* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* added STANDARD CURVE type, added option to reverse the xaxis of MFI plot, plots in ggplot2, log scales

* docs

* plate name detection based on filepath

* changed the default log scale into `all`

---------

Co-authored-by: Fersoil <Fersoil>

* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* Add .gitignore

* Add sample files and adequate tests

* Setup package workflow

* Style code (GHA)

* Export remaining objects

* Move dots down

* Add missing usage description

* Disable lint error

* Fix missing import ggplot2

---------

Co-authored-by: Tymoteusz Kwieciński <[email protected]>
Co-authored-by: ZetrextJG <[email protected]>

* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* bug: standard curve sample type (#13)

* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* added STANDARD CURVE type, added option to reverse the xaxis of MFI plot, plots in ggplot2, log scales

* docs

* plate name detection based on filepath

* changed the default log scale into `all`

---------

Co-authored-by: Fersoil <Fersoil>

* Add tests and setup GHA (#18)

* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* Add .gitignore

* Add sample files and adequate tests

* Setup package workflow

* Style code (GHA)

* Export remaining objects

* Move dots down

* Add missing usage description

* Disable lint error

* Fix missing import ggplot2

---------

Co-authored-by: Tymoteusz Kwieciński <[email protected]>
Co-authored-by: ZetrextJG <[email protected]>

* Add dev to GHA for R check and test coverage (#19)

* fixed sample type recognition; added standard curve to summary

* updated example script with Covid OISE dataset

* updated example script

---------

Co-authored-by: Jakub Grzywaczewski <[email protected]>
Co-authored-by: ZetrextJG <[email protected]>
Co-authored-by: Fersoil <Fersoil>

* Add covid and external data

* Rename file and add a second plate from Covid OISE

* description of available datasets

---------

Co-authored-by: Fersoil <Fersoil>

* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* added simple nplr model

* standard curve as plate attribute; simple plot of fitted model

* standard curve model fitting

* enchanced standard curve fitting, fixed reading Covid oise files, added docs

* expanded example script with Covid oise dataset and curve fitting

* predictions in example script

* minor fixes of predictions script

* covid oise datasets

* add `nplr` to `DESCRIPTION`

* vignette engine fixes

* added `ggplot2` import

* error fixes

* add imports to vignettes

* add docs

* CMD check fixes

* CMD check warning fixes

* correct license formatting

* datasets description

* add covid oise layout file

* restore `qpdf` import

---------

Co-authored-by: Fersoil <Fersoil>

* Add JakubG to DESCRIPTION

* Set only one maintainer

* add automatic documentation

* add github bot as author of the GHA commits

* trigger build for docs

* Update documentation (GHA)

* limit roxygenize on main and dev branch only

---------

Co-authored-by: Fersoil <Fersoil>
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

* added myself and bug reports section

* typo fixes

since there won't be a lot of changes on this branch I think it's a good idea to fix typos here

* typo fixes

* Update DESCRIPTION

---------

Co-authored-by: nizwant <[email protected]>
Co-authored-by: Fersoil <Fersoil>

* add NEWS.md with updates

* bioconductor compatibility

* documentation according to the bioconductor requirements

* remove imports from R code

* add PvSTATEM.Rproj to .gitignore

* cmd check notes

* license according to guidelines

* small fixes + docs

* typos fixed

* missing dependencies

* add docs

* restored imports to original

* remove double BugReports

---------

Co-authored-by: Fersoil <Fersoil>
Co-authored-by: Mateusz Nizwantowski <[email protected]>

* Update style.yaml

* Add ssh-key to roxygenise GHA

* Remove styler from precommit

* Styling changes

* Add missing layout file

* Fix latex inside docs

* Upload complied man and vignettes

* Capitalize sentences in docs

* Merge latex solutions

* added support of documentation for non latex environments

* bugfix issue 52 missing plots

---------

Co-authored-by: nizwant <[email protected]>

* Remove styler from precommit

* Styling changes

* Add missing layout file

* Fix latex inside docs

* Upload complied man and vignettes

* Capitalize sentences in docs

* Merge latex solutions

* initialisation of new files

* splitting classes into separate files

* removed classes file and new documentation

* docs for helpers functions

* added support of documentation for non latex environments

* bugfix issue 52 missing plots

* recompiled documentation and small fixes

* removed unnecessary example, that causes trouble

* recompile documentation

* Remove old classes

---------

Co-authored-by: ZetrextJG <[email protected]>
Co-authored-by: Jakub Grzywaczewski <[email protected]>

* docs update

* print equation and latex components correctly

* initialisation of new files

* splitting classes into separate files

* removed classes file and new documentation

* docs for helpers functions

* added support of documentation for non latex environments

* bugfix issue 52 missing plots

* recompiled documentation and small fixes

* removed unnecessary example, that causes trouble

* recompile documentation

* moved duplicated verbose_cat to helper file

* list of colors moved to helpers file

* Styling changes

---------

Co-authored-by: nizwant <[email protected]>

* new plate class

* add layout function description

* added definition of translate_sample_names_to_sample_types function

* Remove old classes

* Remove all examples

* Builder pattern for Plate. New standard_curve.R implementations (#62)

