Philipp Baumann
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2888f7c955
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add first version of `join_spc_chem()` to join spectral and chemical tibbles
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8 years ago |
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Philipp Baumann
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cb19c32e81
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fix error in conditional offset definition for reading correct spectra
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8 years ago |
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Philipp Baumann
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c7ec013322
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adapt binary OPUS file reader function to differering block position structures in OPUS files of ALPHA spectrometers at ETH Zuerich and ICRAF. Redefine offsets for upper and lower frequencies, number of points, and spectral information offsets for sample spectra.
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8 years ago |
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Philipp Baumann
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d53c207bac
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fix error in `read_spectra()` that readOPUS function is not found. This is a result from renaming `readOPUS` to `read_opus()` in the `load-spectra.R` file
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8 years ago |
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Philipp Baumann
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bf1aa0ff8a
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Update documentation using `devtools::document()`
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8 years ago |
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Philipp Baumann
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17d33541fa
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Update documentation using `devtools::document()`
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8 years ago |
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Philipp Baumann
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50a9abaf45
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Update NAMESPACE file due to changed export from `load-spectra.R` function renaming
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8 years ago |
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Philipp Baumann
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4c176e8dc8
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change names of binary OPUS file reading functions adapted from soil.spec package. Current `read_spectra()` function based on exported spectra text files from OPUS software macro is not affected. Change `readOPUS` to `read_opus`, `readOPUS_bin` to `read_opus_bin`, `readOPUS_text` to `read_opus_text`
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8 years ago |
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Philipp Baumann
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ece6a882a7
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delete file because it has been renamed to `gather-spc.R`
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8 years ago |
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Philipp Baumann
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8d6c498f7a
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first version of tibble interface functions that aim to streamline the spectral data reading, gathering, resampling, averaging, and preprocessing by using tidy data structures in the form tibble class outputs and inputs. This makes printing of the spectral data streamline more user-friendly, stores spectral information in list-columns (list of data.table objects) of tibbles.
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8 years ago |
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Philipp Baumann
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eba693aa20
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Add R script file for function `preprocess_spc()` that preprocesses spectra in tibble column
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8 years ago |
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Philipp Baumann
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1e9f084a5e
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Add R script file for function `averages_spc()` that averages spectra in tibble column
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8 years ago |
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Philipp Baumann
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da7b9f7c32
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add R script file for function `resample_spc()` that resamples spectra in tibble column
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8 years ago |
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Philipp Baumann
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4e59826c20
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add R script file for fuction `gather_spc()` that gathers list of spectra into a tibble class object
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8 years ago |
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Philipp Baumann
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4995af3966
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add wrapper functions for handling tibble class data input for modeling
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8 years ago |
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Philipp Baumann
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34255f37a6
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update documentation using devtools::document()
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8 years ago |
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Philipp Baumann
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d3930d199d
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add default argument for maximal number of pls components evaluated
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8 years ago |
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Philipp Baumann
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a5a17d1dd0
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add default option for maximal number of PLS Regression components
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8 years ago |
Philipp Baumannit config --global user.email philipp.baumann@usys.ethz.ch
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b3374b92f9
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add tidyverse package in Imports field via devtools::add_package()
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8 years ago |
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Philipp Baumann
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cf82410085
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change block positions for lx (frequency of lowest point) and offsets for spectral information to extract correct wavenumbers and specktra. Fix works for ETH and ICRAF Ivory Coast OPUS spectra at current OPUS software versions, exact versions to be checked).
