diff --git a/404.html b/404.html index 1f111e6..33e736c 100644 --- a/404.html +++ b/404.html @@ -20,7 +20,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -30,6 +30,7 @@ Reference +Changelog diff --git a/authors.html b/authors.html index e2650a9..00c6a7b 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -16,6 +16,7 @@ Reference +Changelog @@ -38,7 +39,7 @@ Authors - Thomas Braun. Contributor. + Thomas Braun. Contributor. @@ -49,13 +50,13 @@ Citation Jefferis G (2024). IgorR: Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic' Data). -R package version 0.8.2.9000, https://jefferis.github.io/IgorR/, https://github.com/jefferis/IgorR. +R package version 0.9.0, https://jefferis.github.io/IgorR/, https://github.com/jefferis/IgorR. @Manual{, title = {IgorR: Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic' Data)}, author = {Gregory Jefferis}, year = {2024}, - note = {R package version 0.8.2.9000, https://jefferis.github.io/IgorR/}, + note = {R package version 0.9.0, https://jefferis.github.io/IgorR/}, url = {https://github.com/jefferis/IgorR}, } diff --git a/index.html b/index.html index ecb87bf..5134895 100644 --- a/index.html +++ b/index.html @@ -22,7 +22,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -32,6 +32,7 @@ Reference +Changelog diff --git a/news/index.html b/news/index.html new file mode 100644 index 0000000..c40120a --- /dev/null +++ b/news/index.html @@ -0,0 +1,132 @@ + +Changelog • IgorR + Skip to contents + + + + + IgorR + + 0.9.0 + + + + + + + + Reference +Changelog + + + + + + + + + + + + Changelog + Source: NEWS.md + + + +IgorR 0.9.0 +fix: handling of Igor dates using timechange library (#6) +remove warnings due to recent changes in how readChar handles strings containing embedded nulls +fix URLs for CRAN +dev: switch to github actions for R CMD check and pkgdown (and remove travis) + + +IgorR 0.8.2 +minor: package docs, spelling, author formatting + + +IgorR 0.8.1CRAN release: 2017-05-21 +Fix namespace and canonical URL issues for CRAN + + +IgorR 0.8CRAN release: 2015-05-28 +fix bug in reading igor waves with embedded non-null terminated strings (#3) +fix bug in reading igor pxp files with names that are not valid R names e.g. begining with an underscore. (#2) +Thanks to Troy Margrie, Mateo Velez and Charly Rousseau for the reports/test data +Minor description fixes for R 3.2.0 +dev: switch to tests in tests/testthat (making them an optional install) but keeping some igor waves required for examples in inst/igor +dev: switch to new style travis config +dev: upgrade to roxygen2 4.1.1 + + +IgorR 0.7.2 +minor doc fixes + + +IgorR 0.7.1CRAN release: 2014-02-11 +Fix encoding issue of Igor pxp files containing high bytes. Pointed out by Brian Ripley on Solaris, fixed across all platforms with help from Ashley Manton. +Fix error on R<3.0.0 caused by use of new keep.source argument for parse(). + + +IgorR 0.7CRAN release: 2014-02-11 +Add support for extracting history, procedures and plain text notebooks (contributed by Thomas Braun). See read.pxp() ExtractText argument. +dev: added support for travis continuous integration +dev: repo now includes man files to allow devtools installation +dev: disable unreliable test of date-time parsing + + +IgorR 0.6 +Some significant speed optimisations without any change in functionality up to 2x faster for small waves (<1Mb) on my system +Now imports bitops, tools + + +IgorR 0.5-4 +Add regular expression to restrict ReadAllNclampLogTables() to log files +Package documentation + + +IgorR 0.5-3CRAN release: 2012-09-20 +Minor fix to error checks in tsp.igorwave() + + + +IgorR 0.5-2CRAN release: 2012-06-21 +Minor fixes to remove outstanding NOTES from R 2.15’s check + + +IgorR 0.5-1 +Option to return Igor wave data as time series when reading pxp files. +Fix problem with empty waves often encountered when reading waves in PXP files as time series. + + +IgorR 0.5CRAN release: 2012-01-25 +rename ReadIgorPackedExperiment and ReadIgorBinary functions to read.pxp() and read.ibw(), respectively. +Fix an encoding bug on Windows MAC->macintosh (pointed out by Brian Ripley) +Teach read.pxp() to read string variables with non ASCII characters +Teach read.pxp() to read only waves matching a regex +Teach read.pxp() to read structure only for waves when requested +Documentation changes for github + + +IgorR 0.4CRAN release: 2012-01-14 +First version on CRAN + + + + + + + + + + + + diff --git a/pkgdown.yml b/pkgdown.yml index ca5c5a4..d6c04d7 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 3.1.11 pkgdown: 2.1.0 pkgdown_sha: ~ articles: {} -last_built: 2024-08-05T01:06Z +last_built: 2024-08-05T06:41Z urls: reference: https://jefferis.github.io/IgorR/reference article: https://jefferis.github.io/IgorR/articles diff --git a/reference/IgorR-package.html b/reference/IgorR-package.html index 221931f..2e0f08a 100644 --- a/reference/IgorR-package.html +++ b/reference/IgorR-package.html @@ -13,7 +13,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -22,6 +22,7 @@ Reference +Changelog diff --git a/reference/IgorR-private.html b/reference/IgorR-private.html index 83244b8..aff096b 100644 --- a/reference/IgorR-private.html +++ b/reference/IgorR-private.html @@ -9,7 +9,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -18,6 +18,7 @@ Reference +Changelog diff --git a/reference/ReadAllNclampLogTables.html b/reference/ReadAllNclampLogTables.html index ece5c64..7ef447a 100644 --- a/reference/ReadAllNclampLogTables.html +++ b/reference/ReadAllNclampLogTables.html @@ -7,7 +7,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -16,6 +16,7 @@ Reference +Changelog diff --git a/reference/ReadNclampLogTable.html