* Remove examples from standard_curves

* Use BuilderPattern for plate creation

* Implement test for helper functions

* Make default unset values nullable

* Move the valid checking to non mutable global variables

* Change getter method naming

* Reimplement first standard curve function with new plate structure

* Make dilution encoder more robust. Create better test plate

* Add missing docs for is_valid_*

* Implement creating the analyte model with new plate structure

* Reimplement predict_dilutions

* Rewrite the last standard_curve.R function

* New parser for xponent and intelliflex files (#44)

* Remove examples from standard_curves

* Use BuilderPattern for plate creation

* Implement test for helper functions

* Make default unset values nullable

* Move the valid checking to non mutable global variables

* Change getter method naming

* Reimplement first standard curve function with new plate structure

* Make dilution encoder more robust. Create better test plate

* Add missing docs for is_valid_*

* Implement creating the analyte model with new plate structure

* Reimplement predict_dilutions

* Rewrite the last standard_curve.R function

* Add covid and external data

* Rename file and add a second plate from Covid OISE

* First version of the new parser

* Fix results parsing, add more info to lines

* Add eof parser to validate fully parsing a file

* Implement backbone for error printing

* Adapt all parsers to new error handling

* Add external data tests and fix protocol heater

* Fix edgecase, rename parser function

* Allow changing the separator and encoding of a file

* Make join_parsers more readable

* Remove na rows

* Fix quoting in reading a csv

* Change global variable modification

* Fix quoting

* Implement intelliflex format parsing

* Merge inst from dev

* Add missing comma

* Implement skipping header part of a xPONENT file

* Make is_line_blank more robust

* Remove the need for a global variable

* Fix NAMESPACE

* Add missing documentation and export

* Remove duplicate code

* Rename files to follow the convention

* Remove dummy test

* Better parser (#65)

* Remove examples from standard_curves

* Use BuilderPattern for plate creation

* Implement test for helper functions

* Make default unset values nullable

* Move the valid checking to non mutable global variables

* Change getter method naming

* Reimplement first standard curve function with new plate structure

* Make dilution encoder more robust. Create better test plate

* Add missing docs for is_valid_*

* Implement creating the analyte model with new plate structure

* Reimplement predict_dilutions

* Rewrite the last standard_curve.R function

* Add covid and external data

* Rename file and add a second plate from Covid OISE

* First version of the new parser

* Fix results parsing, add more info to lines

* Add eof parser to validate fully parsing a file

* Implement backbone for error printing

* Adapt all parsers to new error handling

* Add external data tests and fix protocol heater

* Fix edgecase, rename parser function

* Allow changing the separator and encoding of a file

* Make join_parsers more readable

* Remove na rows

* Fix quoting in reading a csv

* Change global variable modification

* Fix quoting

* Implement intelliflex format parsing

* Merge inst from dev

* Add missing comma

* Implement skipping header part of a xPONENT file

* Make is_line_blank more robust

* Remove the need for a global variable

* Fix NAMESPACE

* Add missing documentation and export

* Remove duplicate code

* Rename files to follow the convention

* Remove dummy test

* Layout parser (#64)

* Move tymek implementation

* Generate a real csv file for tests

* Implement the layout parser

* Add parser documentation

* Name form luminex of layout file to sample type (#66)

* temporary place to develop and test function to derive type and dilution

* removed deriving dilutions in this function

* Refactor derive_sample_type function to handle vector of strings

* rename passed arguments to plural

* insert new function implementation into code base

* remove tmp file

* tests of deriving type from names

* positive control more generic recognition and compatibility with newer R versions

* Make roxygen happy

* Parser (#67)

* Base of the parser implementation

* Create parser integration tests

* Remove intermediate functions from user access

* Add R6 to class import

* Integrate parser with validated input

* Fix typo

* Make R6 only importFrom

* Blank adjustment (#68)

* Base of the parser implementation

* Create parser integration tests

* Remove intermediate functions from user access

* Integrate parser with validated input

* Fix typo

* Reimplement blank-adjustment

* Fix parsing dilutions (#70)

* fixed log scale for plots #72 (#75)

Co-authored-by: Fersoil <Fersoil>

* Implement boxplot for MFI (#69)

* Implement boxplot for MFI

* Reimplement mfi plot for test samples

* Encapsulate model (#76)

* Reimplement standard curve model WIP

* Fix model plot_data sequence

* Fix indentation

* Make roxygen happy

* Reimplement standard curve plotting

* Rename SCModel to Model

* Add docs for init, plot_data, predict method for Model

* Move top bottom asymptote to active fields

* Add missing docs for generic functions

* Fix typo

* Add print method and examples

* Rename model to classes-model

* Move replicated code to a private function

* Rename plot_data to get_plot_data

* Fix typo

* Improve performace of a hot loop in the xponent parser (#82)

