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Bring tara-main up to date with mike's 'main' #3

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Bring tara-main up to date with mike's 'main' #3

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b89690d
git glm poisson and qpoisson to song_count, glm_gamma to song_prop
mikegilchrist Oct 27, 2022
a0b95b1
minor change in line spacing
mikegilchrist Oct 31, 2022
43fee72
working with FE models, adding and evaluating round 2 data.
mikegilchrist Oct 31, 2022
6e2e91e
add useful article/lecture notes on poisson regression and its extens…
mikegilchrist Oct 31, 2022
e4e3d01
plot var vs. mean for round 2. Should add error bars for more context.
mikegilchrist Nov 1, 2022
f6b90c8
use bootstraps() and rename file.
mikegilchrist Nov 1, 2022
9c461f5
add round 2 using target temp
mikegilchrist Nov 3, 2022
8a22f6e
minor renaming of folder
mikegilchrist Nov 3, 2022
dde792a
add reference on HMC
mikegilchrist Nov 3, 2022
5564cd6
renamed folder
mikegilchrist Nov 3, 2022
42c7a7e
removing males with extremely high variances suggests var = phi mean.
mikegilchrist Nov 4, 2022
0559988
add evaluation of var vs. mean using repeated measures at 40C
mikegilchrist Nov 4, 2022
2c1bf53
working on brms fittings.
mikegilchrist Nov 4, 2022
862f41b
minor tweaks to printing of mean vs. var analysis.
mikegilchrist Nov 4, 2022
5eaf3c1
minor edit: add dispersion term.
mikegilchrist Nov 9, 2022
516adbc
add references for regression and thermal experience.
mikegilchrist Nov 9, 2022
b08dcdc
move processing of raw data to own folder
mikegilchrist Nov 9, 2022
82aace4
begin working on rTPC fitting to filtered data.
mikegilchrist Nov 9, 2022
5cb32a1
minor tweaks to data processing
mikegilchrist Nov 11, 2022
49e93ff
rTPC fits running to combined data. Ugly.
mikegilchrist Nov 11, 2022
ac03caa
add some references
mikegilchrist Nov 11, 2022
1a60c38
brms runs but ofetn get memory issues.
mikegilchrist Nov 11, 2022
fc0efac
add 46C augmented data & more progress in working with nls
mikegilchrist Nov 14, 2022
d8c3a27
working on getting all model fits to examine consistency of best fit.
mikegilchrist Nov 21, 2022
9e10208
add Padfield and LevesqueAndMarshshall2021 references
mikegilchrist Nov 29, 2022
489cd51
stan normal and poisson routines running
mikegilchrist Nov 30, 2022
9d42d1b
more progress in fitting piecewise function with stan.
mikegilchrist Nov 30, 2022
447ad46
poisson piecewise model using stan directly is working
mikegilchrist Dec 1, 2022
d0d39a2
work on plotting of model predictions and data
mikegilchrist Dec 1, 2022
a12d646
add references on segmented and qpoisson vs. nb
mikegilchrist Dec 2, 2022
98a5210
abandon plotting for now. Move on to using brms.
mikegilchrist Dec 2, 2022
aede458
old update to pdf
mikegilchrist Dec 2, 2022
8dc5338
add various old files.
mikegilchrist Dec 2, 2022
496ffdc
Rename folder
mikegilchrist Dec 2, 2022
dbcd871
rename brms folder
mikegilchrist Dec 2, 2022
88328e7
add brms with piecewise fitting
mikegilchrist Dec 5, 2022
d0767ae
continue working on brms version of step wise
mikegilchrist Dec 5, 2022
30ae84b
ensure song_count and song_count_plus_1 are integers
mikegilchrist Dec 6, 2022
b249f60
non-working version of brms_two.piece...
mikegilchrist Dec 9, 2022
faa0740
add references on brms and linking nb to qpoisson
mikegilchrist Dec 9, 2022
ec819e5
simulate data for two piece
mikegilchrist Dec 13, 2022
418a726
update sim code to use observed values for y0
mikegilchrist Dec 13, 2022
a9537ea
stan code for poisson model with a level for male compiles and runs.
