R/make_tracks.R
In darrennorris/rgps: Functions to use gpx files
Defines functions
make_tracks
Documented in
make_tracks
#' @title Import and summarise tracklogs and waypoints.
#' @description Import and summarise tracklogs and waypoints.
#' @param folder_gpx Location of folder containing .gpx files.
#' @param river_shape Location of file containing shapefile to define survey zones
#' @param folder_result Location where results are saved.
#' @param date_start Optional. Character of start date ("dd/mm/yyyy")
#' @param date_end Optional. Character of end date ("dd/mm/yyyy")
#' @param make_shape Optional. Logical (TRUE/FALSE). Write a shapefile with all tracklog points.
#' @param do_waypoints Optional. Logical (TRUE/FALSE). Generate .csv with waypoints.
#' @param make_shape_wp Optional. Logical (TRUE/FALSE). Generate shapefile with waypoints.
#' @param type_csv Required. What type of .csv to export? ".csv" or ".csv2"
#'
#' @return Will generate R objects and export .csv and shapefiles.
#'
#' @export
#' @importFrom "stats" "na.omit" "sd"
#' @importFrom "utils" "write.csv2"
#' @importFrom "utils" "write.csv"
#'
#' @examples
#' \dontrun{
#' # 1) need to specify 3 locations.
#' #1.1) Location of shapefile with river zones
#' #1.2) Location of folder with .gpx files censu
#' #1.3) Location of folder for results
#'
#' rs <- system.file("shapes/riverzones.shp", package = "rgps")
#' fg <- system.file("gpx", package = "rgps")
#' fr <- "/Location/of/result/folder"
#'
#' # 2) run
#' list_track_data <- rgps::make_tracks(
#' folder_gpx = fg, folder_result = fr, river_shape = rs,
#' do_waypoints = TRUE, make_shape = FALSE,
#' make_shape_wp = FALSE,
#' type_csv = ".csv")
#' }
make_tracks <- function(folder_gpx, river_shape, folder_result,
date_start = NA, date_end = NA, make_shape = FALSE,
do_waypoints = FALSE, make_shape_wp = FALSE,
type_csv = NA){
# 1) load gpx
# 1.1) list of .gpx files
setwd(folder_gpx)
input_path<-getwd() # target directory
myfileinfo<-file.info(list.files(input_path, pattern= ".gpx",
ignore.case=TRUE,full.names=TRUE))
myfileinfo$aname <- rownames(myfileinfo)
# 1.2 run
gc()
#library(plyr)
df_tracks_in <- plyr::ddply(myfileinfo, .variables="aname",
.fun = load_tracks)
# 2) cleaning, should clean tracklogs, remove duplicates and common import errors
gc()
#library(plyr)
df_tracks_out <- plyr::ddply(df_tracks_in, .variables="aname",
.fun = clean_tracks)
# 2.1 finish
selg <- which(is.na(df_tracks_out$lon)==FALSE)
df_tracks_out <- df_tracks_out[selg, ]
#remove duplicates
df_tracks_out <- df_tracks_out[!duplicated(df_tracks_out$adtnum), ]
# drop first distance
selSt <- which(df_tracks_out$trip_start_flag == 1)
df_tracks_out[selSt, 'dist_m_census'] <- NA
## 3) add zones
#library(raster)
s1 <- raster::shapefile(river_shape)
#library(sp)
sp1 <- df_tracks_out
sp::coordinates(sp1) <- ~lon+lat
# assign CRS/projection
sp::proj4string(sp1) <- sp::proj4string(s1)
df_tracks_out$zone <- sp::over(sp1, s1)[,2]
df_tracks_out <- df_tracks_out[order(df_tracks_out$adtnum), ]
rownames(df_tracks_out) <- NULL
# 4) summary
all_tracks_summary <- plyr::ddply(df_tracks_out,
.variables=c("aname", "seg_id", "zone"),
plyr::summarize,
transect = NA,
Day = NA,
min_t = min(adt),
max_t = max(adt),
aname = min(aname),
ayear = min(ayear),
adate = as.Date(format(min(adt),"%d/%m/%Y",tz="America/Belem"),
format="%d/%m/%Y"),
anomes = format(min(adt),"%Y%m",tz="America/Belem"),
trip_start = format(min(adt), tz="America/Belem"),
trip_end = format(max(adt), tz="America/Belem"),
trip_time_sec = (max(as.numeric(adt)) - min(as.numeric(adt))),
trip_time_hr = ((max(as.numeric(adt)) - min(as.numeric(adt)))/60)/60,
speed_mean = round(mean(na.omit(vel)),3),
V_min = round(min(na.omit(vel)),2),
V_max = round(max(na.omit(vel)),2),
V_sd = round(sd(na.omit(vel)),2),
dist_tot_km = sum(na.omit(dist_m_clean))/1000,
dist_tot_census_km = sum(na.omit(dist_m_census))/1000
)
all_tracks_summary$trip_id <- paste(all_tracks_summary$zone,
all_tracks_summary$trip_start, sep="_")
# select dates
if (is.na(date_start)==FALSE){
stoptext <- "No .gpx tracklogs in specified dates. Check dates are valid.
