-
Notifications
You must be signed in to change notification settings - Fork 31
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #212 from lawinslow/master
Switch over to Sparkling example
- Loading branch information
Showing
21 changed files
with
40,280 additions
and
23,333 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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| Package: glmtools | ||
| Type: Package | ||
| Title: glmtools | ||
| Version: 0.14.2 | ||
| Version: 0.14.3 | ||
| Date: 2016-05-22 | ||
| Authors@R: c( person("Jordan", "Read", role = c("aut","cre"), | ||
| email = "[email protected]"), | ||
|
|
||
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
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 +1,165 @@ | ||
|
|
||
|
|
||
| library(glmtools) | ||
| sim_dir = run_example_sim() | ||
|
|
||
| Sys.setenv(tz='UTC') | ||
|
|
||
| #compare temps | ||
| ncfile = file.path(sim_dir, 'output.nc') | ||
| tempfield = file.path(sim_dir, 'field_data.csv') | ||
| plot_temp_compare(ncfile, tempfield, resample = FALSE) | ||
|
|
||
| rmse = validate_sim(ncfile, tempfield, 'water.temperature', fig_path=FALSE, report = TRUE) | ||
|
|
||
| ################################################################################ | ||
| #Ice compare | ||
| ################################################################################ | ||
| ice_obs = read.table(file.path(sim_dir, 'snow_ice_depth_obs.csv'), sep=',', header=TRUE) | ||
| ice_obs$DateTime = as.POSIXct(ice_obs$sampledate, tz="GMT") | ||
| ice_obs$avsnow = ice_obs$avsnow/100 | ||
| ice_obs$whiteice = ice_obs$whiteice/100 | ||
| ice_obs$blueice = ice_obs$blueice/100 | ||
|
|
||
|
|
||
| snow = get_var(ncfile, 'hsnow') | ||
| attributes(snow$DateTime)$tzone = 'GMT' | ||
| wice = get_var(ncfile, 'hwice') | ||
| attributes(wice$DateTime)$tzone = 'GMT' | ||
| bice = get_var(ncfile, 'hice') | ||
| attributes(bice$DateTime)$tzone = 'GMT' | ||
| wtr = get_temp(ncfile, reference='surface') | ||
| attributes(wtr$DateTime)$tzone = 'GMT' | ||
|
|
||
| all_ice = merge(snow, ice_obs, all.x=TRUE, by='DateTime') | ||
| all_ice = merge(wice, all_ice, all.x=TRUE) | ||
| all_ice = merge(bice, all_ice, all.x=TRUE) | ||
| all_ice$yday = as.POSIXlt(all_ice$DateTime)$yday | ||
| all_ice$year = as.POSIXlt(all_ice$DateTime)$year + 1900 | ||
|
|
||
| ice = get_ice(ncfile) | ||
| attributes(ice$DateTime)$tzone = 'GMT' | ||
| ice_on_off = mda.lakes::get_ice_onoff(ice, wtr) | ||
|
|
||
| lter_on_off = read.table(file.path(sim_dir,'ice_duration_obs.csv'), sep=',', header=TRUE) | ||
| all_ice = merge(all_ice, ice_on_off, all.x=TRUE) | ||
| all_ice = merge(all_ice, lter_on_off, all.x=TRUE) | ||
|
|
||
| all_ice = all_ice[order(all_ice$DateTime), ] | ||
|
|
||
| ################################################################################ | ||
| ## Now plots | ||
| ################################################################################ | ||
| plot(all_ice$avsnow, all_ice$hsnow) | ||
| abline(0,1) | ||
|
|
||
| plot(all_ice$whiteice, all_ice$hwice) | ||
| abline(0,1) | ||
|
|
||
| plot(all_ice$blueice, all_ice$hice) | ||
| abline(0,1) | ||
|
|
||
| plot(hice~DateTime, subset(all_ice, year < 1990), type='l') | ||
| points(all_ice$DateTime, all_ice$blueice) | ||
|
|
||
| #png('figures/sp_bice.png', res=300, width=2000, height=2000) | ||
| par(mfrow=c(3,1)) | ||
| plot(hice~DateTime, subset(all_ice, year < 1990), type='l') | ||
| title('Blue Ice') | ||
| points(all_ice$DateTime, all_ice$blueice) | ||
| plot(hice~DateTime, subset(all_ice, year > 1990 & year < 2000), type='l') | ||
| points(all_ice$DateTime, all_ice$blueice) | ||
| plot(hice~DateTime, subset(all_ice, year > 2000 & year < 2010), type='l') | ||
| points(all_ice$DateTime, all_ice$blueice) | ||
| #dev.off() | ||
|
|
||
| #png('figures/sp_wice.png', res=300, width=2000, height=2000) | ||
