Changelog for cmsafops package

1.2.1

1.2.0

1.1.1

1.1.0

1.0.0

2.0.1 (originally in cmsaf package)

Published 2019-08-26

1.9.5 (originally in cmsaf package)

timsum: bug fix - zero instead of NA new na.rm option of treatment of NA values box_mergetime, cmsaf.cat, levbox_mergetime: bug fix - now merging of files with more than one time step is allowed timmean: new na.rm option of treatment of NA values seassum: new function for seasonal sums seas.anomaly, seasmean, seassum: bug fix - only monthly input was working

Apply.Function.R: bug fix - timpctl default was not working seassum operator added CMSAF-R-TOOLBOX.R: browsing from last file’s position CMSAF_Visualizer.R: bug fix - caption of colorbar was not saved properly

1.9.4 (originally in cmsaf package)

ydaymean: bug fix because function caused an error on two of ten test platforms Prep.Data.R: bug fix for no plot in case of longitude instead of lon (same for lat) shinyApp_toolbox.R: bug fix for problem with file selection after update to shinyFiles 0.7.0 minor bug fixes

1.9.3 (originally in cmsaf package)

ydaymean: function caused an error on two of ten test platforms; first bug fix unfortunately did not work

1.9.2 (originally in cmsaf package)

read_ncvar: renamed because of conflicts with other packages output as list including time dimension (if applicable) all functions with file output: export of global attributes to output file fldmean, fldmin, fldmax, wfldmean: lon and lat are set to the mid-point of the applied field timsum: new function for all-time sums ydaymean: new function for multi-year daily sums multimonmean, multimonsum, seasmean: bug fix if used with daily or even higher resolved data cmsaf.addc, cmsaf.mulc, cmsaf.divc, cmsaf.subc: added info about used function in meta data multimonmean: bug fix in cmsaf.info attribute CMSAF_Visualizer: additional color palette; error check for ppt; exit button to stop app; bug fix for saving analyse.timeseries plot; clean up at end; Analyse.TimeSeriesTrend.R is now included in Analyse.TimeSeries; option to plot data from R-Instat RData files; plot own locations Prep.Data.R: preview of available and chosen region; clean up at end; show standard name Apply.Function.R: clean up at end; more functions of cmsaf packages added; option for nc4 CMSAF-R-TOOLBOX: add script that controls all main toolbox scripts by shinyApp_toolbox.R - this includes minor modifications on Prep.Data.R, Apply.Function.R, CMSAF_Visualizer.R as file.choose works only in interactive sessions, additional way to choose files with shinyFiles; remember last selected file Adapted folder structure in R-scripts Minor performance improvements in R-scripts

1.9.1 (originally in cmsaf package)

all operators with var input: no case sensitivity for var and if var not found default var is used; operator name is included in output NetCDF selpoint: file extension is checked; if problems occur, nc is used as default selpoint.multi: file extension is checked; if problems occur, nc is used as default checkfile: nc file extension of outfile is checked; if problems occur, nc is used as default Prep.Data.R & Apply.Function.R: bug fix if path contains identical entries; path length under Windows is restricted to < 260 added check for startdate and enddate input variable SATID will be no default variable Apply.Function.R: operator cmsaf.mulc added option for operator trend added when applying another function, user can choose to which one Apply.Function.R & CMSAF_Visualizer: add options to improve the visualization add tabs for additional information bug fix for wrong imagesize of analyze.timeseries plot additional projection (orthographic) added

1.9.0 (originally in cmsaf package)

box_mergetime: bug fix in time_sorting if applied to just one file box_mergetime: if given variable is not included in file, the first included one will be used box_mergetime: bug fix if time_bnds are included levbox_mergetime: include time_sorting levbox_mergetime: if given variable is not included in file, the first included one will be used levbox_mergetime: bug fix if time_bnds are included selpoint.multi: bug fix: tbnds was not correctly defined in case of a given infile multimonmean: bug fix: Error in seas[j, i] <- dum : replacement has length zero fldmin: bug fix if applied to just one time step fldmax: bug fix if applied to just one time step trend: bug fix: Error for NA values trend: bug fix for maxval warning and increased sample number (3 to 5) trend: include option keyword for option 1 (faster trend calculation, but whole data field is read in) and option 2 (same calculation, but sequential, if data file is too big for memory; needs much more time) checkfile: bug fix: in some cases a wrong status was given timpctl: new function to determine a given percentile cmsaf.cat: new function to concatenate datasets of several input files Apply.Function.R and Prep.Data.R: put sys.frame intp try-function to avoid error, when scripts are started from terminal

