## ---- include = FALSE---------------------------------------------------- library(data.table) library(magrittr) library(servosphereR) ## ---- include = FALSE, echo = FALSE-------------------------------------- servosphere_data <- read.csv2("317_03212018_servosphere.csv") ## ---- echo = FALSE, eval = TRUE------------------------------------------ head(servosphere_data, n = 4) ## ---- include = FALSE---------------------------------------------------- servosphere_data <- getFiles(path = ".", pattern = "_servosphere") ## ---- eval = FALSE, echo = TRUE------------------------------------------ # servosphere_data <- getFiles(path = "C:/Users/Jake/thesis_project/servosphere_data", # pattern = "_servosphere") ## ---- eval = TRUE, echo = TRUE------------------------------------------- servosphere_data <- cleanNames(list = servosphere_data, colnames = c("stimulus", "dT", "dx", "dy")) head(servosphere_data[[1]], n = 4) # Return the first 4 rows of the 1st file in the list ## ---- echo = FALSE, eval = TRUE------------------------------------------ experiment_info <- read.csv("trial_id.csv") ## ---- echo = TRUE, eval = TRUE------------------------------------------- head(experiment_info) ## ---- echo = TRUE, eval = TRUE------------------------------------------- servosphere_data <- mergeTrialInfo(list = servosphere_data, trial.data = experiment_info, col.names = c("id", "treatment"), stimulus.keep = c(0, 1, 2)) head(servosphere_data[[1]], n = 4) # Return the first 4 rows of the 1st file in the list ## ---- echo = FALSE, eval = TRUE------------------------------------------ servosphere_data <- getFiles(path = ".", pattern = "_servosphere") %>% cleanNames(colnames = c("stimulus", "dT", "dx", "dy")) ## ---- echo = TRUE, eval = TRUE------------------------------------------- servosphere_data <- mergeTrialInfo(list = servosphere_data, trial.data = experiment_info, col.names = c("id", "treatment"), stimulus.keep = c(1)) head(servosphere_data[[1]], n = 4) ## ---- echo = FALSE, eval = TRUE------------------------------------------ experimental_info_stim_split <- read.csv("trial_id_stimulus.csv") %>% dplyr::arrange(id) ## ---- echo = TRUE, eval = TRUE------------------------------------------- head(experimental_info_stim_split) ## ---- echo = FALSE, eval = TRUE------------------------------------------ servosphere_data <- getFiles(path = ".", pattern = "_servosphere") %>% cleanNames(colnames = c("stimulus", "dT", "dx", "dy")) ## ---- echo = TRUE, eval = TRUE------------------------------------------- servosphere_data <- mergeTrialInfo(list = servosphere_data, trial.data = experimental_info_stim_split, col.names = c("id_stim", "treatment"), stimulus.keep = c(1, 2), stimulus.split = TRUE) head(servosphere_data[[1]], n = 4) ## ---- echo = FALSE, eval = TRUE------------------------------------------ servosphere_data <- getFiles(path = ".", pattern = "_servosphere") %>% cleanNames(colnames = c("stimulus", "dT", "dx", "dy")) %>% mergeTrialInfo(trial.data = experiment_info, col.names = c("id", "treatment"), stimulus.keep = c(1)) ## ---- echo = TRUE, eval = TRUE------------------------------------------- servosphere_data <- aggregateData(list = servosphere_data, n = 60) head(servosphere_data[[1]], n = 4) ## ---- echo = TRUE, eval = TRUE------------------------------------------- servosphere_data <- servosphere_data %>% calcXY() %>% calcDistance() %>% calcBearing() %>% calcTurnAngle() %>% calcTurnVelocity() %>% calcVelocity() head(servosphere_data[[1]]) # Displays first rows of 1st dataframe in list ## ---- echo = TRUE, eval = TRUE------------------------------------------- summary_data_frame <- summaryTotalDistance(list = servosphere_data, summary.df = NA) summary_data_frame ## ---- echo = TRUE, eval = TRUE------------------------------------------- summary_data_frame <- summaryNetDisplacement(list = servosphere_data, summary.df = summary_data_frame) summary_data_frame ## ---- echo = TRUE, eval = TRUE------------------------------------------- summary_data_frame <- summaryTortuosity(summary.df = summary_data_frame, total.distance = total_distance, net.displacement = net_displacement, inverse = FALSE) summary_data_frame ## ---- echo = TRUE, eval = TRUE------------------------------------------- summary_data_frame <- summaryStops(list = servosphere_data, summary.df = summary_data_frame, stop.threshold = 0.1) summary_data_frame ## ---- echo = TRUE, eval = TRUE------------------------------------------- summary_data_frame <- summaryAvgBearing(list = servosphere_data, summary.df = summary_data_frame) summary_data_frame <- summaryAvgVelocity(list = servosphere_data, summary.df = summary_data_frame) summary_data_frame ## ---- echo = TRUE, eval = FALSE------------------------------------------ # # Get files, clean file column names, and merge relevant experimental info # servosphere_data <- getFiles(path = ".", pattern = "_servosphere") %>% # cleanNames(colnames = c("stimulus", # "dT", # "dx", # "dy")) %>% # mergeTrialInfo(trial.data = experiment_info, # col.names = c("id", "treatment"), # stimulus.keep = c(1)) %>% # aggregateData(n = 100) %>% # # Calculate derived movement variables # calcDistance() %>% # calcBearing() %>% # calcTurnAngle() %>% # calcTurnVelocity() %>% # calcVelocity() # # # Summarize derived variables # summary_data_frame <- summaryTotalDistance(list = servosphere_data, # summary.df = NA) # # summary_data_frame <- summaryNetDisplacement(list = servosphere_data, # summary.df = summary_data_frame) # # summary_data_frame <- summaryTortuosity(summary.df = summary_data_frame, # total.distance = total_distance, # net.displacement = net_displacement, # inverse = FALSE) # # summary_data_frame <- summaryStops(list = servosphere_data, # summary.df = summary_data_frame, # stop.threshold = 0.1) # # summary_data_frame <- summaryStops(list = servosphere_data, # summary.df = summary_data_frame, # stop.threshold = 0.1) # # summary_data_frame <- summaryAvgBearing(list = servosphere_data, # summary.df = summary_data_frame) # # summary_data_frame <- summaryAvgVelocity(list = servosphere_data, # summary.df = summary_data_frame)