b/reference/ReadNclampLogTable.html index 923b71e..499b4dc 100644 --- a/reference/ReadNclampLogTable.html +++ b/reference/ReadNclampLogTable.html @@ -11,7 +11,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -20,6 +20,7 @@ Reference +Changelog diff --git a/reference/SummariseSweepFile.html b/reference/SummariseSweepFile.html index 499dc78..46504cd 100644 --- a/reference/SummariseSweepFile.html +++ b/reference/SummariseSweepFile.html @@ -7,7 +7,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -16,6 +16,7 @@ Reference +Changelog diff --git a/reference/SweepFilesToDataFrame.html b/reference/SweepFilesToDataFrame.html index 8531445..83028c8 100644 --- a/reference/SweepFilesToDataFrame.html +++ b/reference/SweepFilesToDataFrame.html @@ -9,7 +9,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -18,6 +18,7 @@ Reference +Changelog diff --git a/reference/UpdateSweepDataFrame.html b/reference/UpdateSweepDataFrame.html index 6d0c6e2..82e5dbc 100644 --- a/reference/UpdateSweepDataFrame.html +++ b/reference/UpdateSweepDataFrame.html @@ -7,7 +7,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -16,6 +16,7 @@ Reference +Changelog diff --git a/reference/WaveToTimeSeries.html b/reference/WaveToTimeSeries.html index a9a2ad5..f2f3ec5 100644 --- a/reference/WaveToTimeSeries.html +++ b/reference/WaveToTimeSeries.html @@ -9,7 +9,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -18,6 +18,7 @@ Reference +Changelog diff --git a/reference/index.html b/reference/index.html index 083c359..6794a8d 100644 --- a/reference/index.html +++ b/reference/index.html @@ -7,7 +7,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -16,6 +16,7 @@ Reference +Changelog diff --git a/reference/read.ibw.html b/reference/read.ibw.html index d68d34c..24ecfa3 100644 --- a/reference/read.ibw.html +++ b/reference/read.ibw.html @@ -7,7 +7,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -16,6 +16,7 @@ Reference +Changelog diff --git a/reference/read.pxp.html b/reference/read.pxp.html index e92b53d..f676cc4 100644 --- a/reference/read.pxp.html +++ b/reference/read.pxp.html @@ -13,7 +13,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -22,6 +22,7 @@ Reference +Changelog diff --git a/reference/tsp.igorwave.html b/reference/tsp.igorwave.html index 1b343a9..4fb0b80 100644 --- a/reference/tsp.igorwave.html +++ b/reference/tsp.igorwave.html @@ -7,7 +7,7 @@ IgorR - 0.8.2.9000 + 0.9.0 @@ -16,6 +16,7 @@ Reference +Changelog diff --git a/search.json b/search.json index 714d715..6701cd5 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://jefferis.github.io/IgorR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Gregory Jefferis. Author, maintainer. Thomas Braun. Contributor.","code":""},{"path":"https://jefferis.github.io/IgorR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Jefferis G (2024). IgorR: Read Binary Files Saved 'Igor Pro' (Including 'Neuromatic' Data). R package version 0.8.2.9000, https://jefferis.github.io/IgorR/, https://github.com/jefferis/IgorR.","code":"@Manual{, title = {IgorR: Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic' Data)}, author = {Gregory Jefferis}, year = {2024}, note = {R package version 0.8.2.9000, https://jefferis.github.io/IgorR/}, url = {https://github.com/jefferis/IgorR}, }"},{"path":[]},{"path":"https://jefferis.github.io/IgorR/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Read Binary Files Saved by Igor Pro (Including Neuromatic Data)","text":"IgorR package R provides routines read binary files generated Igor Pro. includes standalone .ibw Igor Binary Wave format (v2 latest v5) .pxp Packed Experiment Format including waves variables. addition package provides functions read files generated Neuromatic analysis suite written Jason Rothman Igor Pro.","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/index.html","id":"standard-install","dir":"","previous_headings":"","what":"Standard Install","title":"Read Binary Files Saved by Igor Pro (Including Neuromatic Data)","text":"NB IgorR CRAN due unfixed bug windows text tecent versions R. Whenever back can install release version CRAN","code":"install.packages('IgorR')"},{"path":"https://jefferis.github.io/IgorR/index.html","id":"github-install","dir":"","previous_headings":"","what":"Github Install","title":"Read Binary Files Saved by Igor Pro (Including Neuromatic Data)","text":"install latest development version github","code":"# install remotes package if required if(!require('remotes')) install.packages('remotes') remotes::install_github('jefferis/IgorR')"},{"path":"https://jefferis.github.io/IgorR/index.html","id":"development-install","dir":"","previous_headings":"","what":"Development Install","title":"Read Binary Files Saved by Igor Pro (Including Neuromatic Data)","text":"checkout version can used development (RStudio strongly recommended), terminal application. R","code":"cd /some/suitable/dir git clone https://github.com/jefferis/IgorR.git install.packages('devtools') # install hadley's devtools library(devtools) load_all('/some/suitable/dir/IgorR') test() #hack load_all() # ready for release check() build_win() # test for Windows release()"},{"path":"https://jefferis.github.io/IgorR/index.html","id":"details","dir":"","previous_headings":"","what":"Details","title":"Read Binary Files Saved by Igor Pro (Including Neuromatic Data)","text":"Details ibw file format derived Igor Technical Note 003. interested source code, ReadIgorBinary.R provides code standard pxp ibw files, ReadNclamp.R provides routines read packed experiment files generated Nclamp data acquisition package.