updating analysis for co study

2025-02-07 10:10:31 -08:00 · 2025-02-07 10:10:31 -08:00 · c643329597
commit c643329597
parent 0e40718a7e
16 changed files with 5016 additions and 4981 deletions
--- a/020425_contributing_crescendo_model.rda
+++ b/020425_contributing_crescendo_model.rda
--- a/cleaning_scripts/verifying_count_on_manifest.R
+++ b/cleaning_scripts/verifying_count_on_manifest.R
@ -0,0 +1,19 @@
 library(dplyr)
 count_path <- "/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/final_data/metadata/co_0205_CONTRIBUTING_weekly_count_data.csv"
 manifest_path <- "validation/020525_CONTRIBUTING_manifest.csv"
 count_df <- read.csv(count_path)
 manifest_df <- read.csv(manifest_path)
 length(unique(count_df$project_id))
 unique_project_ids <- unique(count_df$project_id)
 missing_project_ids <- setdiff(unique_project_ids, manifest_df$repo_id)
 missing_project_ids
 count_df_filtered <- count_df %>% filter(!project_id %in% missing_project_ids)
 length(unique(count_df_filtered$project_id))
 missing_repo_ids <- setdiff(manifest_df$repo_id, count_df_filtered$project_id)
 write.csv(count_df_filtered, "/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/final_data/metadata/final_0207_CONTRIBUTING_weekly_count_data.csv", row.names =FALSE)
--- a/mlm/contributing_did_prep.R
+++ b/mlm/contributing_did_prep.R
@ -1,18 +1,19 @@
 library(dplyr)
 library(lubridate)
 library(rdd)
 library(tidyr)
-contributing_df_filepath <- "/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/final_data/CONTRIBUTING_weekly_count_data.csv"
+contributing_df_filepath <- "/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/final_data/metadata/final_0207_CONTRIBUTING_weekly_count_data.csv"
 df = read.csv(contributing_df_filepath, header = TRUE) 
 #EDA 
-var(df$commit_count) # 325.5261
+var(df$commit_count) # 349.06
-mean(df$commit_count) # 7.743385
+mean(df$commit_count) # 8.371495
 median(df$commit_count) # 1
-mean(df$age) # 4838.649 days
+mean(df$age) # 4939.859
-mean(df$age_at_commit) # 2141.996 days
+mean(df$age_at_commit) # 2286.772 days
-median(df$age) # 4597 days
+median(df$age) #4738 says
-median(df$age_at_commit) # 1603 days
+median(df$age_at_commit) # 1806 days
 # scale and log-transform
 df$scaled_age <- scale(df$age)
@ -21,10 +22,17 @@ df$log1p_count <- log1p(df$commit_count)
 #getting IK Bandwidth
 get_optimal_bandwidth <- function(df){
-  IKbandwidth(df$week_index, df$log1p_count, cutpoint = 0, verbose = FALSE, kernel = "triangular")
+  bw <- tryCatch({
    IKbandwidth(df$relative_week, df$log1p_count, cutpoint = 0, verbose = FALSE, kernel = "triangular")
  }, error = function(e) {
    NA
  })
 }
 mean_optimal_bandwidth <- df %>%
  group_by(project_id) %>%
  summarise(optimal_bandwidth = get_optimal_bandwidth(cur_data())) %>%
  drop_na(optimal_bandwidth) |>
  summarise(mean_optimal_bandwidth = mean(optimal_bandwidth))
 #5.676423
--- a/mlm/data/0201_contributing_dweek_ranefs.csv
+++ b/mlm/data/0201_contributing_dweek_ranefs.csv
@ -1,716 +0,0 @@
 "","effect","group","level","term","estimate","std.error","conf.low","conf.high","ranef_grouping","rank"
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 "655","ran_vals","project_id","tpope_vim-pathogen.git","before_after:week_index",-0.290308941345517,0.143050686696824,-0.570683135235015,-0.00993474745601819,0,129
 "656","ran_vals","project_id","tqdm_tqdm.git","before_after:week_index",0.053296792380904,0.0864337468535963,-0.116110238500997,0.222703823262805,1,378
 "657","ran_vals","project_id","trevorld_r-optparse.git","before_after:week_index",-0.499145276412738,0.181690814996526,-0.855252730127659,-0.143037822697817,0,22
 "658","ran_vals","project_id","trezor_trezor-firmware.git","before_after:week_index",0.381154217142729,0.0490109142346569,0.28509459039342,0.477213843892038,2,681
 "659","ran_vals","project_id","troglobit_inadyn","before_after:week_index",0.0826483926266794,0.0823345562308339,-0.078724372268843,0.244021157522202,1,411
 "660","ran_vals","project_id","Tux_Text-CSV_XS.git","before_after:week_index",-0.189977387287352,0.124663554541083,-0.43431346437262,0.0543586897979155,1,192
 "661","ran_vals","project_id","twbs_bootstrap-sass","before_after:week_index",0.0119300086628006,0.0928648173039842,-0.1700816886839,0.193941706009502,1,342
