-
Notifications
You must be signed in to change notification settings - Fork 63
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
#871 move initialisation of object ts to a separate function
1 parent
e392cf1
commit 8acaa96
Showing
4 changed files
with
100 additions
and
60 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| g.part5_initialise_ts = function(IMP, M, params_247, params_general) { | ||
|
|
||
| # extract key variables from the mile-stone data: time, acceleration and elevation angle | ||
| # note that this is imputed ACCELERATION because we use this for describing behaviour: | ||
| scale = ifelse(test = grepl("^Brond|^Neishabouri|^ZC", params_general[["acc.metric"]]), yes = 1, no = 1000) | ||
| # if (length(which(names(IMP$metashort) == "anglez")) == 0 & verbose == TRUE) { | ||
| # cat("Warning: anglez not extracted. Please check that do.anglez == TRUE") | ||
| # } | ||
|
|
||
| if ("anglez" %in% names(IMP$metashort)) { | ||
| ts = data.frame(time = IMP$metashort[,1], ACC = IMP$metashort[,params_general[["acc.metric"]]] * scale, | ||
| guider = rep("unknown", nrow(IMP$metashort)), | ||
| angle = as.numeric(as.matrix(IMP$metashort[,which(names(IMP$metashort) == "anglez")]))) | ||
| } else { | ||
| ts = data.frame(time = IMP$metashort[,1], ACC = IMP$metashort[,params_general[["acc.metric"]]] * scale, | ||
| guider = rep("unknown", nrow(IMP$metashort))) | ||
| } | ||
| Nts = nrow(ts) | ||
| # add non-wear column | ||
| nonwear = IMP$rout[,5] | ||
| nonwear = rep(nonwear, each = (IMP$windowsizes[2]/IMP$windowsizes[1])) | ||
| if (length(nonwear) > Nts) { | ||
| nonwear = nonwear[1:Nts] | ||
| } else if (length(nonwear) < Nts) { | ||
| nonwear = c(nonwear, rep(0, (Nts - length(nonwear)))) | ||
| } | ||
| ts$nonwear = 0 # initialise column | ||
| ts$nonwear = nonwear | ||
| lightpeak_available = "lightpeak" %in% colnames(M$metalong) | ||
| # Check if temperature and light are availble | ||
| if (lightpeak_available == TRUE) { | ||
| luz = M$metalong$lightpeak | ||
| if (length(params_247[["LUX_cal_constant"]]) > 0 & | ||
| length(params_247[["LUX_cal_exponent"]]) > 0) { # re-calibrate light | ||
| luz = params_247[["LUX_cal_constant"]] * exp(params_247[["LUX_cal_exponent"]] * luz) | ||
| } | ||
| handle_luz_extremes = g.part5.handle_lux_extremes(luz) | ||
| luz = handle_luz_extremes$lux | ||
| correction_log = handle_luz_extremes$correction_log | ||
| # repeate values to match resolution of other data | ||
| repeatvalues = function(x, windowsizes, Nts) { | ||
| x = rep(x, each = (windowsizes[2]/windowsizes[1])) | ||
| if (length(x) > Nts) { | ||
| x = x[1:Nts] | ||
| } else if (length(x) < Nts) { | ||
| x = c(x, rep(0, (Nts - length(x)))) | ||
| } | ||
| return(x) | ||
| } | ||
| luz = repeatvalues(x = luz, windowsizes = IMP$windowsizes, Nts) | ||
| correction_log = repeatvalues(x = correction_log, windowsizes = IMP$windowsizes, Nts) | ||
| ts$lightpeak_imputationcode = ts$lightpeak = 0 # initialise column | ||
| ts$lightpeak = luz | ||
| ts$lightpeak_imputationcode = correction_log | ||
| } | ||
| return(ts) | ||
| } | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| \name{g.part5_initialise_ts} | ||
| \alias{g.part5_initialise_ts} | ||
| \title{ | ||
| Initialise time series data from for part 5 | ||
| } | ||
| \description{ | ||
| Initialise time series dataframe ts, part of \link{g.part5}. | ||
| } | ||
| \usage{ | ||
| g.part5_initialise_ts(IMP, M, params_247, params_general) | ||
| } | ||
| \arguments{ | ||
| \item{IMP}{ | ||
| Object derived from \link{g.part2} | ||
| } | ||
| \item{M}{ | ||
| Object derived from \link{g.part1}. | ||
| } | ||
| \item{params_247}{ | ||
| See \link{GGIR} | ||
| } | ||
| \item{params_general}{ | ||
| See \link{GGIR} | ||
| } | ||
| } | ||
| \value{ | ||
| Data.frame ts | ||
| } | ||
| \keyword{internal} |