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-package.html","id":null,"dir":"Reference","previous_headings":"","what":"Read binary files saved by Igor Pro (including Neuromatic data) — IgorR-package","title":"Read binary files saved by Igor Pro (including Neuromatic data) — IgorR-package","text":"package provides function read data Igor Pro data analysis program Wavemetrics. data formats supported Igor packed experiment format (.pxp) Igor binary wave (.ibw). See: https://www.wavemetrics.com/ details.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read binary files saved by Igor Pro (including Neuromatic data) — IgorR-package","text":"also includes functions load special pxp files produced Neuromatic/Nclamp packages recording analysing neuronal #data. See https://github.com/SilverLabUCL/NeuroMatic details. Key functions package include read.ibw, read.pxp.","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read binary files saved by Igor Pro (including Neuromatic data) — IgorR-package","text":"Maintainer: Gregory Jefferis jefferis@gmail.com (ORCID) contributors: Thomas Braun [contributor]","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":null,"dir":"Reference","previous_headings":"","what":"Private functions in IgorR Package — IgorR-private","title":"Private functions in IgorR Package — IgorR-private","text":".ReadPackedHeader reads short record header current location PXP file","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Private functions in IgorR Package — IgorR-private","text":"","code":".ReadPackedHeader(con, endian)"},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Private functions in IgorR Package — IgorR-private","text":"con R connection file reading endian either little big","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Private functions in IgorR Package — IgorR-private","text":"list containing information current record","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Private functions in IgorR Package — IgorR-private","text":"Note recordType one constants Igor's enum PackedFileRecordType","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Private functions in IgorR Package — IgorR-private","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":null,"dir":"Reference","previous_headings":"","what":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"Read Nclamp log tables directory list","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"","code":"ReadAllNclampLogTables(logfiledir, pattern = \"_log[0-9]+[.]pxp$\", ...)"},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"logfiledir path directory containing log files (pxp files). pattern optional regular expression – see list.files. ... additional parameters ReadNclampLogTable.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"named list containing one dataframe parsed log file.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"","code":"if (FALSE) { # \\dontrun{ logfiles <- ReadAllNclampLogTables(\"/GD/projects/PhysiologyData/logs\") str(logfiles) } # }"},{"path":"https://jefferis.github.io/IgorR/reference/ReadNclampLogTable.html","id":null,"dir":"Reference","previous_headings":"","what":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","title":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","text":"log tables special Igor .pxp files contain variables. entry corresponds single run Nclamp protocol, storing information like protocol name, run time etc.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadNclampLogTable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","text":"","code":"ReadNclampLogTable(f, Verbose = FALSE)"},{"path":"https://jefferis.github.io/IgorR/reference/ReadNclampLogTable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","text":"f path log file. Verbose whether print status information reading file.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadNclampLogTable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","text":"dataframe containing row acquisition protocol run.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadNclampLogTable.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"e.g. import Physiology database","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"","code":"SummariseSweepFile(f, Verbose = FALSE)"},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"f path Nclamp/Igor PXP format sweep file. Verbose TRUE, print details parsing underlying PXP file.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"list 25 fields summarising sweep file.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"","code":"l <- SummariseSweepFile(system.file(\"igor\", \"WedJul407c2_001.pxp\", package=\"IgorR\")) cat(\"There are\", l$NumWaves, \"waves in the file each of total duration\", l$StimWaveLength, \"ms and sample duration\", l$StimSampleInterval, \"ms \\n\") #> There are 100 waves in the file each of total duration 20 ms and sample duration 0.025 ms"},{"path":"https://jefferis.github.io/IgorR/reference/SweepFilesToDataFrame.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","title":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","text":"Note still little fragile lists produced SummariseSweepFile consistent field names.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SweepFilesToDataFrame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","text":"","code":"SweepFilesToDataFrame(ff)"},{"path":"https://jefferis.github.io/IgorR/reference/SweepFilesToDataFrame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","text":"ff paths set sweep files.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SweepFilesToDataFrame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","text":"dataframe rows sweep file.","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/SweepFilesToDataFrame.