Check date format is valid (dd/mm/yyyy). Change dates to NA to run all days."
mdates <- seq(as.Date(date_start, format="%d/%m/%Y",tz="America/Belem"),
as.Date(date_end, format="%d/%m/%Y",tz="America/Belem"), by ="day")
selD <- which(all_tracks_summary$adate %in% mdates)
if(length(selD) > 0) {all_tracks_summary <- all_tracks_summary[selD, ]}else{stop(stoptext)}
#all_tracks_summary <- all_tracks_summary[selD, ]
}
# select trips lasting 3 minutes or more
selT <- which(all_tracks_summary$trip_time_sec > 179)
all_tracks_summary <- all_tracks_summary[selT, ]
# count of number of survey days, plus sorts by date
all_tracks_summary <- merge(all_tracks_summary,
data.frame(adate = unique(all_tracks_summary$adate),
day_count = rank(unique(all_tracks_summary$adate))), all.x = TRUE)
all_tracks_summary <- all_tracks_summary[order(all_tracks_summary$trip_start), ]
rownames(all_tracks_summary) <- NULL
# 5) select only valid track points
# Result = data frame with track points for trips in all_tracks_summary
t_seq <- function(x){
df1 <- data.frame(mydt = seq(from = x$min_t, to = x$max_t, by = "sec"))
}
#require(plyr)
d_seq <- plyr::ddply(all_tracks_summary,
.variables=c("aname", "seg_id", "zone",
"trip_start", "trip_id"), .fun = t_seq)
# data frame with track points for trips in all_tracks_summary
dt <- merge(df_tracks_out, d_seq, by.x=c("zone", "adt" ), by.y=c("zone","mydt"))
dt <- dt [order(dt$adtnum), ]
rownames(dt ) <- NULL
df_tracks_out2 <- data.frame(aname = dt$aname.x, trip_id = dt$trip_id,
trip_start = dt$trip_start, zone = dt$zone,
gpstime = dt$time, adt = dt$adt, adtnum = dt$adtnum,
adtAP = dt$adtAP, ayear = dt$ayear, adate = dt$adate,
ele = dt$ele,
lon = dt$lon, lat = dt$lat, lon_lead = dt$lon_lead,
lat_lead = dt$lat_lead,
tdiff_clean = dt$tdiff_clean,
bear_deg_clean = dt$bear_deg_clean, vel = dt$vel,
dist_m_clean = dt$dist_m_clean, dist_m_census = dt$dist_m_census
)
all_tracks_summary_out <- data.frame(aname = all_tracks_summary$aname,
trip_id = all_tracks_summary$trip_id,
day_count = all_tracks_summary$day_count,
ayear = all_tracks_summary$ayear,
anomes = all_tracks_summary$anomes,
adate = all_tracks_summary$adate,
zone = all_tracks_summary$zone,
transect = all_tracks_summary$transect,
Day = all_tracks_summary$Day,
trip_start = all_tracks_summary$trip_start,
trip_end = all_tracks_summary$trip_end,
trip_time_sec = all_tracks_summary$trip_time_sec,
trip_time_hr = all_tracks_summary$trip_time_hr,
speed_mean = all_tracks_summary$speed_mean,
V_min = all_tracks_summary$V_min,
V_max = all_tracks_summary$V_max,
V_sd = all_tracks_summary$V_sd,
dist_tot_km = all_tracks_summary$dist_tot_km,
dist_tot_census_km = all_tracks_summary$dist_tot_census_km)
list_track <- list(track_summary = all_tracks_summary_out,
tracks = df_tracks_out2)
# 6) make waypoints
if(do_waypoints!=FALSE){
list_waypoints <- make_waypoints( folder_gpx = folder_gpx, river_shape = river_shape,