 "662","ran_vals","project_id","twilio_twilio-python","before_after:week_index",0.0916777058518811,0.0813813904877355,-0.0678268885158709,0.251182300219633,1,420
 "663","ran_vals","project_id","twisted_pydoctor","before_after:week_index",0.376553426498389,0.0498868681811727,0.278776961561793,0.474329891434985,2,676
 "664","ran_vals","project_id","ua-parser_uap-core.git","before_after:week_index",0.090301897074397,0.0817511208955456,-0.0699273555766523,0.250531149725446,1,417
 "665","ran_vals","project_id","ukui_peony","before_after:week_index",0.333048338047732,0.0530792523691061,0.229014915077972,0.437081761017493,2,645
 "666","ran_vals","project_id","Ultimaker_Cura","before_after:week_index",0.362148082836441,0.0505244365325766,0.263122006893411,0.461174158779471,2,666
 "667","ran_vals","project_id","un33k_django-ipware","before_after:week_index",-0.529361166651499,0.187075747563832,-0.896022894257517,-0.16269943904548,0,5
 "668","ran_vals","project_id","unknown-horizons_unknown-horizons.git","before_after:week_index",0.419992104766536,0.0458547831817979,0.330118381211319,0.509865828321753,2,705
 "669","ran_vals","project_id","untitaker_python-atomicwrites","before_after:week_index",-0.152834899728803,0.117019575119352,-0.382189052448913,0.0765192529913063,1,214
 "670","ran_vals","project_id","varietywalls_variety.git","before_after:week_index",0.0774144449856542,0.0825633974438188,-0.0844068404454971,0.239235730416805,1,401
 "671","ran_vals","project_id","varvet_pundit","before_after:week_index",-0.0909420940275992,0.108596506434927,-0.303787335486929,0.121903147431731,1,256
 "672","ran_vals","project_id","vcr_vcr","before_after:week_index",0.300346100044626,0.0566323935201245,0.189348648386883,0.41134355170237,2,606
 "673","ran_vals","project_id","vim-airline_vim-airline.git","before_after:week_index",0.250794279220423,0.062208056175112,0.128868729568959,0.372719828871887,2,557
 "674","ran_vals","project_id","vim-syntastic_syntastic","before_after:week_index",0.314366414566401,0.0552940138801542,0.205992138800641,0.422740690332161,2,620
 "675","ran_vals","project_id","virt-manager_virt-manager","before_after:week_index",0.304379939778706,0.0568849542579229,0.192887478170968,0.415872401386443,2,614
 "676","ran_vals","project_id","voxpupuli_beaker","before_after:week_index",0.348990913830841,0.0519492924185047,0.247172171668232,0.45080965599345,2,660
 "677","ran_vals","project_id","voxpupuli_librarian-puppet.git","before_after:week_index",-0.39422551323252,0.162053783935859,-0.71184509330524,-0.076605933159801,0,77
 "678","ran_vals","project_id","voxpupuli_pypuppetdb","before_after:week_index",-0.296897304660233,0.144628391440308,-0.580363743025198,-0.0134308662952685,0,126
 "679","ran_vals","project_id","watson-developer-cloud_python-sdk.git","before_after:week_index",-0.00466489730332885,0.0951357687263136,-0.191127577648435,0.181797783041778,1,319
 "680","ran_vals","project_id","webcamoid_webcamoid.git","before_after:week_index",-0.037041763400456,0.0999757201043483,-0.232990574133436,0.158907047332524,1,296
 "681","ran_vals","project_id","webrtchacks_adapter","before_after:week_index",0.291563349220042,0.0572926942629675,0.179271731887362,0.403854966552723,2,595
 "682","ran_vals","project_id","websocket-client_websocket-client","before_after:week_index",0.197776682968342,0.067642776549638,0.0651992771167612,0.330354088819923,2,509
 "683","ran_vals","project_id","WoLpH_numpy-stl","before_after:week_index",-0.0877980950901149,0.10536403537173,-0.294307809684511,0.118711619504281,1,260
 "684","ran_vals","project_id","wtforms_flask-wtf.git","before_after:week_index",-0.0896057377295899,0.108416284955035,-0.30209775157909,0.12288627611991,1,258
 "685","ran_vals","project_id","X0rg_CPU-X.git","before_after:week_index",0.100819116462142,0.0795716427928496,-0.0551384376025291,0.256776670526814,1,428
 "686","ran_vals","project_id","Xastir_Xastir.git","before_after:week_index",0.0604885496605608,0.0832039581603247,-0.102588211704853,0.223565311025975,1,383
 "687","ran_vals","project_id","Xaviju_inkscape-open-symbols","before_after:week_index",-0.0840533586580127,0.107471745431413,-0.294694109059238,0.126587391743213,1,263
 "688","ran_vals","project_id","xonsh_xonsh.git","before_after:week_index",0.343590234792073,0.0522108731709255,0.241258803775671,0.445921665808476,2,653