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/UpdateSweepDataFrame.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","title":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","text":"Update CSV file summarising sweeps Nclamp data folder","code":""},{"path":"https://jefferis.github.io/IgorR/reference/UpdateSweepDataFrame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","text":"","code":"UpdateSweepDataFrame( folder, outfile = NULL, action = c(\"update\", \"force\"), DryRun = FALSE )"},{"path":"https://jefferis.github.io/IgorR/reference/UpdateSweepDataFrame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","text":"folder path folder. outfile path outfile (default: /path//datafolder/datafolder.csv). action update newer (default) force update (yet implemented). DryRun TRUE, report files processed, nothing.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/UpdateSweepDataFrame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","text":"TRUE something happened, FALSE otherwise.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/UpdateSweepDataFrame.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/WaveToTimeSeries.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","title":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","text":"multiple waves, assumed compatible lengths can joined together cbind.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/WaveToTimeSeries.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","text":"","code":"WaveToTimeSeries(WaveData, ReturnOriginalDataOnError = TRUE)"},{"path":"https://jefferis.github.io/IgorR/reference/WaveToTimeSeries.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","text":"WaveData, wave list waves ReturnOriginalDataOnError make time series, return return original data (default TRUE)","code":""},{"path":"https://jefferis.github.io/IgorR/reference/WaveToTimeSeries.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","text":"time series multi time series (ts, mts)","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/WaveToTimeSeries.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":null,"dir":"Reference","previous_headings":"","what":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"Read binary files Igor Binary Wave format (IBW)","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"","code":"read.ibw( wavefile, Verbose = FALSE, ReturnTimeSeries = FALSE, MakeWave = FALSE, HeaderOnly = FALSE )"},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"wavefile either character vector containing path file R connection. Verbose TRUE, print status information reading file. ReturnTimeSeries TRUE, return R time series (package ts). MakeWave TRUE, assign wave list global user environment. HeaderOnly TRUE, return header Igor Wave.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"vector containing wave data , MakeWave == TRUE, returns name new R vector containing data made user environment","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"","code":"# return a list containing the wave wavedata=read.ibw(system.file(\"igor\",\"version5.ibw\",package=\"IgorR\")) sum(wavedata) #> [1] 15 # make a list containing the wave's data in the users's environment wavename=read.ibw(system.file(\"igor\",\"version5.ibw\",package=\"IgorR\"),MakeWave=TRUE) sum(get(wavename)) #> [1] 15"},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":null,"dir":"Reference","previous_headings":"","what":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"Note PXP files partially documented contents parsed (e.g. image data). function currently reads data records (Igor waves variables), history, procedures, recreation macros plain text notebooks. Formatted notebooks read.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"","code":"read.pxp( pxpfile, regex, ReturnTimeSeries = FALSE, Verbose = FALSE, StructureOnly = FALSE, ExtractText = FALSE, IgorPlatform = NULL, ... )"},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"pxpfile character vector naming PXP file R connection. regex TRUE, read records (e.g. waves) PXP file whose names match regex. ReturnTimeSeries TRUE, Igor waves returned link{ts} object sensible x scaling (FALSE default). Verbose whether print information console loading (numeric values also allowed 0=none, 1=basic, 2=). StructureOnly (TODO) TRUE, structure PXP file inspection. ExtractText whether extract procedures, recreation macros, history plain text notebooks (FALSE default). IgorPlatform OS Igor file saved (windows macintosh). ... optional parameters passed read.ibw.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"list containing individual waves variables PXP file.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"IgorPlatform determine encoding text read (WINDOWS-1252 windows macintosh macintosh). Unique abbreviations acceptable. Defaults \"windows\" Windows, \"macintosh\" otherwise. Note Igor Pro 5.5 added PlatformRecord PXP file format used determine file's platform origin available. Since information straight horse's mouth override IgorPlatform argument.","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"","code":"r=read.pxp(system.file(\"igor\",\"testexpt.pxp\",package=\"IgorR\"))"},{"path":"https://jefferis.github.io/IgorR/reference/tsp.igorwave.html","id":null,"dir":"Reference","previous_headings":"","what":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","title":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","text":"Note end = (npts-1) * deltat","code":""},{"path":"https://jefferis.github.io/IgorR/reference/tsp.igorwave.