Single(data, order.q = c(1, 2), Alltime = TRUE, start_T = NULL, end_T = NULL) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # iSTAY_Multiple(data, order.q = c(1, 2), Alltime = TRUE, start_T = NULL, end_T = NULL) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # iSTAY_Hier(data, structure, order.q = c(1, 2), Alltime = TRUE, start_T = NULL, end_T = NULL) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # ggiSTAY_qprofile(output) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # ggiSTAY_analysis(output, x_variable, by_group = NULL, model = "LMM") ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # data("Data_Jena_20_metacommunities") # metacommunities <- Data_Jena_20_metacommunities # head(round(metacommunities[[1]][,1:5],2), 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data("Data_Jena_20_metacommunities") metacommunities <- Data_Jena_20_metacommunities head(round(metacommunities[[1]][,1:5],2), 10) ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # data("Data_Jena_20_metacommunities") # individual_plots <- do.call(rbind, Data_Jena_20_metacommunities) # head(round(individual_plots[,1:5],2), 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data("Data_Jena_20_metacommunities") individual_plots <- do.call(rbind, Data_Jena_20_metacommunities) head(round(individual_plots[,1:5],2), 10) ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # data("Data_Jena_76_metapopulations") # metapopulations <- Data_Jena_76_metapopulations # head(round(metapopulations[[1]][,1:5],2), 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data("Data_Jena_76_metapopulations") metapopulations <- Data_Jena_76_metapopulations head(round(metapopulations[[1]][,1:5],2), 10) ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # data("Data_Jena_76_metapopulations") # individual_populations <- do.call(rbind, Data_Jena_76_metapopulations) # head(round(individual_populations[,1:5],2), 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data("Data_Jena_76_metapopulations") individual_populations <- do.call(rbind, Data_Jena_76_metapopulations) head(round(individual_populations[,1:5],2), 10) ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # data("Data_Jena_462_populations") # head(round(Data_Jena_462_populations[,1:5],2), 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data("Data_Jena_462_populations") head(round(Data_Jena_462_populations[,1:5],2), 10) ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # data("Data_Jena_hierarchical_structure") # head(Data_Jena_hierarchical_structure, 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data("Data_Jena_hierarchical_structure") head(Data_Jena_hierarchical_structure, 10) ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # individual_plots <- do.call(rbind, Data_Jena_20_metacommunities) # output_two_plots_q <- iSTAY_Single(data = individual_plots[which(rownames(individual_plots) %in% c("B1_4.B1A04", "B4_2.B4A14")),], # order.q=seq(0.1,2,0.1), # Alltime = TRUE) # head(output_two_plots_q, 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- individual_plots <- do.call(rbind, Data_Jena_20_metacommunities) output_two_plots_q <- iSTAY_Single(data = individual_plots[which(rownames(individual_plots) %in% c("B1_4.B1A04", "B4_2.B4A14")),], order.q=seq(0.1,2,0.1), Alltime = TRUE) head(cbind(output_two_plots_q[,1:2],"Stability"=round(output_two_plots_q[,3],3)), 10) ## ----fig.align='center'------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ggiSTAY_qprofile(output = output_two_plots_q) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # output_individual_plots_div <- iSTAY_Single(data = individual_plots, order.q = c(1,2), Alltime = TRUE) # output_individual_plots_div <- data.frame(output_individual_plots_div, # log2_sowndiv = log2(as.numeric(do.call(rbind, # strsplit(output_individual_plots_div[,1],"[._]+"))[,2])), # block=do.call(rbind, strsplit(output_individual_plots_div[,1],"[._]+"))[,1]) # colnames(output_individual_plots_div)[1] <- c("Dataset") # head(output_individual_plots_div, 10) ## ----echo=FALSE, digits=3----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- output_individual_plots_div <- iSTAY_Single(data = individual_plots, order.q = c(1,2), Alltime = TRUE) output_individual_plots_div <- data.frame(output_individual_plots_div, log2_sowndiv = log2(as.numeric(do.call(rbind, strsplit(output_individual_plots_div[,1],"[._]+"))[,2])), block=do.call(rbind, strsplit(output_individual_plots_div[,1],"[._]+"))[,1]) colnames(output_individual_plots_div)[1] <- c("Dataset") head(cbind(output_individual_plots_div[,1:2],"Stability"=round(output_individual_plots_div[,3],3),output_individual_plots_div[,4:5]), 10) ## ----fig.width = 7------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ggiSTAY_analysis(output = output_individual_plots_div, x_variable = "log2_sowndiv", by_group = "block", model = "LMM") ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # individual_populations <- do.call(rbind, Data_Jena_76_metapopulations) # output_two_populations_q <- iSTAY_Single(data = individual_populations[which(rownames(individual_populations) %in% c("B1A06_B1_16.BM_Ant.odo", "B1A06_B1_16.BM_Cam.pat")),], # order.q=seq(0.1,2,0.1), Alltime=TRUE) # head(output_two_populations_q, 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- individual_populations <- do.call(rbind, Data_Jena_76_metapopulations) output_two_populations_q <- iSTAY_Single(data = individual_populations[which(rownames(individual_populations) %in% c("B1A06_B1_16.BM_Ant.odo", "B1A06_B1_16.BM_Cam.pat")),], order.q=seq(0.1,2,0.1), Alltime=TRUE) head(cbind(output_two_populations_q[,1:2],"Stability"=round(output_two_populations_q[,3],3)), 10) ## ----fig.align='center'------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ggiSTAY_qprofile(output = output_two_populations_q) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # output_individual_populations_div <- iSTAY_Single(data = individual_populations, # order.q = c(1,2), Alltime=TRUE) # output_individual_populations_div <- data.frame(output_individual_populations_div, # log2_sowndiv = log2(as.numeric(do.call(rbind, # strsplit(output_individual_populations_div[,1],"[._]+"))[,3])), # block = do.call(rbind, # strsplit(output_individual_populations_div[,1],"[._]+"))[,2]) # head(output_individual_populations_div, 10) ## ----echo=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- output_individual_populations_div <- iSTAY_Single(data = individual_populations, order.q = c(1,2), Alltime=TRUE) output_individual_populations_div <- data.frame(output_individual_populations_div, log2_sowndiv = log2(as.numeric(do.call(rbind, strsplit(output_individual_populations_div[,1],"[._]+"))[,3])), block = do.call(rbind, strsplit(output_individual_populations_div[,1],"[._]+"))[,2]) head(cbind(output_individual_populations_div[,1:2],"Stability"=round(output_individual_populations_div[,3],3),output_individual_populations_div[,4:5]), 10) ## ----fig.width = 7------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ggiSTAY_analysis(output=output_individual_populations_div, x_variable="log2_sowndiv", by_group="block", model="LMM") ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # metacommunities <- Data_Jena_20_metacommunities # output_two_metacommunities_q <- iSTAY_Multiple(data = metacommunities[which(names(metacommunities) %in% c("B1_1", "B3_2"))], # order.q = seq(0.1,2,0.1), Alltime=TRUE) # head(output_two_metacommunities_q, 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- metacommunities <- Data_Jena_20_metacommunities output_two_metacommunities_q <- iSTAY_Multiple(data = metacommunities[which(names(metacommunities) %in% c("B1_1", "B3_2"))], order.q = seq(0.1,2,0.1), Alltime=TRUE) head(output_two_metacommunities_q, 10) ## ----fig.align='center', fig.width = 7, fig.height = 4.5---------------------------------------------------------------------------------------------------------------------------------------------- ggiSTAY_qprofile(output = output_two_metacommunities_q) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # output_metacommunities_div <- iSTAY_Multiple(data = metacommunities, order.q=c(1,2), Alltime=TRUE) # # output_metacommunities_div <- data.frame(output_multi_div, # log2_sowndiv = log2(as.numeric(do.call(rbind, strsplit(output_metacommunities_div[, 1], "_"))[, 2])), # block = do.call(rbind, strsplit(output_metacommunities_div[, 1], "_"))[, 1]) # rownames(output_metacommunities_div) <- NULL # head(cbind(output_metacommunities_div[,1:2], round(output_metacommunities_div[3:6],3), output_metacommunities_div[,7:8]), 10) ## ----echo=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- output_metacommunities_div <- iSTAY_Multiple(data = metacommunities, order.q = c(1,2), Alltime = TRUE) output_metacommunities_div <- data.frame(output_metacommunities_div, log2_sowndiv = log2(as.numeric(do.call(rbind, strsplit(output_metacommunities_div[, 1], "_"))[, 2])), block = do.call(rbind, strsplit(output_metacommunities_div[, 1], "_"))[, 1]) rownames(output_metacommunities_div) <- NULL head(cbind(output_metacommunities_div[,1:2], round(output_metacommunities_div[3:6],3), output_metacommunities_div[,7:8]), 10) ## ----fig.width = 8, fig.height=9.5-------------------------------------------------------------------------------------------------------------------------------------------------------------------- ggiSTAY_analysis(output = output_metacommunities_div, x_variable = "log2_sowndiv", by_group = "block", model = "LMM") ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # metapopulations <- Data_Jena_76_metapopulations # output_two_metapopulations_q <- iSTAY_Multiple(data = metapopulations[which(names(metapopulations) %in% c("B1A04_B1_4", "B4A14_B4_2"))], # order.q = seq(0.1,2,0.1), Alltime = TRUE) # head(output_two_metapopulations_q, 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- metapopulations <- Data_Jena_76_metapopulations output_two_metapopulations_q <- iSTAY_Multiple(data = metapopulations[which(names(metapopulations) %in% c("B1A04_B1_4", "B4A14_B4_2"))], order.q = seq(0.1,2,0.1), Alltime = TRUE) head(output_two_metapopulations_q, 10) ## ----fig.align='center', fig.width = 7, fig.height = 4.5---------------------------------------------------------------------------------------------------------------------------------------------- ggiSTAY_qprofile(output = output_two_metapopulations_q) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # output_metapopulations_div <- iSTAY_Multiple(data = metapopulations, # order.q = c(1,2), Alltime = TRUE) # output_metapopulations_div <- data.frame(output_metapopulations_div, # log2_sowndiv = log2(as.numeric(do.call(rbind, # strsplit(output_metapopulations_div[,1],"[._]+"))[,3])), # block = do.call(rbind, # strsplit(output_metapopulations_div[,1],"_"))[,2]) # head(output_metapopulations_div, 10) ## ----echo=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- output_metapopulations_div <- iSTAY_Multiple(data = metapopulations, order.q = c(1,2), Alltime = TRUE) output_metapopulations_div <- data.frame(output_metapopulations_div, log2_sowndiv = log2(as.numeric(do.call(rbind, strsplit(output_metapopulations_div[,1],"[._]+"))[,3])), block = do.call(rbind, strsplit(output_metapopulations_div[,1],"_"))[,2]) head(output_metapopulations_div, 10) ## ----fig.width = 8, fig.height=9.5-------------------------------------------------------------------------------------------------------------------------------------------------------------------- ggiSTAY_analysis(output=output_metapopulations_div, x_variable="log2_sowndiv", by_group="block", model="LMM") ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # data("Data_Jena_462_populations") # data("Data_Jena_hierarchical_structure") # output_hier_q <- iSTAY_Hier(data = Data_Jena_462_populations, # structure = Data_Jena_hierarchical_structure, # order.q=seq(0.1,2,0.1), Alltime=TRUE) # head(cbind(output_hier_q[,1:2], round(output_hier_q[,3:6],3)), 10) ## ----echo=F------------------------------------------------------------------- data("Data_Jena_462_populations") data("Data_Jena_hierarchical_structure") output_hier_q <- iSTAY_Hier(data = Data_Jena_462_populations, structure = Data_Jena_hierarchical_structure, order.q=seq(0.1,2,0.1), Alltime=TRUE) head(cbind(output_hier_q[,1:2], round(output_hier_q[,3:6],3)), 10) on.exit(options(old_options)) # Restore user options to comply with CRAN policy ## ----fig.align='left', fig.width = 5, fig.height = 3-------------------------- hierplot <- ggiSTAY_qprofile(output=output_hier_q) hierplot[[1]] ## ----fig.align='left', fig.width = 9.5, fig.height = 3------------------------ hierplot[[2]]