Commit Graph

68 Commits (678a6ce4b73b2b839539020d4c44f79bfda15ed5)
 

Author SHA1 Message Date
Taha Ahmed 678a6ce4b7 Fixed circ dependency created in last commit
Goofed and declared dependency on photoec in previous commit. Fixed it by removing it and the non-exported function that used it.
Note to self: this package should not import any of my other packages.
TA a11f59eb22 Added function simpleCap()
Taha Ahmed 3f4462aae8 Added more data and squashed a few bugs.
Taha Ahmed b1bed60d40 Potentials vs SHE now converted to SHE.
Previous behaviour returned NAs for values that were already vs SHE. That issue now fixed. The fix included added SHE (zero at all temperatures) to as.SHE.data.
Taha Ahmed 82f635f3a3 as.SHE() now supports arguments with arbitrary length.
Ended up completely rewriting as.SHE() and some of the companion functions.
Taha Ahmed dc0fcb0629 Function that converts scale names is now accessible (exported).
Capitalised scale names so they match more variations (remember, matching uses tolower(), so no need to start with lowercase).
Taha Ahmed 1dee1918c1 Deprecated the old electrochemical conversion functions
AVS2SHE, SHE2AVS,ConvertRefPotEC and ConvertRefPot
Taha Ahmed 5d7230ebaf Completely reworked electrochemical scale converter
by adding a new family of functions.
Corrected package version number to dev. A few other smaller (older) changes.
Taha Ahmed e22546cb3c Refactored code into a rudimentary R package.
Taha Ahmed c00fcc54a9 Added functions for converting to/from wavelength and wavenumbers.
Taha Ahmed e2d0d21236 Lots of changes, apparently ... Note previous commit missed files.
Latest change: addition of generic Xtable handler functions
    (GenericXtableSetAttributes(), TabularXtableHeader(), and the longtable
    version of that one, which is LongtableXtableHeader()).
Taha Ahmed a67ce80e2b Lots of changes, apparently ...
Latest change: addition of generic Xtable handler functions
(GenericXtableSetAttributes(), TabularXtableHeader(), and the longtable
version of that one, which is LongtableXtableHeader()).
Taha Ahmed 203bd6cfbe Added an extra arg (mainlabel) plus other minor changes so that LaTeX doesnot complain
about "multiply-defined labels".
Taha Ahmed d0044d87ed New function SubfigureGenerator() takes a vector of images and captions and creates a LaTeX subfigure.
Taha Ahmed 1a52116071 Added the small utility function hms2seconds()
Converts character strings of hours, minutes, seconds to seconds (as numeric).
Taha Ahmed 7d6044143b Implemented a switch (arg) that allows new behaviour (optional) ...
without breaking code that relies on old behaviour (default).
Taha Ahmed ca87357da3 Changed implementation to dirname(basename()). This should be more robust. ...
This should be more robust as the dirname follows a more stringent format
than the filename itself.
Taha Ahmed 16faf22b9f numbers2words() converts numbers into their spelled names. capitalize is...
... a simple function for capitalizing the first letter of a string.
It should work well in conjunction with numbers2words() at the beginning
of sentences.
Taha Ahmed d36666ac24 Made regex more specific (now matches "\\labreport...}{").
Previous behaviour matched first part of \SI{}{} as well and was unwanted.
Taha Ahmed b6383eb556 Function that fetches the substrate-history from the sample-matrix,
and prettifies the dataframe a little (removes empty columns) before returning it.
Taha Ahmed a6466ddc02 Split original git repo by subdirectory.
Taha Ahmed 5ee85d580e Added function to read Perkin-Elmer spectra files.
This function reads *.SP files (ASCII), and currently fetches only data (no meta-data).
Taha Ahmed 98dcf3b7a3 Updated to reflect change (long time ago) in folder structure.
Taha Ahmed f0ed360c0d Ok, no commits since a while. Last change was remake of init.R to improve readability.
Taha Ahmed 70c39b9145 xrdpkWrapper.R now correctly handles situations where file already exists,
override = TRUE, and run > 1. Previously only the latest run was actually saved,
although the created list had the right length.
Works correctly and as intended now, as far as I can tell.
Taha Ahmed 3d4244f1fd Added XRD peak wrapper functions (as done previously for XRF and Raman).
Also put the short R-data loading function I wrote into the
common directory.