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","text":"","code":"tsp.igorwave(wave)"},{"path":"https://jefferis.github.io/IgorR/reference/tsp.igorwave.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","text":"wave Igor wave loaded read.ibw orread.pxp","code":""},{"path":"https://jefferis.github.io/IgorR/reference/tsp.igorwave.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","text":"numeric vector elements start, end, frequency","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/tsp.igorwave.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","text":"jefferis","code":""}] +[{"path":"https://jefferis.github.io/IgorR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Gregory Jefferis. Author, maintainer. Thomas Braun. Contributor.","code":""},{"path":"https://jefferis.github.io/IgorR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Jefferis G (2024). IgorR: Read Binary Files Saved 'Igor Pro' (Including 'Neuromatic' Data). R package version 0.9.0, https://jefferis.github.io/IgorR/, https://github.com/jefferis/IgorR.","code":"@Manual{, title = {IgorR: Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic' Data)}, author = {Gregory Jefferis}, year = {2024}, note = {R package version 0.9.0, https://jefferis.github.io/IgorR/}, url = {https://github.com/jefferis/IgorR}, }"},{"path":[]},{"path":"https://jefferis.github.io/IgorR/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Read Binary Files Saved by Igor Pro (Including Neuromatic Data)","text":"IgorR package R provides routines read binary files generated Igor Pro. includes standalone .ibw Igor Binary Wave format (v2 latest v5) .pxp Packed Experiment Format including waves variables. addition package provides functions read files generated Neuromatic analysis suite written Jason Rothman Igor Pro.","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/index.html","id":"standard-install","dir":"","previous_headings":"","what":"Standard Install","title":"Read Binary Files Saved by Igor Pro (Including Neuromatic Data)","text":"NB IgorR CRAN due unfixed bug windows text tecent versions R. Whenever back can install release version CRAN","code":"install.packages('IgorR')"},{"path":"https://jefferis.github.io/IgorR/index.html","id":"github-install","dir":"","previous_headings":"","what":"Github Install","title":"Read Binary Files Saved by Igor Pro (Including Neuromatic Data)","text":"install latest development version github","code":"# install remotes package if required if(!require('remotes')) install.packages('remotes') remotes::install_github('jefferis/IgorR')"},{"path":"https://jefferis.github.io/IgorR/index.html","id":"development-install","dir":"","previous_headings":"","what":"Development Install","title":"Read Binary Files Saved by Igor Pro (Including Neuromatic Data)","text":"checkout version can used development (RStudio strongly recommended), terminal application. R","code":"cd /some/suitable/dir git clone https://github.com/jefferis/IgorR.git install.packages('devtools') # install hadley's devtools library(devtools) load_all('/some/suitable/dir/IgorR') test() #hack load_all() # ready for release check() build_win() # test for Windows release()"},{"path":"https://jefferis.github.io/IgorR/index.html","id":"details","dir":"","previous_headings":"","what":"Details","title":"Read Binary Files Saved by Igor Pro (Including Neuromatic Data)","text":"Details ibw file format derived Igor Technical Note 003. interested source code, ReadIgorBinary.R provides code standard pxp ibw files, ReadNclamp.R provides routines read packed experiment files generated Nclamp data acquisition package.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-package.html","id":null,"dir":"Reference","previous_headings":"","what":"Read binary files saved by Igor Pro (including Neuromatic data) — IgorR-package","title":"Read binary files saved by Igor Pro (including Neuromatic data) — IgorR-package","text":"package provides function read data Igor Pro data analysis program Wavemetrics. data formats supported Igor packed experiment format (.pxp) Igor binary wave (.ibw). See: https://www.wavemetrics.com/ details.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read binary files saved by Igor Pro (including Neuromatic data) — IgorR-package","text":"also includes functions load special pxp files produced Neuromatic/Nclamp packages recording analysing neuronal #data. See https://github.com/SilverLabUCL/NeuroMatic details. Key functions package include read.ibw, read.pxp.","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read binary files saved by Igor Pro (including Neuromatic data) — IgorR-package","text":"Maintainer: Gregory Jefferis jefferis@gmail.com (ORCID) contributors: Thomas Braun [contributor]","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":null,"dir":"Reference","previous_headings":"","what":"Private functions in IgorR Package — IgorR-private","title":"Private functions in IgorR Package — IgorR-private","text":".ReadPackedHeader reads short record header current location PXP file","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Private functions in IgorR Package — IgorR-private","text":"","code":".ReadPackedHeader(con, endian)"},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Private functions in IgorR Package — IgorR-private","text":"con R connection file reading endian either little big","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Private functions in IgorR Package — IgorR-private","text":"list containing information current record","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Private functions in IgorR Package — IgorR-private","text":"Note recordType one constants Igor's enum PackedFileRecordType","code":""},{"path":"https://jefferis.github.io/IgorR/reference/IgorR-private.