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8 years ago |
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Philipp Baumann
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3d406c45a5
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rename argument `max_ncomp_pls` to `pls_ncomp_max`
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8 years ago |
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Philipp Baumann
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be16896378
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fix wrong selection of `val_set` and `cal_set` for inverted calibration sampling
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8 years ago |
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Philipp Baumann
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3ed972af98
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add `invert` argument from quoted function `ken_stone_q` to pls modeling function `pls_ken_stone` using non-standard evaluation
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8 years ago |
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Philipp Baumann
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3b4b39cca2
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simplify and add better comments to function `ken_stone_q`, add an option to invert selection of calibration and validation spectra for the Kennard-Stones calibration sampling
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8 years ago |
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Philipp Baumann
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20d2d56cb8
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fixed error message for `select_ref_samples()` because `MIR0` was used as spectra, now changed to `MIR_pre`
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8 years ago |
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Philipp Baumann
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46bdd8b6b0
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update documentation for `do_pretreatment` with new name of spectral output matrix `MIR_pre`
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8 years ago |
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Philipp Baumann
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f24f686018
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update documentation for `do_pretreatment` with new name preprocessed spectra element
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8 years ago |
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Philipp Baumann
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c74c137d7e
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change name of preprocessed from `MIR0` to MIR_pre` in preprocessing function `do_pretreatment(), implement consistent names of processed spectral data matrices inputs and outputs of `resample_spectra()`and `join_chem_spec()`
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8 years ago |
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Philipp Baumann
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03191b77fc
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implement window size of 13 with first derivative, option called `MIR1_w13`
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8 years ago |
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Philipp Baumann
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751979f78c
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fix bug in `predictions_caret` and use `model_list` from function argument
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8 years ago |
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Philipp Baumann
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4170115772
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fix typo in `rf_ken_stone`
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8 years ago |
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Philipp Baumann
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3ae8a15f4a
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update NAMESPACE and manual
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8 years ago |
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Philipp Baumann
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68dbd35c82
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automatically created R documentation file for `select_ref_samples`
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8 years ago |
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Philipp Baumann
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3011670500
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change title description of random forest function
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8 years ago |
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Philipp Baumann
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31e36a109f
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add random forest in one function called `rf_ken_stone`
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8 years ago |
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Philipp Baumann
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396a5396d7
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add random forest model function fit_rf_q
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8 years ago |
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Philipp Baumann
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cc82db514d
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swap calibration and validation samples for ken_stone_q function in order to cover maximum spectral diversity in PC space
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8 years ago |
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Philipp Baumann
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81f8e017c9
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specify default value for pc (=2) for pls_ken_stone function
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8 years ago |
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Philipp Baumann
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f777a10bdc
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add new first derivative preprocessing option to that corresponds to ICRAF routine
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8 years ago |
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Philipp Baumann
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b5f261e25b
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rename metadata and spectra list element to simpler description
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8 years ago |
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Philipp Baumann
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5f81ef85de
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swap colours for model prediction and reference analysis in PCA space
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8 years ago |
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Philipp Baumann
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c17fbcc36f
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changed sel_df_cal to sel_df_ref
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8 years ago |
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Philipp Baumann
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c7dc4390ad
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add code to select_ref_samples to print selection of reference and predition samples in PC space
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8 years ago |
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Philipp Baumann
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bee6c97d25
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delete ken_stone from manual because function was renamed to ken_stone_q as it is a quoted version for non-standard evaluation
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8 years ago |
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Philipp Baumann
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0894ad5175
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add missing title for calibration sampling function
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8 years ago |
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Philipp Baumann
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44568f6df1
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add function to select reference samples to be measured by reference analysis method. Use Kennard-Stones algorithm.
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8 years ago |
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Philipp Baumann
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121311750f
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create quoted version of ken_stone as ken_stone_q and test option to use non-standard evaluation for passing the number of components for calibration sampling
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8 years ago |
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Philipp Baumann
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715db56dcc
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complete list of packages built upon, add credits to people
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8 years ago |
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Philipp Baumann
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8fc39e0120
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add pipes in example workflow and code for spectral model development
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8 years ago |
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Philipp Baumann
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9a04f0ff92
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fix typos and add sections <Key conceps and data analysis workflow>, <Example workflow>, and <Details on Functions>
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8 years ago |