mikegilchrist Dec 14, 2022
0e34d37
pooled poisson works
mikegilchrist Dec 14, 2022
439365d
Combine pars_sim and pars_est into single tibble
mikegilchrist Dec 15, 2022
a90e49c
plot sim (truth) vs. est using facet wrap
mikegilchrist Dec 15, 2022
b80c829
Merge pull request #1 from KMesserly/main
mikegilchrist Dec 15, 2022
99bd9f4
renamed data folders to be more concise and accurate
mikegilchrist Dec 15, 2022
addace2
replace 'raw_data' with 'collated' in *.Rmd files
mikegilchrist Dec 15, 2022
f09b7cc
add xls and exported .csv files with temp and humidity data
mikegilchrist Dec 15, 2022
0dbecd1
reformatted and copied data for round 1 to file previously used file …
mikegilchrist Dec 15, 2022
f75236a
replace 'song_count' with 'motif_count'
mikegilchrist Dec 15, 2022
840e144
update repeatability (round 2 in R code) file with temp and humidity …
mikegilchrist Dec 15, 2022
12ee4fa
minor edit: replace song_rate with motif_rate
mikegilchrist Dec 15, 2022
06e6325
replace 'song_*' with 'motif_*' to match updated data files
mikegilchrist Dec 15, 2022
96a63aa
update folder name
mikegilchrist Dec 15, 2022
a278e84
update data.processing files and .Rda output to use motif_count
mikegilchrist Dec 15, 2022
9e25239
working on qpoisson model.
mikegilchrist Dec 19, 2022
9fe0f55
Qpoisson not running
mikegilchrist Dec 19, 2022
2268dad
qpoisson model working! at least the pooled version.
mikegilchrist Dec 19, 2022
952f9cc
Analysis of simulated data with qpoisson and male effects working!
mikegilchrist Dec 20, 2022
9b5f522
renamed simulation folder
mikegilchrist Dec 20, 2022
90b15d9
analyzed real data and got somewhat dispiriting results
mikegilchrist Dec 21, 2022
9d024af
additional work with plotting results
mikegilchrist Dec 21, 2022
43f183f
rename folders and add today's folder
mikegilchrist Dec 21, 2022
5b924a7
add input folder
mikegilchrist Dec 21, 2022
4cc06ae
minor edit: comment out cmdstan
mikegilchrist Dec 22, 2022
c820565
flexible qpoisson where grouping x0, y0, and theta can be specified
mikegilchrist Dec 22, 2022
1f950f6
Begin working on consistent and compact use of qpoisson 2.0
mikegilchrist Dec 23, 2022
eb02cb2
model comparison working, still need to add plotting
mikegilchrist Dec 23, 2022
da54111
advance loo for qpoisson models, compilable nb model
mikegilchrist Dec 24, 2022
c95077f
Rename various folders and files more accurately.
mikegilchrist Jan 3, 2023
2862663
refine code so that qpoisson and nb fits can be easily compared.
mikegilchrist Jan 9, 2023
3e9cc39
add work using brms and piecewise function
mikegilchrist Jan 11, 2023
d41da79
minor edits related to rendering .Rmd, add pdf
mikegilchrist Jan 11, 2023
03cc000
begin generating simulated data to ensure models fitting as expected.
mikegilchrist Jan 12, 2023
721b398
changed phi prior from a exponential to a gamma distribution
mikegilchrist Jan 12, 2023
9cc5ec3
fix issues with simulating data
mikegilchrist Jan 12, 2023
b928a2f
refine simulation routines
mikegilchrist Jan 12, 2023
dd74730
begin work on MWE for quesitons on brms
mikegilchrist Jan 12, 2023
9a15e26
add analysis of var(temp_mean) vs temp_target
mikegilchrist Jan 13, 2023
83684c8
improve temp vs var
mikegilchrist Jan 13, 2023
22adfb3
add more realistic simulation routines
mikegilchrist Jan 13, 2023
fd35bd9
Add `print(fit)` to qpoisson and nb model fits
mikegilchrist Jan 13, 2023
1602c3a
create large simulated dataset structured by x/y_flags and n_reps
mikegilchrist Jan 17, 2023
9f15243
update data_sim to one `motif_count` col, add `sampling_dist` col
mikegilchrist Jan 17, 2023
8eccd0a
BRMS fit to simulation data seems to work
mikegilchrist Jan 17, 2023
7a368a6
split simulation work from analysis of real data
mikegilchrist Jan 18, 2023
31566c6
add *.rds, *.html, and #* to .gitignore
mikegilchrist Jan 18, 2023
864722d
updated folder name
mikegilchrist Jan 18, 2023
7405bdf
rename files in preparation of future merge
mikegilchrist Jan 18, 2023
180e133
revisit and revise previous brms fittings.