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Private functions in IgorR Package — IgorR-private","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":null,"dir":"Reference","previous_headings":"","what":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"Read Nclamp log tables directory list","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"","code":"ReadAllNclampLogTables(logfiledir, pattern = \"_log[0-9]+[.]pxp$\", ...)"},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"logfiledir path directory containing log files (pxp files). pattern optional regular expression – see list.files. ... additional parameters ReadNclampLogTable.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"named list containing one dataframe parsed log file.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read all Nclamp log tables from a directory into a list — ReadAllNclampLogTables","text":"","code":"if (FALSE) { # \\dontrun{ logfiles <- ReadAllNclampLogTables(\"/GD/projects/PhysiologyData/logs\") str(logfiles) } # }"},{"path":"https://jefferis.github.io/IgorR/reference/ReadNclampLogTable.html","id":null,"dir":"Reference","previous_headings":"","what":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","title":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","text":"log tables special Igor .pxp files contain variables. entry corresponds single run Nclamp protocol, storing information like protocol name, run time etc.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadNclampLogTable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","text":"","code":"ReadNclampLogTable(f, Verbose = FALSE)"},{"path":"https://jefferis.github.io/IgorR/reference/ReadNclampLogTable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","text":"f path log file. Verbose whether print status information reading file.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadNclampLogTable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","text":"dataframe containing row acquisition protocol run.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/ReadNclampLogTable.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read the log table produced by Nclamp acquisition software for Igor — ReadNclampLogTable","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"e.g. import Physiology database","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"","code":"SummariseSweepFile(f, Verbose = FALSE)"},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"f path Nclamp/Igor PXP format sweep file. Verbose TRUE, print details parsing underlying PXP file.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"list 25 fields summarising sweep file.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SummariseSweepFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract summary information from an Nclamp/Igor Sweep File — SummariseSweepFile","text":"","code":"l <- SummariseSweepFile(system.file(\"igor\", \"WedJul407c2_001.pxp\", package=\"IgorR\")) cat(\"There are\", l$NumWaves, \"waves in the file each of total duration\", l$StimWaveLength, \"ms and sample duration\", l$StimSampleInterval, \"ms \\n\") #> There are 100 waves in the file each of total duration 20 ms and sample duration 0.025 ms"},{"path":"https://jefferis.github.io/IgorR/reference/SweepFilesToDataFrame.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","title":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","text":"Note still little fragile lists produced SummariseSweepFile consistent field names.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SweepFilesToDataFrame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","text":"","code":"SweepFilesToDataFrame(ff)"},{"path":"https://jefferis.github.io/IgorR/reference/SweepFilesToDataFrame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","text":"ff paths set sweep files.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/SweepFilesToDataFrame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","text":"dataframe rows sweep file.","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/SweepFilesToDataFrame.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Summarise multiple sweep files into a single dataframe — SweepFilesToDataFrame","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/UpdateSweepDataFrame.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","title":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","text":"Update CSV file summarising sweeps Nclamp data folder","code":""},{"path":"https://jefferis.github.io/IgorR/reference/UpdateSweepDataFrame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","text":"","code":"UpdateSweepDataFrame( folder, outfile = NULL, action = c(\"update\", \"force\"), DryRun = FALSE )"},{"path":"https://jefferis.github.io/IgorR/reference/UpdateSweepDataFrame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","text":"folder path folder. outfile path outfile (default: /path//datafolder/datafolder.csv). action update newer (default) force update (yet implemented). DryRun TRUE, report files processed, nothing.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/UpdateSweepDataFrame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","text":"TRUE something happened, FALSE otherwise.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/UpdateSweepDataFrame.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Update the CSV file summarising the sweeps in an Nclamp data folder — UpdateSweepDataFrame","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/WaveToTimeSeries.