1.8.3 (originally in cmsaf package)

multimonsum: bug fix: NA values were converted into zero multimonsum: bug fix: Error in seas[j, i] <- dum : replacement has length zero

1.8.2 (originally in cmsaf package)

selpoint.multi: bug fix if only one location is selected selpoint.multi: bug fix remove ‘any’ command Apply.Function.R and CMSAF_Visualizer.R: improved plotting of 1D-timeseries; additional plotting options; bug fix for wrong latitude in HLW and HSH data; requires additional package ‘colourpicker’ Prep.Data.R: no need for path information; path and file will be chosen by file.chose and depending on current file directory; if NetCDF contains only one variable no need for input; option for internal tar function if problems under Windows occur; error message if sinusoidal projection is used; fix dums warning; bug fix because of undefined slash; no case sensitive input anymore; additional checks for correct input otherwise defaults are used; start- and enddate are not needed - push ENTER is enough; Apply.Function.R: no need for path information; path and file will be chosen by file.chose and depending on current file directory; if NetCDF contains only one variable no need for input; close all graphic devices in the end; bug fix because of undefined slash; no case sensitive input anymore; additional checks for correct input otherwise defaults are used; bug fix: HOAPS figures could be upside down because of latitude sorting data file can be in any folder (not only data or output) CMSAF_Visualizer.R: no need for path information; path and file will be chosen by file.chose and depending on current file directory; if NetCDF contains only one variable no need for input; longname in title as default; proper display of HOAPS data; fix warning for RB-colorbar; close all graphic devices in the end; include AnalyzeTimeseries; dynamic width and height; bug fix because of undefined slash include new CM SAF R Toolbox logo; interactive Analyse.Timeseries; bug fix: error if trend line for daily data

1.8.1 (originally in cmsaf package)

all functions with file output: bug fix for wrong reading of dimensional variables yseasmean: bug fix - now daily data can be used yseasmax: bug fix - now daily data can be used yseasmin: bug fix - now daily data can be used yseassd: bug fix - now daily data can be used

1.8.0 (originally in cmsaf package)

box_mergetime: bug fix if only one file corresponds to pattern box_mergetime: order of timesteps will be checked all functions with file output: bug fix for use with CRU data due to missing standard_name of longitude all functions with file output: bug fix for input files with dimension nb2 cmsaf.sub: bug fix variable precision and setting of fill value; will be done for other functions, too selpoint.multi: new function to select multiple locations from a single file or a bunch of files all functions with file output: new option for NetCDFv4 output trend: additional output field for trend without multiplication with length of time series trend: bug fix in trend calculation, which could lead to wrong trend values trend: faster trend calculation multimonmean: bug fix wrong if statement could lead to error of month not included multimonsum: bug fix wrong if statement could lead to error of month not included Prep.Data.R: all tar-files with same ORD number are handled in one step

1.7.2 (originally in cmsaf package)

Prep.Data.R: remove functionality to avoid overwriting; now capable to handle daily and hourly data; HSH data can be used; extracted files can be deleted Apply.Function.R: bug fix for choice 26; add option for CM SAF R Visualizer; more info messages added Plot.TimeSeries.R: bug fix for HLW and HSH products Analyse.TimeSeries.R: bug fix for HLW and HSH products Install.Packages4Toolbox.R: new script for easier installation of necessary packages timmean: bug fix if lon x lat x time is too large selmon: bug fix matching months where not found yearsum: bug fix sum of NA values is now NA instead of 0 box_mergetime: bug fix wrong time bounds levbox_mergetime: bug fix wrong time bounds extract.levels: new function to extract one or all levels from 4D NetCDF files

1.7.1 (originally in cmsaf package)

Bug fix: Precision info in netcdf, which is not conform to standard, could lead to error Prep.Data.R: Adaptations to netcdf4 were done

1.7.0 (originally in cmsaf package)

