# spatialFDA 1.3.3
* rewrote `summary.functionalGam` and added a new `coef.functionalGam` to have no 
breaking changes in `spatialFDA` due to changes in `refund::pffr` naming.
* this makes `spatialFDA` again compatible with the `OSTA` chapter.

# spatialFDA 1.3.2
* covariance matrices are now corrected for cluster-correlations along
the domain $r$ with sandwich-estimators by default - thank you @fabianscheipl
for implementing this in `refund::pffr`
* models can now also be fit with `gamm4`
* Experimental: implemented an AR(1) penalty along the domain $r$ in `bam` fits. This
is to some extent already adressed by the cluster-robust sandwich estimators so 
might be removed in the future. 

# spatialFDA 1.3.1
* option to square-root transform the weights in the functional Gam
* changes to cutoff calculations at the saturating end of $G$ functions
* fix `as.formula` calls by passing an `empty.env` call
* cleaned up `spatialInference` from exploratory code.

# spatialFDA 1.1.22
* fix sample_id call if model is a GAM instead of GAMM.
* added the option to define a ridge penalty parameter which is added to the matrix $H$ as defined in `mgcv::gam`. In order to do this we need the number of parameters `p` from a prefit of the model.

# spatialFDA 1.1.21
* allowing for the explicit passing of `correction` in `spatialInference`
and `crossSpatialInference` to fix issues with calculating `Lcross`.
* passing messages with verbose logical for better usage
* bug fix in tests with removed `subsetby` argument

# spatialFDA 1.1.20
* only returning the transformed curves in `spatialInference` plus removing
the assays and the rowData for faster computations.

# spatialFDA 1.1.19
* fixing `plotFbPlot` ylims across conditions to have the same range-

# spatialFDA 1.1.18
* removed the argument `subsetby` from `spatialInference` and 
`crossSpatialInference` as this will always be the same as `image_id` in this 
function
* indicated in the documentation that `...` in `spatialInference` and 
`crossSpatialInference` is passed to both `spatstat.explore` functions and
to `refund::pffr`. 

# spatialFDA 1.1.17
* added an assertion that the maximum radius considered must always be smaller
than the maximum window length of each image.
* added a test for this case
* add a heuristic to check for a convenient and good rMax to consider
* added heuristic to the vignettes

# spatialFDA 1.1.16
* adjusted that all failed `calcMetricPerFov` output NA in the dimension
of rSeq, clearly stating which values in `metricRes` where NA. 
* return the raw non-filtered `metricResRaw` in `spatialInference` as well as 
the filtered `metricRes` for comparison.
* implemented option to add different QC metrics of the functional model and
plot them with different shapes in `plotCrossHeatmap`
* adapted the overview vignette to plot the raw spatial statistics curves 
* accelerated all examples and tests with functional GAM via `algorithm = "bam"`

# spatialFDA 1.1.15
* added a test to check the edf values and order from the RSE calculation. 
Made the RSE code more robust.
* added progressbar in `crossSpatialInference`.
* adapted the overview vignette to reflect the recent changes.

# spatialFDA 1.1.14
* change the sum of mean residuals per condition to be the residual standard
error. The main reason is to have a more comparable estimator of model fit
by dividing by the degrees of freedom per condition. The degrees of freedom
are the no. of data points per condition (no. of curves * data points per curve)
- the sum of the estimated degrees of freedom of the parameters per condition as
provided by the summary.pffr() output.

# spatialFDA 1.1.13
* provide the condition-wise sum of mean residuals across the curves. This is a 
measure to judge the quality of the fitted functional GAM by condition.
* allow for an automated threshold selection `delta` in `spatialInference`
based on the mean over all images of the minimum nearest neighbour distance
between points. Added test for this use case

# spatialFDA 1.1.12
* changed the thresholding in `calcMetricPerFov` from having at least 1 point
per (sub)point pattern to at least two in order to avoid having images with 
way to uncertain curves. In order to accommodate for this change some tests and
examples had to be adapted
* `spatialInference` now prints the adjusted R squared to quickly assess overall
model fit. As this is just one summary, still rigorous assessment via qq plots
and autocorrelation should be performed.

