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Update location_barnett_metrics.R to handle empty dataframes and location sequences without flights

replace/824459cbe305bb36cfc46176947fb2a999206055
JulioV 2019-11-13 14:54:24 -05:00
parent d2e9b79af6
commit 44bbe17435
1 changed files with 33 additions and 7 deletions
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36
src/features/location_barnett_metrics.R
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@ -2,6 +2,26 @@ source("packrat/init.R")
library(dplyr) library(dplyr)
write_empty_file <- function(file_path){
write.csv(data.frame(local_date= character(),
hometime= numeric(),
disttravelled= numeric(),
rog= numeric(),
maxdiam= numeric(),
maxhomedist= numeric(),
siglocsvisited= numeric(),
avgflightlen= numeric(),
stdflightlen= numeric(),
avgflightdur= numeric(),
stdflightdur= numeric(),
probpause= numeric(),
siglocentropy= numeric(),
minsmissing= numeric(),
circdnrtn= numeric(),
wkenddayrtn= numeric()
), file_path, row.names = F)
}
# Load Ian Barnett's code. Taken from https://scholar.harvard.edu/ibarnett/software/gpsmobility # Load Ian Barnett's code. Taken from https://scholar.harvard.edu/ibarnett/software/gpsmobility
file.sources = list.files(c("src/features/location_barnett"), pattern="*.R$", full.names=TRUE, ignore.case=TRUE) file.sources = list.files(c("src/features/location_barnett"), pattern="*.R$", full.names=TRUE, ignore.case=TRUE)
sapply(file.sources,source,.GlobalEnv) sapply(file.sources,source,.GlobalEnv)
@ -12,13 +32,19 @@ timezone <- snakemake@params[["timezone"]]
location <- read.csv(snakemake@input[[1]], stringsAsFactors = F) %>% location <- read.csv(snakemake@input[[1]], stringsAsFactors = F) %>%
select(timestamp, latitude = double_latitude, longitude = double_longitude, altitude = double_altitude, accuracy) select(timestamp, latitude = double_latitude, longitude = double_longitude, altitude = double_altitude, accuracy)
if (nrow(location) > 0){ if (nrow(location) > 1){
features <- MobilityFeatures(location, ACCURACY_LIM = accuracy_limit, tz = timezone) features <- MobilityFeatures(location, ACCURACY_LIM = accuracy_limit, tz = timezone)
if(is.null(features)){
write_empty_file(snakemake@output[[1]])
} else{
# Copy index (dates) as a column # Copy index (dates) as a column
outmatrix = cbind(rownames(features$featavg), features$featavg) outmatrix <- cbind(rownames(features$featavg), features$featavg)
outmatrix <- as.data.frame(outmatrix)
outmatrix[-1] <- lapply(lapply(outmatrix[-1], as.character), as.numeric)
colnames(outmatrix)=c("local_date",tolower(colnames(features$featavg))) colnames(outmatrix)=c("local_date",tolower(colnames(features$featavg)))
write.csv(outmatrix,snakemake@output[[1]], row.names = F) write.csv(outmatrix,snakemake@output[[1]], row.names = F)
} else { }
write.csv(data.frame(),snakemake@output[[1]])
} else {
write_empty_file(snakemake@output[[1]])
} }