mikegilchrist Jan 19, 2023
a4e6eaa
merged in updated data analysis, need to add in early one from 01-09
mikegilchrist Jan 20, 2023
ec55bea
restored folder 2023-01-09 from commit d74730 on Jan 12 2023
mikegilchrist Jan 20, 2023
d3e1fc4
resolved merge conflicts in individual files.
mikegilchrist Jan 20, 2023
0148935
More edits to resolve merge
mikegilchrist Jan 23, 2023
f988e09
add work from 2022-12-31.
mikegilchrist Jan 23, 2023
32753b9
begin working on loops for model fitting to largest dataset.
mikegilchrist Jan 24, 2023
14c727a
restored rstan.and.brms_two.piece_fit.various.models.to.real.data.Rmd…
mikegilchrist Jan 24, 2023
0368a46
add to .gitignore
mikegilchrist Jan 30, 2023
6c344d7
Prevent listing of pdf files by default.
mikegilchrist Jan 30, 2023
ad58c1e
Complete analysis of `groups_2, groups_2` data
mikegilchrist Jan 31, 2023
ab8e509
improving quality of simulations
mikegilchrist Feb 2, 2023
d18a970
add initial and incomplete visualization code
mikegilchrist Feb 2, 2023
513adae
Remove cruft at end of brms_.. simulated data file
mikegilchrist Feb 2, 2023
eab4c6e
Replace xx and yy with x_group and y_group
mikegilchrist Feb 2, 2023
7b5aef8
more tweaking of variable names x_group -> x0_group in brms create sim
mikegilchrist Feb 2, 2023
dc55f2e
propagate x_group to x0_group in plotting file
mikegilchrist Feb 2, 2023
276f34e
believe I have model correctly specified for brms
mikegilchrist Feb 3, 2023
8a3ba82
Fix error of previous commit. model formulation is correct here
mikegilchrist Feb 3, 2023
e6f3c52
working generation and analysis of simulated data.
mikegilchrist Feb 7, 2023
719f70d
working version for analyzing real data. Results are not promising.
mikegilchrist Feb 7, 2023
37e31a3
Begin making fitting function that can use columns in fit_tbl
mikegilchrist Feb 7, 2023
4ead300
Revert "Begin making fitting function that can use columns in fit_tbl"
mikegilchrist Feb 8, 2023
c74bd62
working analysis of real data
mikegilchrist Feb 8, 2023
1aeec6b
correct date for fitting folder
mikegilchrist Feb 8, 2023
148894f
add summary notes to file.
mikegilchrist Feb 8, 2023
e6ba417
standardize folder names
mikegilchrist Feb 8, 2023
3dadcac
minor change in parameter values
mikegilchrist Feb 9, 2023
4dccd79
fix minor typo in knitr settings
mikegilchrist Feb 9, 2023
6724230
Fix erroneous statement about upper bound to `x0`'s CI
mikegilchrist Feb 9, 2023
eb4cb7a
add *tmp to .gitignore
mikegilchrist Feb 10, 2023
11a4c07
Add possibility of saving of data_stan and have most R output saved a…
mikegilchrist Feb 10, 2023
b189421
removed 01-09 folder that was replaced with 01-16 folder
mikegilchrist Feb 13, 2023
15b3674
minor update to .gitignore
mikegilchrist Feb 16, 2023
dbf2748
Merge branch 'main' of ssh://github.com/mikegilchrist/ZEFI-Thermal-Cu…
mikegilchrist Feb 16, 2023
b95788e
update .gitignore to include .stan files.
mikegilchrist Feb 21, 2023
4c1fef9
add new plotting routines.