Plot.Region.R no RNetCDF dependency anymore Plot.Region.Multi.R no RNetCDF dependency anymore Analyse.TimeSeries.R no RNetCDF dependency anymore Analyse.TimeSeriesTrend.R no RNetCDF dependency anymore Plot.Region.R round thick labels to be shorter Plot.Region.Multi.R round thick labels to be shorter Export.TimeSeries.R deleted from toolbox, as selpoint function can export to netcdf or csv ncinfo: info=“l” returns info and list Precision of time bounds: bug fix set precision to double The default precision was set from “double” to “float” to reduce file size Functions, which do not change the original values, check for variable precision monmax: new function to get monthly maxima monmin: new function to get monthly minima monsd: new function to get monthly standard deviations ymonmax: new function to get multi-year monthly maxima ymonmin: new function to get multi-year monthly minima ymonsd: new function to get multi-year monthly standard deviations yseasmax: new function to get multi-year seasonal maxima yseasmin: new function to get multi-year seasonal minima yseassd: new function to get multi-year seasonal standard deviations timmax: new function to get all-time maxima timmin: new function to get all-time minima timsd: new function to get all-time seasonal standard deviations remapbil: grids with coordinates 0-360 can be used now as infile1 fldmean: bug fix if infile has only one timestep mon.anomaly: bug fix adaptation of fill values (e.g.-1 could lead to errors) seas.anomaly: bug fix adaptation of fill values (e.g.-1 could lead to errors) monsum: bug fix sum of NA values is now NA instead of 0

1.6.1 (originally in cmsaf package)

selpoint: bug fix in strsplit “\.” instead of “.” Apply.Function.R: bug fix l.57 go_on=“n” has to be set to go_on=“y”

1.6

get_time: get_time can now handle Julian date get_time: higher precision for time unit ‘months’ get_time: time units without ‘since’ give an error message box_mergetime: error message if coordinates are outside the target area levbox_mergetime: error message if coordinates are outside the target area cmsaf.addc: new function to add a constant cmsaf.divc: new function to divide by a constant cmsaf.mulc: new function to multiply with a constant cmsaf.subc: new function to subtract a constant selpoint: add option for output of a csv-file selpoint: add check for correct file extension read_nc: new function to read data into R

1.5

Due to some problems with the installation of the ‘RNetCDF’ package, the ‘RNetCDF’ function ‘utcal.nc’ was replaced by an own, quite simple, function to extract the time information. The function ‘get_time’ converts the time step and time unit information into POSIXct times. Thus, the ‘RNetCDF’ package is no more required for the ‘cmsaf’ package.

1.4

levbox_mergetime: change back from as.Date to as.POSIXct to keep hourly timesteps levbox_mergetime: difftime can only handle units up to “weeks”, now “months” are possible box_mergetime: change back from as.Date to as.POSIXct to keep hourly timesteps box_mergetime: difftime can only handle units up to “weeks”, now “months” are possible Prep.Data.light.R: same as Prep.Data.R but without untar and unzip ymonsum: new function to calculate multi-year monthly sums multimonmean: new function to calculate multi-monthly means multimonsum: new function to calculate multi-monthly sums year.anomaly: new function to calculate annual anomalies seas.anomaly: new function to calculate seasonal anomalies mon.anomaly: ymonsub was renamed to mon.anomaly all functions: standard precision is set to double, the previous automatically check could lead to imprecisions selperiod: new function to select periods of dates from a timeseries extract.period: new function to remove periods of dates from a timeseries trend: wrong line break to show progress was corrected Prep.Data.R: if files are already unzipped, they will be overwritten, deleting is not necessary anymore Prep.Data.R: default for the functions loop is set to n Prep.Data.R: HLW data are recognized and levbox_mergetime is used in this case Prep.Data.R: ymonsub is renamed to mon.anomaly Apply.Function.R: new cmsaf_1.4 functions added Apply.Function.R: default for the functions loop is set to n Apply.Function.R: HLW data are recognized and levbox_mergetime is used in this case Apply.Function.R: ymonsub is renamed to mon.anomaly Plot.Region.R: add option to plot user defined locations

1.3.4 (originally in cmsaf package)

Final version for the 2015 CM SAF Training Workshop in Pretoria, South Africa.