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","title":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","text":"multiple waves, assumed compatible lengths can joined together cbind.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/WaveToTimeSeries.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","text":"","code":"WaveToTimeSeries(WaveData, ReturnOriginalDataOnError = TRUE)"},{"path":"https://jefferis.github.io/IgorR/reference/WaveToTimeSeries.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","text":"WaveData, wave list waves ReturnOriginalDataOnError make time series, return return original data (default TRUE)","code":""},{"path":"https://jefferis.github.io/IgorR/reference/WaveToTimeSeries.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","text":"time series multi time series (ts, mts)","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/WaveToTimeSeries.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Convert an Igor wave (wave list) loaded by read.ibw into an R time series — WaveToTimeSeries","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":null,"dir":"Reference","previous_headings":"","what":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"Read binary files Igor Binary Wave format (IBW)","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"","code":"read.ibw( wavefile, Verbose = FALSE, ReturnTimeSeries = FALSE, MakeWave = FALSE, HeaderOnly = FALSE )"},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"wavefile either character vector containing path file R connection. Verbose TRUE, print status information reading file. ReturnTimeSeries TRUE, return R time series (package ts). MakeWave TRUE, assign wave list global user environment. HeaderOnly TRUE, return header Igor Wave.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"vector containing wave data , MakeWave == TRUE, returns name new R vector containing data made user environment","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.ibw.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read binary files in the Igor Binary Wave format (IBW) — read.ibw","text":"","code":"# return a list containing the wave wavedata=read.ibw(system.file(\"igor\",\"version5.ibw\",package=\"IgorR\")) sum(wavedata) #> [1] 15 # make a list containing the wave's data in the users's environment wavename=read.ibw(system.file(\"igor\",\"version5.ibw\",package=\"IgorR\"),MakeWave=TRUE) sum(get(wavename)) #> [1] 15"},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":null,"dir":"Reference","previous_headings":"","what":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"Note PXP files partially documented contents parsed (e.g. image data). function currently reads data records (Igor waves variables), history, procedures, recreation macros plain text notebooks. Formatted notebooks read.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"","code":"read.pxp( pxpfile, regex, ReturnTimeSeries = FALSE, Verbose = FALSE, StructureOnly = FALSE, ExtractText = FALSE, IgorPlatform = NULL, ... )"},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"pxpfile character vector naming PXP file R connection. regex TRUE, read records (e.g. waves) PXP file whose names match regex. ReturnTimeSeries TRUE, Igor waves returned link{ts} object sensible x scaling (FALSE default). Verbose whether print information console loading (numeric values also allowed 0=none, 1=basic, 2=). StructureOnly (TODO) TRUE, structure PXP file inspection. ExtractText whether extract procedures, recreation macros, history plain text notebooks (FALSE default). IgorPlatform OS Igor file saved (windows macintosh). ... optional parameters passed read.ibw.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"list containing individual waves variables PXP file.","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"IgorPlatform determine encoding text read (WINDOWS-1252 windows macintosh macintosh). Unique abbreviations acceptable. Defaults \"windows\" Windows, \"macintosh\" otherwise. Note Igor Pro 5.5 added PlatformRecord PXP file format used determine file's platform origin available. Since information straight horse's mouth override IgorPlatform argument.","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/reference/read.pxp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reads an Igor Pro Packed Experiment (.pxp) file — read.pxp","text":"","code":"r=read.pxp(system.file(\"igor\",\"testexpt.pxp\",package=\"IgorR\"))"},{"path":"https://jefferis.github.io/IgorR/reference/tsp.igorwave.html","id":null,"dir":"Reference","previous_headings":"","what":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","title":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","text":"Note end = (npts-1) * deltat","code":""},{"path":"https://jefferis.github.io/IgorR/reference/tsp.igorwave.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","text":"","code":"tsp.igorwave(wave)"},{"path":"https://jefferis.github.io/IgorR/reference/tsp.igorwave.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","text":"wave Igor wave loaded read.ibw orread.pxp","code":""},{"path":"https://jefferis.github.io/IgorR/reference/tsp.igorwave.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","text":"numeric vector elements start, end, frequency","code":""},{"path":[]},{"path":"https://jefferis.github.io/IgorR/reference/tsp.igorwave.