mikegilchrist Feb 21, 2023
cc14deb
working on com_poisson fitting.
mikegilchrist Feb 22, 2023
fc866e9
add file examining standard and constrained (qpoisson) nb regression.
mikegilchrist Feb 25, 2023
46626ac
build custom_family for overdispersed poisson.
mikegilchrist Feb 26, 2023
50c4dc9
add mathematica file looking at replacing shape with mu/(theta-1).
mikegilchrist Feb 26, 2023
2e0e8ce
minor renaming of variables for qqpoisson family in brms
mikegilchrist Feb 27, 2023
3bd6c36
edits prior to working on version for repo
mikegilchrist Feb 28, 2023
3faf4cb
added note about nature of NB I'm using
mikegilchrist Feb 28, 2023
06b1c19
minor changes in unpromising approach.
mikegilchrist Feb 28, 2023
5592162
add separate folder for processing data for focused fittings.
mikegilchrist Feb 28, 2023
cb0f90d
minor updates to files examining type I nb.
mikegilchrist Feb 28, 2023
8b05921
dealt with missing (really renamed) .nb file.
mikegilchrist Feb 28, 2023
37ab1b8
suppress plot warnings
mikegilchrist Mar 3, 2023
3bf7c17
Progress!! Figured out what was wrong with (some) of my brms runs
mikegilchrist Mar 3, 2023
d1d1010
minor edits and newly rendered pdf.
mikegilchrist Mar 4, 2023
8da8dd7
added generated on Feb 28th
mikegilchrist Mar 4, 2023
5d90593
Direct knitr output to own folder.
mikegilchrist Mar 4, 2023
3cb8d62
fix typo that kept groups_1 fittings from working.
mikegilchrist Mar 6, 2023
f4a557d
many changes, not convinced it's all working right
mikegilchrist Mar 8, 2023
bad525e
Few more fixes and code is running well again.
mikegilchrist Mar 8, 2023
f5684e7
Set up fitting slope like parameter `s0` instead of threshold `x0`.
mikegilchrist Mar 9, 2023
358c131
Minor tweaks to get runs to work as desired
mikegilchrist Mar 9, 2023
7e5eb71
fixed mistake in file name (was type2, now type1)
mikegilchrist Mar 9, 2023
208463f
Thought I committed these minor tweaks in last commit.
mikegilchrist Mar 9, 2023
bf316a1
Created separate file for visualizing 2022-02-28 nb ytpe 1 fits
mikegilchrist Mar 9, 2023
c052fc6
Create two nice options for plotting posterior samples
mikegilchrist Mar 10, 2023
561a021
minor edit to deal with plotting cruft at end of for loops
mikegilchrist Mar 10, 2023
a5c5972
minor fix to output file names, version used with flat y0 prior
mikegilchrist Mar 10, 2023
8fcf13c
add switch for individual prior of y0
mikegilchrist Mar 10, 2023
3af0e90
html for output with uniform y0 prior (or so I think)
mikegilchrist Mar 10, 2023
a6a1c67
Merge remote-tracking branch 'refs/remotes/origin/main'
mikegilchrist Mar 10, 2023
349ae7d
minor modifications to run settings
mikegilchrist Mar 13, 2023
963c35d
add plots of samples, model predictions, and data
mikegilchrist Mar 13, 2023
92ed3fd
minor plot update. Still can't plot predicted range, likely due to Na…
mikegilchrist Mar 18, 2023
df93e6e
add notes about qpoisson really being nb and few other tweaks.
mikegilchrist Mar 18, 2023
65b67ee
add README.md with notes on qpoisson.
mikegilchrist Mar 18, 2023
c133819
add local .gitignore using echo command
mikegilchrist Mar 18, 2023
dc20169
rename type2 to type1
mikegilchrist Mar 18, 2023
c40466b
add new analysis allowing disp to vary b/w individuals
mikegilchrist Mar 20, 2023
e6e04e2
add directory structure
mikegilchrist Mar 20, 2023
dd8cb14
add asymptotic model and filtering of males with large disp values.