folder_result = folder_result, track_data = list_track,
date_start = date_start, date_end = date_end,
make_shape_wp = make_shape_wp,
way_csv = type_csv)
}
# 7) export tracks and summary
fileend <- paste(format(Sys.time(),"%Y%m%d"), format(Sys.time(),"%H%M%S"), sep="_")
if(type_csv == ".csv2"){
# 7.1 tracks .csv
setwd(folder_result)
namet <- paste(paste("all_tracks", fileend, sep="_"),".csv",sep="")
write.csv2(df_tracks_out2, namet)
# 7.2 summary .csv
namesum <- paste(paste("summary_all_tracks", fileend, sep="_"),".csv",sep="")
write.csv2(all_tracks_summary_out, namesum)
}else{
# 7.1 tracks .csv
setwd(folder_result)
namet <- paste(paste("all_tracks", fileend, sep="_"),".csv",sep="")
write.csv(df_tracks_out2, namet)
# 7.2 summary .csv
namesum <- paste(paste("summary_all_tracks", fileend, sep="_"),".csv",sep="")
write.csv(all_tracks_summary_out, namesum)
}
#7.3 write shape
if(make_shape!=FALSE){
setwd(folder_result)
dir.create(paste("shapes_tracks", fileend, sep="_"))
newf <- paste(getwd(),paste("shapes_tracks", fileend, sep="_"), sep="/")
setwd(newf)
sppoint <- df_tracks_out2[, c('aname', 'trip_id', 'trip_start','zone','gpstime', 'adtAP',
'ayear', 'adate', 'ele','lon', 'lat', 'bear_deg_clean',
'vel', 'dist_m_clean', 'dist_m_census')]
sp::coordinates(sppoint) <- ~lon+lat
sp::proj4string(sppoint) <- sp::CRS("+init=epsg:4326")
namepoint <- paste(paste("trackpoints", fileend, sep="_"),".shp",sep="")
raster::shapefile(sppoint, filename = namepoint)
}
# 8) export as list
return(list_track <- list(track_summary = all_tracks_summary_out,
tracks = df_tracks_out2))
}
darrennorris/rgps documentation built on Sept. 17, 2019, 9:23 a.m.
R Package Documentation
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Defines functions make_tracks
Documented in make_tracks
#' @title Import and summarise tracklogs and waypoints.
#' @description Import and summarise tracklogs and waypoints.
#' @param folder_gpx Location of folder containing .gpx files.
#' @param river_shape Location of file containing shapefile to define survey zones
#' @param folder_result Location where results are saved.
#' @param date_start Optional. Character of start date ("dd/mm/yyyy")
#' @param date_end Optional. Character of end date ("dd/mm/yyyy")
#' @param make_shape Optional. Logical (TRUE/FALSE). Write a shapefile with all tracklog points.
#' @param do_waypoints Optional. Logical (TRUE/FALSE). Generate .csv with waypoints.
#' @param make_shape_wp Optional. Logical (TRUE/FALSE). Generate shapefile with waypoints.
#' @param type_csv Required. What type of .csv to export? ".csv" or ".csv2"
#'
#' @return Will generate R objects and export .csv and shapefiles.
#'
#' @export
#' @importFrom "stats" "na.omit" "sd"
#' @importFrom "utils" "write.csv2"
#' @importFrom "utils" "write.csv"
#'
#' @examples
#' \dontrun{
#' # 1) need to specify 3 locations.