* Improve performace of a hot loop in the xponent parser

* fixed quotation marks

---------

Co-authored-by: Tymoteusz Kwieciński <[email protected]>

* Dilution detection (#80)

* updated the extraction of dilutions

* renamed setters for dilutions and types as `set_*` instead of `extract_*`; added active field for converting the layout into the vector; verbosity; error fixes

* fixed errors; added warnings

* added tests, verbosity parameter to the reading function

* update docs

* fixes of indicated bugs

---------

Co-authored-by: Fersoil <Fersoil>

* Add more information to standard curve plots (#87)

* Improve performace of a hot loop in the xponent parser

* Allow extracting data for all analytes

* Model: Allow setting min and max mfi for scaling

* Improve the quality of the sc plots

* Model: Adjust lower bound

* fix typos

* plot labeling

* additional plot parameters

---------

Co-authored-by: Tymoteusz Kwieciński <[email protected]>
Co-authored-by: Fersoil <Fersoil>

* validation and docs after refactor (#85)

* docs and validation for `Plate` class

* additional documentation - better display of available sample and data types

* typos

* reuse the data types from plate class

* added `...` documentation

* minor docs changes

* verbose options for main reading function

* suppress verbosity during tests

* add sample example script

* consistency in naming the function parameters `analyte` -> `analyte_name`

* removed doubled output during plate creating

* updated the vignette with example script

* set `plate_name` as the filename, the old plate name is now called `batch_name` #77

* added tests for #77

* changes made according to the comments

---------

Co-authored-by: Fersoil <Fersoil>

* More detailed plate summary (#84)

* copying the old summary method

* add S3 style summary function

* extensive summary

* S3 method proper implementation

---------

Co-authored-by: nizwant <[email protected]>
Co-authored-by: Fersoil <Fersoil>

* plots of plate - counts and layout  (#71)

* initial plot_plate functionality

* code refactoring

* creating a function out of code for plotting

* handle plotting numbers in wells and finally path to image that works

* handling errors

* install packages moved to description

* plot counts

* plot layout

* Add dependencies properly and remove code use for tests

* documentation for plot plate functionalities

* new colours and refactoring

* added scaling of numbers size

* bold title font and slight tweaks to points size

* finally legend (it was a pain)

* updated docs and stylistic changes

* examples in docs

* plate as an argument

* bugfix

* count plot is working

* layout is working

* add examples to plot layout and plot count

* rerun roxygen

* fixes pt.1

* fixes pt.2

* docs update

* better documentation

* better documentation pt.2

* automatic dosc generation

* fixes of documentation

* Plate layout (#94)

* sample names from layout

* simple layout validation

* some simple docs

---------

Co-authored-by: Fersoil <Fersoil>

* feat: model carrying more info (#92)

* add analyte into the model

* `plot_standard_curve_with_model` adapted to the changes

* fix error #90

---------

Co-authored-by: Fersoil <Fersoil>

* Our plots vignette (#97)

* introduction to our plots

* plot layout

* plot counts description

* remove ggplot dependency

* renaming of plots file

* mfi

* roxygen update

* change to valid antibody and bug fix

* standard curve without model

* plot with model pl1

* plot with model pt2

* typos pt1

* typos pt2

* typos pt3

* error fixes: removed `dilutions_from` parmeter

* error fixes: fixed the `plot_standard_curve_analyte` syntax in tests

* fix dependencies

* fix errors: examples in internal functions

* supplementing the documentation

* fix errors: internal function in docs examples

* added plate tests

* added tests

* typo fixes

* tests for `plot_plate` removed `require` statement

---------

Co-authored-by: nizwant <[email protected]>
Co-authored-by: Tymoteusz Kwieciński <[email protected]>
Co-authored-by: Fersoil <Fersoil>

* Display outliers only for boxplot

* Alternate the outlier label to avoid overcrowding

---------

Co-authored-by: Mateusz Nizwantowski <[email protected]>

* remove overlap

* add dependencies

* Clamp method implementation

* Reimplement blank adjustment

* Small visual fix for vignettes

* added new blank adjustment test

* test fixes

* Update R/classes-plate.R

Co-authored-by: Tymoteusz Kwieciński <[email protected]>

---------

Co-authored-by: Fersoil <Fersoil>
Co-authored-by: Tymoteusz Kwieciński <[email protected]>

* Fix: layout indeed can be longer the samples

* Update docs

* Fix: layout indeed can be longer the samples

* Update docs

* Basic implementation of process plate function

)

* Make plot_layout and plot_counts look a little better in vignetts

* fixed the plate plot generation

* typo fix

---------

Co-authored-by: Fersoil <Fersoil>

* news and package version update

* fix #108

* tests for #108 fix

* fix typos

---------

Co-authored-by: Fersoil <Fersoil>

* correct mistakes in vignettes

* styling

* grammar mistakes

* how to link your own files

---------

Co-authored-by: Tymoteusz Kwieciński <[email protected]>