Taha Ahmed 0579b5ea52 Many small changes and updates. Need separate git repo for each instrument.
Taha Ahmed beab0b9e64 Solved the issue with repeating diffractometry analyses by wrapper functions.
Caught some errors and made some improvements in the other functions.
Taha Ahmed 4fff82be0c Complete re-write of tifftags2df (only internal changes).
No changes in input or output of this function, only of the internal
mechanism with which tags are chosen and formatted for output.
init.R contains the sourceDir() function which is necessary for sourcing
all .R files in a directory.
Taha Ahmed b55af5d478 Re-wrote muxd2df() from scratch.
To make it able to include parameters as well as data in the returned df.
muxd2df() now works satisfactorily, outputs parameters such as steptime,
theta, and cps as well as thth and counts.
Other minor changes mostly updates of source file pointers.
Taha Ahmed b976bd3fa4 Split all files into their separate functions, put each former file in a directory.
The idea is to better expose each function, since some functions tended
to drown in the larger files.
Note that dependecies are are not resolved yet.
Many functions are probably broken right now, especially those who point
to common.R.
Taha Ahmed f12fe6306c Added empirical_formula to attributes of pdf2df().
Since chemicalformula can be quite a mess for some PDFs.
Taha Ahmed ed1853b706 Changed from factors to strings in pdf2df().
Added stringsAsFactors = FALSE to dataframe.
Taha Ahmed 52adff796b Added ocp2df() function to AUTOLAB.R.
ocp2df() is a straight-forward, no-frills function.
Taha Ahmed 77fd0b5aef Renamed chronoamp2df() to amp2df(). Added stringsAsFactors.
Renamed because the technique I have used so far is regular amperometry,
not chronoamperometry. Whatever the distinction is, I am not really sure.
Anyway, this function corresponds to the amperometry2df() function for CHI760.
Taha Ahmed ab65adee9d Fixed the problem with multiple-potential steps in mps2df().
Taha Ahmed e6eb2b9544 Created the chronoamp function for AUTOLAB.
Small changes in the chronoamp2df() for CHI.
Taha Ahmed 8e7eb9e9b1 In chronoamp2df(), changed the naming for the two "step" parameters.
This way, it should be more clear which is the dynamic counter, and which
is the static counter.
Also removed factor() around the dynamic step counter.
Taha Ahmed e3a7e20ff8 Updated chronoamp2df() to the new attributes system. Also improved docs.
Taha Ahmed b687e77eb5 ConvertRefPot() now handles AVS scale too.
Taha Ahmed 1d0dd666b0 Moved baseline args gam and scl.factor to Ramanpk() function arg.
Taha Ahmed 6a312409c3 Removed re-calc to evenly spaced shift from Raman2df().
The first test showed that such an approach would not work
(see comment in Raman2df()).
Taha Ahmed 9d67dbfad2 Raman2df() now includes evenly spaced spectrum in return dataframe.
It appears this will be such a common operation that it is worth
including in the fetch function itself.
Taha Ahmed aadd16e605 Raman spectrum are now sorted by increasing Raman shift by Raman2df().
INCA.R deals with EDS data.
Minor updates to CHI.R (check the diff logs for details).
Taha Ahmed 2287b7f57f Updated lsv2df(). Now includes attributes in dataframe columns.
Added calculation of charge density.
Also updated the description.
Taha Ahmed 0f936f1e62 Updated ocp2df() in CHI.R to put attributes in the dataframe columns.
Taha Ahmed bd2b1731fc Major update in CHI.R, function amperometry2df() improved, fixed.
There was an error in amperometry2df(), whereby the timediff calculated
was way too low. Was possibly related to the It2charge() function
used to calculate those values. That function (in common.R) is no longer
used by amperometry2df().
Also updated amperometry2df() so it now includes the data attributes
in the return dataframe itself, as columns (compare cv2df()).

common.R: do not use the It2charge() function in the future.
Do such calculations inline instead.
Taha Ahmed fd62a103c8 Created LEO1550.R: created tifftags2df() function.
In common.R: marked LinearBaseline() as deprecated.
Taha Ahmed 8e0733d03e Added function LinearBaseline().
Taha Ahmed fa6ac99fa5 Changed attribute name Segment to Segments (stores no of segments).
Because we already have the counter "segment", which stores the
current segment (so for Segments = 10, segment = 1:10).