#' #1.1) Location of shapefile with river zones
#' #1.2) Location of folder with .gpx files censu
#' #1.3) Location of folder for results
#'
#' rs <- system.file("shapes/riverzones.shp", package = "rgps")
#' fg <- system.file("gpx", package = "rgps")
#' fr <- "/Location/of/result/folder"
#'
#' # 2) run
#' list_track_data <- rgps::make_tracks(
#' folder_gpx = fg, folder_result = fr, river_shape = rs,
#' do_waypoints = TRUE, make_shape = FALSE,
#' make_shape_wp = FALSE,
#' type_csv = ".csv")
#' }
make_tracks <- function(folder_gpx, river_shape, folder_result,
date_start = NA, date_end = NA, make_shape = FALSE,
do_waypoints = FALSE, make_shape_wp = FALSE,
type_csv = NA){
# 1) load gpx
# 1.1) list of .gpx files
setwd(folder_gpx)
input_path<-getwd() # target directory
myfileinfo<-file.info(list.files(input_path, pattern= ".gpx",
ignore.case=TRUE,full.names=TRUE))
myfileinfo$aname <- rownames(myfileinfo)
# 1.2 run
gc()
#library(plyr)
df_tracks_in <- plyr::ddply(myfileinfo, .variables="aname",
.fun = load_tracks)
# 2) cleaning, should clean tracklogs, remove duplicates and common import errors
gc()
#library(plyr)
df_tracks_out <- plyr::ddply(df_tracks_in, .variables="aname",
.fun = clean_tracks)
# 2.1 finish
selg <- which(is.na(df_tracks_out$lon)==FALSE)
df_tracks_out <- df_tracks_out[selg, ]
#remove duplicates
df_tracks_out <- df_tracks_out[!duplicated(df_tracks_out$adtnum), ]
# drop first distance
selSt <- which(df_tracks_out$trip_start_flag == 1)
df_tracks_out[selSt, 'dist_m_census'] <- NA
## 3) add zones
#library(raster)
s1 <- raster::shapefile(river_shape)
#library(sp)
sp1 <- df_tracks_out
sp::coordinates(sp1) <- ~lon+lat
# assign CRS/projection
sp::proj4string(sp1) <- sp::proj4string(s1)
df_tracks_out$zone <- sp::over(sp1, s1)[,2]
df_tracks_out <- df_tracks_out[order(df_tracks_out$adtnum), ]
rownames(df_tracks_out) <- NULL
# 4) summary
all_tracks_summary <- plyr::ddply(df_tracks_out,
.variables=c("aname", "seg_id", "zone"),
plyr::summarize,
transect = NA,
Day = NA,
min_t = min(adt),
max_t = max(adt),
aname = min(aname),
ayear = min(ayear),
adate = as.Date(format(min(adt),"%d/%m/%Y",tz="America/Belem"),
format="%d/%m/%Y"),
anomes = format(min(adt),"%Y%m",tz="America/Belem"),
trip_start = format(min(adt), tz="America/Belem"),
trip_end = format(max(adt), tz="America/Belem"),
trip_time_sec = (max(as.numeric(adt)) - min(as.numeric(adt))),
trip_time_hr = ((max(as.numeric(adt)) - min(as.numeric(adt)))/60)/60,
speed_mean = round(mean(na.omit(vel)),3),
V_min = round(min(na.omit(vel)),2),
V_max = round(max(na.omit(vel)),2),
V_sd = round(sd(na.omit(vel)),2),
dist_tot_km = sum(na.omit(dist_m_clean))/1000,
dist_tot_census_km = sum(na.omit(dist_m_census))/1000
)
all_tracks_summary$trip_id <- paste(all_tracks_summary$zone,
all_tracks_summary$trip_start, sep="_")
# select dates
if (is.na(date_start)==FALSE){
stoptext <- "No .gpx tracklogs in specified dates. Check dates are valid.
Check date format is valid (dd/mm/yyyy). Change dates to NA to run all days."
mdates <- seq(as.Date(date_start, format="%d/%m/%Y",tz="America/Belem"),
as.Date(date_end, format="%d/%m/%Y",tz="America/Belem"), by ="day")
selD <- which(all_tracks_summary$adate %in% mdates)
if(length(selD) > 0) {all_tracks_summary <- all_tracks_summary[selD, ]}else{stop(stoptext)}
#all_tracks_summary <- all_tracks_summary[selD, ]
}
# select trips lasting 3 minutes or more
selT <- which(all_tracks_summary$trip_time_sec > 179)
all_tracks_summary <- all_tracks_summary[selT, ]
# count of number of survey days, plus sorts by date
all_tracks_summary <- merge(all_tracks_summary,
data.frame(adate = unique(all_tracks_summary$adate),
day_count = rank(unique(all_tracks_summary$adate))), all.x = TRUE)