mikegilchrist Mar 21, 2023
94b80de
rename file to reflect changes in previous commit
mikegilchrist Mar 21, 2023
42afab3
Fix minor typo
mikegilchrist Mar 21, 2023
df9c803
add creation of .csv files to data processing output
mikegilchrist Mar 22, 2023
ae1ebad
Many changes. Code *should* run, but having sampling issues.
mikegilchrist Mar 23, 2023
3578b3f
Code form Feb with single, common disp value seems to work well.
mikegilchrist Mar 23, 2023
1d04cfb
adjust prior for y0 results in similar behavior to 02-28 fits.
mikegilchrist Mar 23, 2023
5626eac
state prior to splitting one and two piece analyses
mikegilchrist Mar 27, 2023
c0ff567
fix problematic typo and a few more tweaks
mikegilchrist Mar 27, 2023
a535bb5
Working code base for two piece model
mikegilchrist Mar 29, 2023
411c313
Add output from script in most recent commit.
mikegilchrist Mar 29, 2023
75d96d6
add plotting form 2023-03-18 model fits
mikegilchrist Mar 29, 2023
aa2d7c4
Replace model fits from earlier today w/ more complete fit_tbl & code
mikegilchrist Mar 29, 2023
397bf77
Improve visualization routines of two_piece fits using 2023-03 code
mikegilchrist Apr 4, 2023
9bea1d7
rerun code 'process.data.for.x0...' and add figures
mikegilchrist Apr 5, 2023
fc01204
Update data procesing routines to work with all of the males
mikegilchrist Apr 5, 2023
03f2d43
Add plotting routines to try and categorize males based on disp
mikegilchrist Apr 5, 2023
f62d534
Additional model fits.
mikegilchrist Apr 7, 2023
0b922c3
improvements in visualizations, but still need to fix
mikegilchrist Apr 7, 2023
587858f
update input structure and printing of prior
mikegilchrist Apr 7, 2023
308f101
add most recent data output
mikegilchrist Apr 7, 2023
d98e611
Load most recent results in input/tibbles
mikegilchrist Apr 7, 2023
1472937
work (incomplete) on plotting of fits.
mikegilchrist Apr 10, 2023
a405da7
Minor improvements to plotting results.
mikegilchrist Apr 10, 2023
ed47140
Improve printing routines, almost done with first set.
mikegilchrist Apr 11, 2023
edc32de
Moved epred and pred plotting and data generation to functions
mikegilchrist Apr 12, 2023
217440e
Improve plotting of pairs plots when there are lots of them/male
mikegilchrist Apr 12, 2023
7b0d753
Add desc_short to top of marrangeGrob, use previous top for bottom
mikegilchrist Apr 12, 2023
39f6651
Reorganize plots, add filtering of chains with mean(lp__) below best
mikegilchrist Apr 13, 2023
43286ae
Add removal of excess chains above `n_chains_target`
mikegilchrist Apr 13, 2023
9766ee9
Rearranged code to improve logical structure
mikegilchrist Apr 13, 2023
a76c7ff
Change fitting values
mikegilchrist Apr 13, 2023
2a15221
move local functions from visualization to own file
mikegilchrist Apr 14, 2023
3aa5bfb
Further improvements & fixes to functions for fitting & plotting
mikegilchrist Apr 14, 2023
8ca7f86
Working local.functions, changes structure of fitting code flow
mikegilchrist Apr 16, 2023
d0f7275
add lp__ violin plots, comment out making of fit obj w/ best chains
mikegilchrist Apr 18, 2023
88f2aa0
Working towards using disp_flags, improve flag setting code
mikegilchrist Apr 18, 2023
306543c
Add disp_flag capabilities while making code more compact
mikegilchrist Apr 18, 2023
3dd4459
Improvement in flow of running/loading fit routines
mikegilchrist Apr 21, 2023
ad050f9
Add last_plot_save() function to my local functions file.
mikegilchrist Apr 21, 2023
67d1290
Add (but not yet tested) list of plots column to fit_tbl
mikegilchrist Apr 21, 2023
870e2df
More fixes to model fitting/displaying routines. Seems to work.
mikegilchrist Apr 21, 2023
ae64d24
Remove "Here" & "There" print() statements used in previous debugging
mikegilchrist Apr 21, 2023
26fdb4f
remove cruft from bottom of model fitting file.