| par(mfrow=c(3,1)) | ||
| plot(hwice~DateTime, subset(all_ice, year < 1990), type='l') | ||
| title('White Ice') | ||
| points(all_ice$DateTime, all_ice$whiteice) | ||
| plot(hwice~DateTime, subset(all_ice, year > 1990 & year < 2000), type='l') | ||
| points(all_ice$DateTime, all_ice$whiteice) | ||
| plot(hwice~DateTime, subset(all_ice, year > 2000 & year < 2010), type='l') | ||
| points(all_ice$DateTime, all_ice$whiteice) | ||
| #dev.off() | ||
|
|
||
| #png('figures/sp_snow.png', res=300, width=2000, height=2000) | ||
| par(mfrow=c(3,1)) | ||
| plot(hsnow~DateTime, subset(all_ice, year < 1990), type='l') | ||
| title('Snow') | ||
| points(all_ice$DateTime, all_ice$avsnow) | ||
| plot(hsnow~DateTime, subset(all_ice, year > 1990 & year < 2000), type='l') | ||
| points(all_ice$DateTime, all_ice$avsnow) | ||
| plot(hsnow~DateTime, subset(all_ice, year > 2000 & year < 2010), type='l') | ||
| points(all_ice$DateTime, all_ice$avsnow) | ||
| #dev.off() | ||
|
|
||
|
|
||
|
|
||
| #### | ||
| #ICE | ||
|
|
||
| mean(abs(all_ice$firstopen - as.POSIXlt(all_ice$off)$yday+1), na.rm=TRUE) | ||
| mean((all_ice$firstopen - as.POSIXlt(all_ice$off)$yday+1), na.rm=TRUE) | ||
|
|
||
| plot(all_ice$firstopen, as.POSIXlt(all_ice$off)$yday+1) | ||
| abline(0,1) | ||
|
|
||
| mean(abs(all_ice$lastopen - as.POSIXlt(all_ice$on)$yday+1), na.rm=TRUE) | ||
| mean((all_ice$lastopen - as.POSIXlt(all_ice$on)$yday+1), na.rm=TRUE) | ||
|
|
||
| plot(all_ice$lastopen, as.POSIXlt(all_ice$on)$yday+1) | ||
| abline(0,1) | ||
|
|
||
|
|
||
| ##figure for Hipsey paper | ||
|
|
||
| #png('figures/sp_bws_plots.png', res=300, width=2000, height=2000) | ||
| par(mfrow=c(3,1), oma=c(5,4,0,0), mar=c(0,0,1,1)) | ||
|
|
||
| plot(hice~DateTime, subset(all_ice, year > 1990 & year < 2001), type='l', ylab='Blue Ice (m)', xaxt='n') | ||
| lines(hice~DateTime, all_ice) | ||
| points(all_ice$DateTime, all_ice$blueice, col=rgb(0, 0, 0, 0.5), pch=16) | ||
| mtext(side=2, text='Blue Ice (m)', line=2.5) | ||
| legend('topright', legend = 'A', bty = 'n', inset = c(-0.01,-0.06), cex=2) | ||
|
|
||
| plot(hwice~DateTime, subset(all_ice, year > 1990 & year < 2001), type='l', ylab='White Ice (m)', xaxt='n') | ||
| lines(hwice~DateTime, all_ice) | ||
| points(all_ice$DateTime, all_ice$whiteice, col=rgb(0, 0, 0, 0.5), pch=16) | ||
| mtext(side=2, text='White Ice (m)', line=2.5) | ||
| legend('topright', legend = 'B', bty = 'n', inset = c(-0.01,-0.06), cex=2) | ||
|
|
||
| legend('topleft', legend = c('Modeled', 'Observed'), pch = c(NA, 16), lty=c(1,NA), col=c('black', rgb(0, 0, 0, 0.5)), inset=c(0.01, 0.05)) | ||
|
|
||
| plot(hsnow~DateTime, subset(all_ice, year > 1990 & year < 2001), type='l', ylab='Snow (m)') | ||
| lines(hsnow~DateTime, all_ice) | ||
| points(all_ice$DateTime, all_ice$avsnow, col=rgb(0, 0, 0, 0.5), pch=16) | ||
| mtext(side=2, text='Snow (m)', line=2.5) | ||
| mtext(side=1, text='Year', line=2.5) | ||
| legend('topright', legend = 'C', bty = 'n', inset = c(-0.01,-0.06), cex=2) | ||
|
|
||
| #dev.off() | ||
|
|
||
|
|
||
| ### Compare ice on and off for Hipsey paper | ||
|
|
||
| library(mda.lakes) | ||
| library(lubridate) | ||
| onoff = lter_on_off | ||
| mod_onoff = get_ice_onoff(get_ice(ncfile), get_temp(ncfile, reference = 'surface')) | ||
|
|
||
| obsmod = merge(onoff, mod_onoff, by='year') | ||
|
|
||
|
|
||
| #png('figures/sp_on_off_plots.png', res=300, width=2400, height=1500) | ||
| par(mfrow=c(1,2), mar=c(5,4,1,1)) | ||
|
|
||
| plot(yday(obsmod$on), yday(as.POSIXct(obsmod$datelastopen)), pch=16, col=rgb(0, 0, 0, 0.5), | ||
| xlab='Modeled Ice On', ylab='Observed Ice On') | ||
| abline(0,1) | ||
| plot(yday(obsmod$off[-1]), yday(as.POSIXct(obsmod$datefirstopen[-1])), pch=16, col=rgb(0, 0, 0, 0.5), | ||
| xlab='Modeled Ice Off', ylab='Observed Ice Off') | ||
| abline(0,1) | ||
|
|
||
| #dev.off() |
Oops, something went wrong.