## ----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 = 5) 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 development version from GitHub # install.packages('devtools') # library(devtools) # install_github("AnneChao/iSTAY") # # ## Load packages # library(iSTAY) # library(ggplot2) ## ----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), equal_weights = FALSE, 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") # communities_aggregated <- do.call(rbind, Data_Jena_20_metacommunities) # head(round(communities_aggregated[,1:5],2), 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data("Data_Jena_20_metacommunities") communities_aggregated <- do.call(rbind, Data_Jena_20_metacommunities) head(round(communities_aggregated[,1:5],2), 10) ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # data("Data_Jena_76_community_populations") # communities <- Data_Jena_76_community_populations # head(round(communities[[1]][,1:5],2), 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data("Data_Jena_76_community_populations") communities <- Data_Jena_76_community_populations head(round(communities[[1]][,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------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # data("Data_Jena_20_metacommunities") # communities_aggregated <- do.call(rbind, Data_Jena_20_metacommunities) # output_two_plots_q <- iSTAY_Single(data = communities_aggregated[which(rownames(communities_aggregated) %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------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- communities_aggregated <- do.call(rbind, Data_Jena_20_metacommunities) output_two_plots_q <- iSTAY_Single(data = communities_aggregated[which(rownames(communities_aggregated) %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_communities_aggregated_div <- iSTAY_Single(data = communities_aggregated, order.q = c(1,2), Alltime = TRUE) # output_communities_aggregated_div <- data.frame(output_communities_aggregated_div, # log2_sowndiv = log2(as.numeric(do.call(rbind, # strsplit(output_communities_aggregated_div[,1],"[._]+"))[,2])), # block=do.call(rbind, strsplit(output_communities_aggregated_div[,1],"[._]+"))[,1]) # colnames(output_communities_aggregated_div)[1] <- c("Dataset") # head(output_communities_aggregated_div, 10) ## ----echo=FALSE, digits=3----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- output_communities_aggregated_div <- iSTAY_Single(data = communities_aggregated, order.q = c(1,2), Alltime = TRUE) output_communities_aggregated_div <- data.frame(output_communities_aggregated_div, log2_sowndiv = log2(as.numeric(do.call(rbind, strsplit(output_communities_aggregated_div[,1],"[._]+"))[,2])), block=do.call(rbind, strsplit(output_communities_aggregated_div[,1],"[._]+"))[,1]) colnames(output_communities_aggregated_div)[1] <- c("Dataset") head(cbind(output_communities_aggregated_div[,1:2],"Stability"=round(output_communities_aggregated_div[,3],3),output_communities_aggregated_div[,4:5]), 10) ## ----fig.width = 7------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ggiSTAY_analysis(output = output_communities_aggregated_div, x_variable = "log2_sowndiv", by_group = "block", model = "LMM") ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # individual_populations <- Data_Jena_462_populations # 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 <- Data_Jena_462_populations 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------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # communities <- Data_Jena_76_community_populations # output_two_communities_equal_q <- iSTAY_Multiple( # data = communities[which(names(communities) %in% c("B1A04_B1_4", "B4A14_B4_2"))], # order.q = seq(0.1, 2, 0.1), # equal_weights = TRUE, # Alltime = TRUE # ) # head(output_two_communities_equal_q, 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- communities <- Data_Jena_76_community_populations output_two_communities_equal_q <- iSTAY_Multiple( data = communities[which(names(communities) %in% c("B1A04_B1_4", "B4A14_B4_2"))], order.q = seq(0.1, 2, 0.1), equal_weights = TRUE, Alltime = TRUE ) head(output_two_communities_equal_q, 10) ## ----fig.align='center', fig.width = 7, fig.height = 4.5---------------------------------------------------------------------------------------------------------------------------------------------- ggiSTAY_qprofile(output = output_two_communities_equal_q) ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # output_two_communities_biomass_q <- iSTAY_Multiple( # data = communities[which(names(communities) %in% c("B1A04_B1_4", "B4A14_B4_2"))], # order.q = seq(0.1, 2, 0.1), # equal_weights = FALSE, # Alltime = TRUE # ) # head(output_two_communities_biomass_q, 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- output_two_communities_biomass_q <- iSTAY_Multiple( data = communities[which(names(communities) %in% c("B1A04_B1_4", "B4A14_B4_2"))], order.q = seq(0.1, 2, 0.1), equal_weights = FALSE, Alltime = TRUE ) head(output_two_communities_biomass_q, 10) ## ----fig.align='center', fig.width = 7, fig.height = 4.5---------------------------------------------------------------------------------------------------------------------------------------------- ggiSTAY_qprofile(output = output_two_communities_biomass_q) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # output_communities_equal_div <- iSTAY_Multiple( # data = communities, # order.q = c(1, 2), # equal_weights = TRUE, # Alltime = TRUE # ) # # output_communities_equal_div <- data.frame( # output_communities_equal_div, # log2_sowndiv = log2(as.numeric(do.call(rbind, # strsplit(output_communities_equal_div[, 1], "[._]+"))[, 3])), # block = do.call(rbind, # strsplit(output_communities_equal_div[, 1], "_"))[, 2] # ) # rownames(output_communities_equal_div) <- NULL # head(cbind(output_communities_equal_div[, 1:2], # round(output_communities_equal_div[, 3:6], 3), # output_communities_equal_div[, 7:9]), 10) ## ----echo=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- output_communities_equal_div <- iSTAY_Multiple( data = communities, order.q = c(1, 2), equal_weights = TRUE, Alltime = TRUE ) output_communities_equal_div <- data.frame( output_communities_equal_div, log2_sowndiv = log2(as.numeric(do.call(rbind, strsplit(output_communities_equal_div[, 1], "[._]+"))[, 3])), block = do.call(rbind, strsplit(output_communities_equal_div[, 1], "_"))[, 2] ) rownames(output_communities_equal_div) <- NULL head(cbind(output_communities_equal_div[, 1:2], round(output_communities_equal_div[, 3:6], 3), output_communities_equal_div[, 7:9]), 10) ## ----fig.width = 8, fig.height = 9.5------------------------------------------------------------------------------------------------------------------------------------------------------------------ ggiSTAY_analysis(output = output_communities_equal_div, x_variable = "log2_sowndiv", by_group = "block", model = "LMM") ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # output_communities_biomass_div <- iSTAY_Multiple( # data = communities, # order.q = c(1, 2), # equal_weights = FALSE, # Alltime = TRUE # ) # # output_communities_biomass_div <- data.frame( # output_communities_biomass_div, # log2_sowndiv = log2(as.numeric(do.call(rbind, # strsplit(output_communities_biomass_div[, 1], "[._]+"))[, 3])), # block = do.call(rbind, # strsplit(output_communities_biomass_div[, 1], "_"))[, 2] # ) # rownames(output_communities_biomass_div) <- NULL # head(cbind(output_communities_biomass_div[, 1:2], # round(output_communities_biomass_div[, 3:6], 3), # output_communities_biomass_div[, 7:9]), 10) ## ----echo=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- output_communities_biomass_div <- iSTAY_Multiple( data = communities, order.q = c(1, 2), equal_weights = FALSE, Alltime = TRUE ) output_communities_biomass_div <- data.frame( output_communities_biomass_div, log2_sowndiv = log2(as.numeric(do.call(rbind, strsplit(output_communities_biomass_div[, 1], "[._]+"))[, 3])), block = do.call(rbind, strsplit(output_communities_biomass_div[, 1], "_"))[, 2] ) rownames(output_communities_biomass_div) <- NULL head(cbind(output_communities_biomass_div[, 1:2], round(output_communities_biomass_div[, 3:6], 3), output_communities_biomass_div[, 7:9]), 10) ## ----fig.width = 8, fig.height = 9.5------------------------------------------------------------------------------------------------------------------------------------------------------------------ ggiSTAY_analysis(output = output_communities_biomass_div, x_variable = "log2_sowndiv", by_group = "block", model = "LMM") ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # metacommunities <- Data_Jena_20_metacommunities # output_two_metacommunities_equal_q <- iSTAY_Multiple( # data = metacommunities[which(names(metacommunities) %in% c("B1_1", "B3_2"))], # order.q = seq(0.1, 2, 0.1), # equal_weights = TRUE, # Alltime = TRUE # ) # head(output_two_metacommunities_equal_q, 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- metacommunities <- Data_Jena_20_metacommunities output_two_metacommunities_equal_q <- iSTAY_Multiple( data = metacommunities[which(names(metacommunities) %in% c("B1_1", "B3_2"))], order.q = seq(0.1, 2, 0.1), equal_weights = TRUE, Alltime = TRUE ) head(output_two_metacommunities_equal_q, 10) ## ----fig.align='center', fig.width = 7, fig.height = 4.5---------------------------------------------------------------------------------------------------------------------------------------------- ggiSTAY_qprofile(output = output_two_metacommunities_equal_q) ## ----eval=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # output_two_metacommunities_biomass_q <- iSTAY_Multiple( # data = metacommunities[which(names(metacommunities) %in% c("B1_1", "B3_2"))], # order.q = seq(0.1, 2, 0.1), # equal_weights = FALSE, # Alltime = TRUE # ) # head(output_two_metacommunities_biomass_q, 10) ## ----echo=F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- output_two_metacommunities_biomass_q <- iSTAY_Multiple( data = metacommunities[which(names(metacommunities) %in% c("B1_1", "B3_2"))], order.q = seq(0.1, 2, 0.1), equal_weights = FALSE, Alltime = TRUE ) head(output_two_metacommunities_biomass_q, 10) ## ----fig.align='center', fig.width = 7, fig.height = 4.5---------------------------------------------------------------------------------------------------------------------------------------------- ggiSTAY_qprofile(output = output_two_metacommunities_biomass_q) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # output_metacommunities_equal_div <- iSTAY_Multiple( # data = metacommunities, # order.q = c(1, 2), # equal_weights = TRUE, # Alltime = TRUE # ) # # output_metacommunities_equal_div <- data.frame( # output_metacommunities_equal_div, # log2_sowndiv = log2(as.numeric(do.call(rbind, # strsplit(output_metacommunities_equal_div[, 1], "_"))[, 2])), # block = do.call(rbind, # strsplit(output_metacommunities_equal_div[, 1], "_"))[, 1] # ) # rownames(output_metacommunities_equal_div) <- NULL # head(cbind(output_metacommunities_equal_div[, 1:2], # round(output_metacommunities_equal_div[, 3:6], 3), # output_metacommunities_equal_div[, 7:9]), 10) ## ----echo=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- output_metacommunities_equal_div <- iSTAY_Multiple( data = metacommunities, order.q = c(1, 2), equal_weights = TRUE, Alltime = TRUE ) output_metacommunities_equal_div <- data.frame( output_metacommunities_equal_div, log2_sowndiv = log2(as.numeric(do.call(rbind, strsplit(output_metacommunities_equal_div[, 1], "_"))[, 2])), block = do.call(rbind, strsplit(output_metacommunities_equal_div[, 1], "_"))[, 1] ) rownames(output_metacommunities_equal_div) <- NULL head(cbind(output_metacommunities_equal_div[, 1:2], round(output_metacommunities_equal_div[, 3:6], 3), output_metacommunities_equal_div[, 7:9]), 10) ## ----fig.width = 8, fig.height = 9.5------------------------------------------------------------------------------------------------------------------------------------------------------------------ ggiSTAY_analysis(output = output_metacommunities_equal_div, x_variable = "log2_sowndiv", by_group = "block", model = "LMM") ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # output_metacommunities_biomass_div <- iSTAY_Multiple( # data = metacommunities, # order.q = c(1, 2), # equal_weights = FALSE, # Alltime = TRUE # ) # # output_metacommunities_biomass_div <- data.frame( # output_metacommunities_biomass_div, # log2_sowndiv = log2(as.numeric(do.call(rbind, # strsplit(output_metacommunities_biomass_div[, 1], "_"))[, 2])), # block = do.call(rbind, # strsplit(output_metacommunities_biomass_div[, 1], "_"))[, 1] # ) # rownames(output_metacommunities_biomass_div) <- NULL # head(cbind(output_metacommunities_biomass_div[, 1:2], # round(output_metacommunities_biomass_div[, 3:6], 3), # output_metacommunities_biomass_div[, 7:9]), 10) ## ----echo=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- output_metacommunities_biomass_div <- iSTAY_Multiple( data = metacommunities, order.q = c(1, 2), equal_weights = FALSE, Alltime = TRUE ) output_metacommunities_biomass_div <- data.frame( output_metacommunities_biomass_div, log2_sowndiv = log2(as.numeric(do.call(rbind, strsplit(output_metacommunities_biomass_div[, 1], "_"))[, 2])), block = do.call(rbind, strsplit(output_metacommunities_biomass_div[, 1], "_"))[, 1] ) rownames(output_metacommunities_biomass_div) <- NULL head(cbind(output_metacommunities_biomass_div[, 1:2], round(output_metacommunities_biomass_div[, 3:6], 3), output_metacommunities_biomass_div[, 7:9]), 10) ## ----fig.width = 8, fig.height = 9.5------------------------------------------------------------------------------------------------------------------------------------------------------------------ ggiSTAY_analysis(output = output_metacommunities_biomass_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]]