# spatialFDA 1.1.11
* Change in the weighting procedure in `spatialInference` and no calculation of 
weights in `calcMetricPerFov`. It is now possible to define custom weights, 
by equal weights, by the total number points, and for multitype processes by the 
smaller point pattern (min) and the larger point pattern (max)
* Option to extract the mean functional coefficient of the functional GAM over
the domain $r$ as a measure of the effect size in `extractCrossInferenceData`
* `plotCrossHeatmap` creates now a bubble plot with the effect size being the
colour and the size of the bubble being the p-value

# spatialFDA 1.1.10
* p-value adjustment option in `plotCrossHeatmap` and filtering of coefficients
for the heatmap. Fix some small global variable defintion errors

# spatialFDA 1.1.9
* enabling Fisher's variance-stabilising transformation in `spatialInference`
as it is recommended for $G$ functions.

# spatialFDA 1.1.8
* adding a constant to the log in `plotCrossHeatmap` to avoid NULL values being
plotted

# spatialFDA 1.1.7
* Fixing error in `plotCrossHeatmap` when the model is NULL.

# spatialFDA 1.1.6
* Error handling in `spatialInference` when one condition has no images with curves.
* Wrote as well a new test for this case

# spatialFDA 1.1.5
* New overview vignette, showing the usability of `spatialInference`
* Plotting of a heatmap from extracted from `crossSpatialInference`
* Adding of the package sticker to the README

# spatialFDA 1.1.4
* `functionalGAM` accepts flexible naming of the intercept column.

# spatialFDA 1.1.3
* changed the default of the GAM estimation to be a Gaussian with log link for
positivty of the response

# spatialFDA 1.1.2
* wrote a new convenience function `crossSpatialInference` which makes the 
estimation across a range of cell types easier.

# spatialFDA 1.1.1
* wrote a new convenience function `spatialInference` which makes the FDA estimation
of the spatial statistics functions simpler
* in order to do this various changes to `prepData` were introduced
* furthermore, small syntactic changes for the retrieval of the functional
intercept were added to `functionalGam` and `plotMdl`
* The vignette was simplified to reflect the changes in `prepData`

# spatialFDA 0.99.14
* changed the example in the Vignette to scaled t-dist. with log link due to 
lower AIC than Gaussian.

# spatialFDA 0.99.13
* changed the example in the vignette to Gaussian with log link and smooth
random intercept.

# spatialFDA 0.99.12
* Changed indexing of spatial coordinates to positional index. Names can differ
between objects, e.g. "x" or "coord_x" etc. therefore, positional index 
generalises better.

# spatialFDA 0.99.11
* major changes in fixing the levels of the mark factors in the point pattern.
Prior to this fix, it could happen that the marks in `selection` do not correspond
to the marks in the point pattern and therefore give the inverse result.

# spatialFDA 0.99.10
* minor bug fix 

# spatialFDA 0.99.9
* remove `imcdatasets` dependency and instead download example data directly
from `ExperimentHub`
* added small reader function `.loadExample` to download the data mentioned 
above

# spatialFDA 0.99.8
* more packages explicitly named
* vignette shows use of PCA based random errors and exchanged one sample

# spatialFDA 0.99.7
* explicit package naming for functions to make compatible with linux distributions
* possible to pass `...` parameters to fPCA method

# spatialFDA 0.99.6
* small error correction in show fPCA method

# spatialFDA 0.99.5
* change in how failures in `calcMetricPerFov` are handled. Works now as well
if `rSeq = NULL`

# spatialFDA 0.99.4
* variable `ID` is no longer created in `calcMetricPerFov`
* adjusted examples and vignette to the above
* added option to extract gene expression directly in `calcMetricPerFov` if
`continuous = TRUE`
* small bug fix in `calcMetricPerFov` to pass `...` in all cases
* added variables `legend.position` and `ncol` to `plotMetricPerFov`

# spatialFDA 0.99.3
* adjusted `by` variable to work with length 1
* adjusted `...` in `plotMetricPerFov` to be passed only to `geom_line`

# spatialFDA 0.99.3
* adjust examples to build in under 10 min

# spatialFDA 0.99.2
* Rewrote vignette with smaller dataset
* Implemented quasi likelihood family in vignette to improve variance estimation
* Adjustd calcMetricPerFov.R to be able to calculate cross functions

# spatialFDA 0.99.1
* Adressed Bioconductor review
* Added unit tests
* Added functional boxplots
* Added diagnostic plots to vignette

# spatialFDA 0.99.0
* Initial Bioconductor submission.