all_tracks_summary <- all_tracks_summary[order(all_tracks_summary$trip_start), ]
rownames(all_tracks_summary) <- NULL
# 5) select only valid track points
# Result = data frame with track points for trips in all_tracks_summary
t_seq <- function(x){
df1 <- data.frame(mydt = seq(from = x$min_t, to = x$max_t, by = "sec"))
}
#require(plyr)
d_seq <- plyr::ddply(all_tracks_summary,
.variables=c("aname", "seg_id", "zone",
"trip_start", "trip_id"), .fun = t_seq)
# data frame with track points for trips in all_tracks_summary
dt <- merge(df_tracks_out, d_seq, by.x=c("zone", "adt" ), by.y=c("zone","mydt"))
dt <- dt [order(dt$adtnum), ]
rownames(dt ) <- NULL
df_tracks_out2 <- data.frame(aname = dt$aname.x, trip_id = dt$trip_id,
trip_start = dt$trip_start, zone = dt$zone,
gpstime = dt$time, adt = dt$adt, adtnum = dt$adtnum,
adtAP = dt$adtAP, ayear = dt$ayear, adate = dt$adate,
ele = dt$ele,
lon = dt$lon, lat = dt$lat, lon_lead = dt$lon_lead,
lat_lead = dt$lat_lead,
tdiff_clean = dt$tdiff_clean,
bear_deg_clean = dt$bear_deg_clean, vel = dt$vel,
dist_m_clean = dt$dist_m_clean, dist_m_census = dt$dist_m_census
)
all_tracks_summary_out <- data.frame(aname = all_tracks_summary$aname,
trip_id = all_tracks_summary$trip_id,
day_count = all_tracks_summary$day_count,
ayear = all_tracks_summary$ayear,
anomes = all_tracks_summary$anomes,
adate = all_tracks_summary$adate,
zone = all_tracks_summary$zone,
transect = all_tracks_summary$transect,
Day = all_tracks_summary$Day,
trip_start = all_tracks_summary$trip_start,
trip_end = all_tracks_summary$trip_end,
trip_time_sec = all_tracks_summary$trip_time_sec,
trip_time_hr = all_tracks_summary$trip_time_hr,
speed_mean = all_tracks_summary$speed_mean,
V_min = all_tracks_summary$V_min,
V_max = all_tracks_summary$V_max,
V_sd = all_tracks_summary$V_sd,
dist_tot_km = all_tracks_summary$dist_tot_km,
dist_tot_census_km = all_tracks_summary$dist_tot_census_km)
list_track <- list(track_summary = all_tracks_summary_out,
tracks = df_tracks_out2)
# 6) make waypoints
if(do_waypoints!=FALSE){
list_waypoints <- make_waypoints( folder_gpx = folder_gpx, river_shape = river_shape,
folder_result = folder_result, track_data = list_track,
date_start = date_start, date_end = date_end,
make_shape_wp = make_shape_wp,
way_csv = type_csv)
}
# 7) export tracks and summary
fileend <- paste(format(Sys.time(),"%Y%m%d"), format(Sys.time(),"%H%M%S"), sep="_")
if(type_csv == ".csv2"){
# 7.1 tracks .csv
setwd(folder_result)
namet <- paste(paste("all_tracks", fileend, sep="_"),".csv",sep="")
write.csv2(df_tracks_out2, namet)
# 7.2 summary .csv
namesum <- paste(paste("summary_all_tracks", fileend, sep="_"),".csv",sep="")
write.csv2(all_tracks_summary_out, namesum)
}else{
# 7.1 tracks .csv
setwd(folder_result)
namet <- paste(paste("all_tracks", fileend, sep="_"),".csv",sep="")
write.csv(df_tracks_out2, namet)
# 7.2 summary .csv
namesum <- paste(paste("summary_all_tracks", fileend, sep="_"),".csv",sep="")
write.csv(all_tracks_summary_out, namesum)
}
#7.3 write shape
if(make_shape!=FALSE){
setwd(folder_result)
dir.create(paste("shapes_tracks", fileend, sep="_"))
newf <- paste(getwd(),paste("shapes_tracks", fileend, sep="_"), sep="/")
setwd(newf)
sppoint <- df_tracks_out2[, c('aname', 'trip_id', 'trip_start','zone','gpstime', 'adtAP',
'ayear', 'adate', 'ele','lon', 'lat', 'bear_deg_clean',
'vel', 'dist_m_clean', 'dist_m_census')]
sp::coordinates(sppoint) <- ~lon+lat
sp::proj4string(sppoint) <- sp::CRS("+init=epsg:4326")
namepoint <- paste(paste("trackpoints", fileend, sep="_"),".shp",sep="")
raster::shapefile(sppoint, filename = namepoint)
}
# 8) export as list
return(list_track <- list(track_summary = all_tracks_summary_out,
tracks = df_tracks_out2))
}
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