mikegilchrist Apr 21, 2023
1332055
Working (but outdated) visual. code to be revised extensively next
mikegilchrist Apr 21, 2023
aaad8e9
Modify generate_epred_data() to allow passing of `group`
mikegilchrist Apr 24, 2023
5e5293d
Combined model fitting and plotting code now appears to run properly
mikegilchrist Apr 28, 2023
adb8e01
Minor edites to local.functions.R
mikegilchrist May 2, 2023
2ec0621
initial fit and plotting routines (appear) to work
mikegilchrist May 2, 2023
742d3f4
Try to improve plotting of fitting runs, still some issues
mikegilchrist May 4, 2023
e789582
Fix issues with plot titles, still an issue with uniform_2 grouping
mikegilchrist May 5, 2023
3124e65
Fixed issue w/disp_group & uniform_2
mikegilchrist May 5, 2023
6388b3e
Knitr compiling now works
mikegilchrist May 9, 2023
f422b3c
fix bug: plotting predictions- replace .epred with .prediction
mikegilchrist May 17, 2023
ae7dc98
working version of code that's running nbinom_typ1 w/o the derivative…
mikegilchrist May 21, 2023
9c1d696
add pdf of previous commit's fittings
mikegilchrist May 21, 2023
deac0cc
add a notes on future runs.
mikegilchrist May 22, 2023
2b40a0d
Post second round of runs with a few additional modifications.
mikegilchrist May 25, 2023
dec064a
add DannerEtAl2021 data and scripts from zenodo.org/record/4437461
mikegilchrist Aug 1, 2023
cdb94a7
Merge remote-tracking branch 'refs/remotes/origin/main'
mikegilchrist Aug 1, 2023
fe4af97
reorganize data folders and files
mikegilchrist Aug 16, 2023
63d5806
minor tweaks to file.
mikegilchrist Aug 16, 2023
c4c5f71
add DannerEtAl2021 code
mikegilchrist Aug 16, 2023
1906333
Add files via upload
taempson Sep 8, 2023
3b18b12
Merge branch 'mikegilchrist:main' into main
taempson Sep 15, 2023
24e258c
Add files via upload
taempson Sep 15, 2023
510a4b3
Delete code/Empson_TA_Code/ZEFI-Thermal-Curves.Rproj
taempson Sep 15, 2023
2d5e7c6
Merge pull request #3 from taempson/main
mikegilchrist Sep 15, 2023
0fc68c8
Making Branch Where Templogger Files were modified
taempson Sep 29, 2023
a335001
fixed issues with bootstrapping function
mikegilchrist Sep 29, 2023
04c542c
Merge pull request #1 from mikegilchrist/debug-tara
taempson Oct 6, 2023
4a15190
add math notes on our formulation of the negative binomial.
mikegilchrist Oct 6, 2023
25ffda4
add recreation of of 2022-10-07 plots
mikegilchrist Oct 6, 2023
8dcd602
update earlier figure
mikegilchrist Oct 6, 2023
bc2a2db
Committing Renamed files and new files
taempson Oct 6, 2023
fdcd72b
changes to earlier runs
mikegilchrist Oct 6, 2023
06bc609
Rename big Rda files to Rdata and modify code accordingly. Add old Rd…
mikegilchrist Oct 6, 2023
7c988d5
Uploading more progress
taempson Oct 13, 2023
199e5da
Deming and Simulating Data
taempson Oct 20, 2023
310ec06
Update 2023.10.20_Deming_and_Simulating_Data.Rmd
taempson Oct 20, 2023
fbcde56
Adding the first row to all the raw temperature reading files (.txt)
taempson Oct 20, 2023
5ec0d67
Clean up code
mikegilchrist Oct 20, 2023
63e6d08
Merge branch 'main-tara'
mikegilchrist Oct 20, 2023
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15 changes: 13 additions & 2 deletions .gitignore
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.Rproj.user
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.RData
.Ruserdata
*.RData
*.Rdata
.Ruserdata
*-2x1.pdf
tmp*.pdf
*.rds
*.html
*.aux
\#*
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*tmp
*.stan
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