mikeblazanin gcplyr issues

mikeblazanin / gcplyr

gcplyr is an R package that facilitates wrangling and analysis of microbial growth curve data

https://mikeblazanin.github.io/gcplyr/

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issues

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Replace \code calls in documentation with \link where appropriate

#216 mikeblazanin closed 2 hours ago
0
Add centroids

#215 mikeblazanin closed 3 days ago
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train_calc_deriv

#214 mikeblazanin opened 1 month ago
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Allow sep when using import_blockdesigns and join_designs = FALSE

#213 mikeblazanin closed 23 hours ago
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Add parallel calculation backend

#212 mikeblazanin opened 2 months ago
1
Explore smooth.spline more to see if I should demo/recommend it in more depth

#211 mikeblazanin opened 3 months ago
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Add method to calculate growth rate using regularization

#210 mikeblazanin opened 4 months ago
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Add regularization smoother

#209 mikeblazanin opened 4 months ago
1
Add moving average with other kernels

#208 mikeblazanin opened 4 months ago
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use stats::runmed for moving_median

#207 mikeblazanin opened 4 months ago
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Build function for cross-validation selection of smoothing parameter

#206 mikeblazanin closed 3 months ago
4
add warn_* arguments to calc_deriv

#205 mikeblazanin closed 4 months ago
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Double warning when log(y) in calc_deriv leads to infinite values

#204 mikeblazanin closed 4 months ago
1
Allow ignoring of warning for infinite values treated as NA in calc_deriv

#203 mikeblazanin closed 4 months ago
2
Better warning for calc_deriv when window width is too narrow and so there are fewer than 2 points present

#202 mikeblazanin closed 4 months ago
0
Add description of other calculation(s) of lag time

#201 mikeblazanin opened 4 months ago
0
Add note that lag_time has a minimum value of min(x[!is.na(x) & !is.na(y)])

#200 mikeblazanin closed 4 months ago
2
use cellranger to permit more flexible specification of input locations in read_ and import_ functions

#199 mikeblazanin opened 4 months ago
0
use cellranger rather than to_excel and from_excel?

#198 mikeblazanin opened 4 months ago
0
bug in lag_time where min density is being calculated as higher than it should be because deriv is NA

#197 mikeblazanin closed 4 months ago
2
Is extr_val behavior with NA's as intended?

#196 mikeblazanin opened 4 months ago
1
Move make_design content to its own vignette

#195 mikeblazanin closed 3 months ago
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Add pasted files to design vignette

#194 mikeblazanin closed 3 months ago
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broken link in design vignette: "[Merging spectrophotometric and design data]"

#193 mikeblazanin closed 4 months ago
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import_blockdesigns doesn't have a file column in output

#192 mikeblazanin closed 4 months ago
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separate_tidy is not run within import_blockdesigns if length(files) == 1

#191 mikeblazanin closed 4 months ago
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make default behavior of first_minima and first_maxima more obvious

#190 mikeblazanin closed 4 months ago
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window_width_frac option for analyze function

#189 mikeblazanin closed 4 months ago
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auc gives a warning when xlim is set to values where the x value is present but the y value is NA

#188 mikeblazanin closed 4 months ago
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Use checkmate to check inputs more thoroughly

#187 mikeblazanin opened 5 months ago
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implement subset argument for lag_time

#186 mikeblazanin opened 5 months ago
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Difference between percap growth rate from gcplyr and from other packages

#185 mikeblazanin closed 5 months ago
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tests for how extr_val handles out-of-range indices?

#184 mikeblazanin closed 5 months ago
0
find_threshold_crosses should treat the first and last subset=TRUE values as the endpoints

#183 mikeblazanin closed 5 months ago
1
Handle NA values in subset argument in all analyze functions

#182 mikeblazanin closed 5 months ago
1
read_blocks has argument for block_name_header, should probably be changed to block_names_header for consistency and block_name_header deprecated

#181 mikeblazanin closed 6 months ago
0
Allow leading or trailing NA in calc_deriv when window_width_n = 2

#180 mikeblazanin opened 6 months ago
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Rename extension argument to filetype

#179 mikeblazanin closed 6 months ago
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Add use of ifelse statements into the multiple plates vignette

#178 mikeblazanin opened 6 months ago
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Add information on experimental setup best practices as vignette

#177 mikeblazanin opened 6 months ago
2
When auto-creating block-name or file-name column, have settings to cut out path/extension

#176 mikeblazanin closed 6 months ago
1
Allow use of other read.table defaults

#175 mikeblazanin closed 7 months ago
0
rename objects like temp throughout to be more function-specific so that error messages are more meaningful

#174 mikeblazanin closed 5 months ago
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error when reading txt files and extension is not specified

#173 mikeblazanin closed 7 months ago
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Better error message when no files are specified to import_ or read_ functions

#172 mikeblazanin closed 7 months ago
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Add message with number of dropped rows when drop = TRUE in merge_dfs

#171 mikeblazanin closed 8 months ago
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separate_tidy tries to coerce NA values into NA

#170 mikeblazanin closed 8 months ago
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read functions don't respect na.strings argument when reading csv files

#169 mikeblazanin closed 8 months ago
0
Add warning when metadata rows/cols are out of range

#168 mikeblazanin closed 8 months ago
0
Allow specification of join type in merge_dfs

#167 mikeblazanin closed 8 months ago
0