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Return tsp attribute of Igor wave (start, end, frequency) — tsp.igorwave","text":"jefferis","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-090","dir":"Changelog","previous_headings":"","what":"IgorR 0.9.0","title":"IgorR 0.9.0","text":"fix: handling Igor dates using timechange library (#6) remove warnings due recent changes readChar handles strings containing embedded nulls fix URLs CRAN dev: switch github actions R CMD check pkgdown (remove travis)","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-082","dir":"Changelog","previous_headings":"","what":"IgorR 0.8.2","title":"IgorR 0.8.2","text":"minor: package docs, spelling, author formatting","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-081","dir":"Changelog","previous_headings":"","what":"IgorR 0.8.1","title":"IgorR 0.8.1","text":"CRAN release: 2017-05-21 Fix namespace canonical URL issues CRAN","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-08","dir":"Changelog","previous_headings":"","what":"IgorR 0.8","title":"IgorR 0.8","text":"CRAN release: 2015-05-28 fix bug reading igor waves embedded non-null terminated strings (#3) fix bug reading igor pxp files names valid R names e.g. begining underscore. (#2) Thanks Troy Margrie, Mateo Velez Charly Rousseau reports/test data Minor description fixes R 3.2.0 dev: switch tests tests/testthat (making optional install) keeping igor waves required examples inst/igor dev: switch new style travis config dev: upgrade roxygen2 4.1.1","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-072","dir":"Changelog","previous_headings":"","what":"IgorR 0.7.2","title":"IgorR 0.7.2","text":"minor doc fixes","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-071","dir":"Changelog","previous_headings":"","what":"IgorR 0.7.1","title":"IgorR 0.7.1","text":"CRAN release: 2014-02-11 Fix encoding issue Igor pxp files containing high bytes. Pointed Brian Ripley Solaris, fixed across platforms help Ashley Manton. Fix error R<3.0.0 caused use new keep.source argument parse().","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-07","dir":"Changelog","previous_headings":"","what":"IgorR 0.7","title":"IgorR 0.7","text":"CRAN release: 2014-02-11 Add support extracting history, procedures plain text notebooks (contributed Thomas Braun). See read.pxp() ExtractText argument. dev: added support travis continuous integration dev: repo now includes man files allow devtools installation dev: disable unreliable test date-time parsing","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-06","dir":"Changelog","previous_headings":"","what":"IgorR 0.6","title":"IgorR 0.6","text":"significant speed optimisations without change functionality 2x faster small waves (<1Mb) system Now imports bitops, tools","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-05-4","dir":"Changelog","previous_headings":"","what":"IgorR 0.5-4","title":"IgorR 0.5-4","text":"Add regular expression restrict ReadAllNclampLogTables() log files Package documentation","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-05-3","dir":"Changelog","previous_headings":"","what":"IgorR 0.5-3","title":"IgorR 0.5-3","text":"CRAN release: 2012-09-20 Minor fix error checks tsp.igorwave()","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-05-2","dir":"Changelog","previous_headings":"","what":"IgorR 0.5-2","title":"IgorR 0.5-2","text":"CRAN release: 2012-06-21 Minor fixes remove outstanding NOTES R 2.15’s check","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-05-1","dir":"Changelog","previous_headings":"","what":"IgorR 0.5-1","title":"IgorR 0.5-1","text":"Option return Igor wave data time series reading pxp files. Fix problem empty waves often encountered reading waves PXP files time series.","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-05","dir":"Changelog","previous_headings":"","what":"IgorR 0.5","title":"IgorR 0.5","text":"CRAN release: 2012-01-25 rename ReadIgorPackedExperiment ReadIgorBinary functions read.pxp() read.ibw(), respectively. Fix encoding bug Windows MAC->macintosh (pointed Brian Ripley) Teach read.pxp() read string variables non ASCII characters Teach read.pxp() read waves matching regex Teach read.pxp() read structure waves requested Documentation changes github","code":""},{"path":"https://jefferis.github.io/IgorR/news/index.html","id":"igorr-04","dir":"Changelog","previous_headings":"","what":"IgorR 0.4","title":"IgorR 0.4","text":"CRAN release: 2012-01-14 First version CRAN","code":""}] diff --git a/sitemap.xml b/sitemap.xml index 215fa2e..54280ed 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -2,6 +2,7 @@ https://jefferis.github.io/IgorR/404.html https://jefferis.github.io/IgorR/authors.html https://jefferis.github.io/IgorR/index.html +https://jefferis.github.io/IgorR/news/index.html https://jefferis.github.io/IgorR/reference/IgorR-package.html https://jefferis.github.io/IgorR/reference/IgorR-private.html https://jefferis.github.io/IgorR/reference/ReadAllNclampLogTables.html
Thomas Braun. Contributor. +
Thomas Braun. Contributor.
Jefferis G (2024). IgorR: Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic' Data). -R package version 0.8.2.9000, https://jefferis.github.io/IgorR/, https://github.com/jefferis/IgorR. +R package version 0.9.0, https://jefferis.github.io/IgorR/, https://github.com/jefferis/IgorR.
@Manual{, title = {IgorR: Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic' Data)}, author = {Gregory Jefferis}, year = {2024}, - note = {R package version 0.8.2.9000, https://jefferis.github.io/IgorR/}, + note = {R package version 0.9.0, https://jefferis.github.io/IgorR/}, url = {https://github.com/jefferis/IgorR}, }
NEWS.md
CRAN release: 2017-05-21
CRAN release: 2015-05-28
CRAN release: 2014-02-11
read.pxp()
ReadAllNclampLogTables()
CRAN release: 2012-09-20
tsp.igorwave()
CRAN release: 2012-06-21
CRAN release: 2012-01-25
read.ibw()
CRAN release: 2012-01-14