 "689","ran_vals","project_id","xtaran_unburden-home-dir","before_after:week_index",-0.0771036692781287,0.105537532368671,-0.283953431737954,0.129746093181696,1,268
 "690","ran_vals","project_id","ycm-core_ycmd","before_after:week_index",-0.000605397284301289,0.0946615699163441,-0.186138665040356,0.184927870471753,1,328
 "691","ran_vals","project_id","ycm-core_YouCompleteMe","before_after:week_index",0.324527083149419,0.0541634904978633,0.218368592496629,0.430685573802208,2,635
 "692","ran_vals","project_id","yrro_command-t","before_after:week_index",-0.20755983067889,0.128814487712847,-0.460031587283048,0.0449119259252668,1,181
 "693","ran_vals","project_id","ytdl-org_youtube-dl.git","before_after:week_index",0.449591992027548,0.0433834492172356,0.364561994036644,0.534621990018452,2,715
 "694","ran_vals","project_id","zaach_jison","before_after:week_index",-0.332005744433942,0.15136793570203,-0.628681446824096,-0.0353300420437893,0,109
 "695","ran_vals","project_id","zeroc-ice_ice-builder-gradle-debian-packaging.git","before_after:week_index",-0.335455388418513,0.151354855240113,-0.632105453574409,-0.0388053232626177,0,107
 "696","ran_vals","project_id","zeroc-ice_ice-debian-packaging.git","before_after:week_index",-0.027148431809379,0.0984513949449932,-0.220109620129294,0.165812756510536,1,303
 "697","ran_vals","project_id","zeromq_czmq.git","before_after:week_index",0.381249216427842,0.0490685492305357,0.285076627162362,0.477421805693323,2,682
 "698","ran_vals","project_id","zeromq_pyzmq.git","before_after:week_index",0.219297261009572,0.0650827149762302,0.0917374836400749,0.346857038379069,2,531
 "699","ran_vals","project_id","zkat_ssri.git","before_after:week_index",-0.137219468453288,0.116022491632154,-0.364619373448909,0.0901804365423333,1,227
 "700","ran_vals","project_id","zloirock_core-js.git","before_after:week_index",0.0286208178547907,0.089960456742353,-0.147698437392995,0.204940073102576,1,355
 "701","ran_vals","project_id","zmartzone_cjose.git","before_after:week_index",-0.337146755776738,0.150737404496958,-0.632586639713821,-0.0417068718396543,0,105
 "702","ran_vals","project_id","zopefoundation_BTrees.git","before_after:week_index",-0.506067068334373,0.182996828739419,-0.864734261948677,-0.147399874720068,0,15
 "703","ran_vals","project_id","zopefoundation_roman","before_after:week_index",-0.497237220569924,0.181809762271757,-0.853577806660357,-0.140896634479492,0,24
 "704","ran_vals","project_id","zopefoundation_zc.lockfile","before_after:week_index",-0.432749289706663,0.17034543413337,-0.766620205538908,-0.0988783738744178,0,60
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 "714","ran_vals","project_id","zsh-users_antigen","before_after:week_index",0.107791818445195,0.0794472420990712,-0.0479219147400187,0.263505551630409,1,438
 "715","ran_vals","project_id","zyga_padme","before_after:week_index",-0.0799196805037215,0.10680930645632,-0.289262074371811,0.129422713364368,1,265
--- a/mlm/data/0203_readme_dweek_ranefs.csv
+++ b/mlm/data/0203_readme_dweek_ranefs.csv
--- a/mlm/models/020125_contributing_model.rda
+++ b/mlm/models/020125_contributing_model.rda
--- a/mlm/models/020325_readme_model.rda
+++ b/mlm/models/020325_readme_model.rda
--- a/mlm/readme_did_prep.R
+++ b/mlm/readme_did_prep.R
@ -3,7 +3,7 @@ library(dplyr)
 library(lubridate)
 library(rdd)
-readme_df_filepath <- "/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/final_data/README_weekly_count_data.csv"
+readme_df_filepath <- "/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/final_data/metadata/final_0207_README_weekly_count_data.csv"
 df = read.csv(readme_df_filepath, header = TRUE)
 #filtered_df <- df |>
@ -13,12 +13,12 @@ df = read.csv(readme_df_filepath, header = TRUE)
 #write.csv(filtered_df, output_filepath, row.names = FALSE)
 #EDA 
-var(df$commit_count) # 112.4945
+var(df$commit_count) #  207.7579
-mean(df$commit_count) # 2.431342
+mean(df$commit_count) # 4.31725
 median(df$commit_count) # 0
-mean(df$age) # 4911.734 days
+mean(df$age) # 5074.828
-mean(df$age_at_commit) # 197.296 days
+mean(df$age_at_commit) # 533.7488
-median(df$age) # 4689 days
+median(df$age) # 4876
 median(df$age_at_commit) # 0 days
 # scale and log-transform
@ -29,12 +29,17 @@ df$log1p_count <- log1p(df$commit_count)
 #getting IK Bandwidth
 get_optimal_bandwidth <- function(df){
-  IKbandwidth(df$week_index, df$log1p_count, cutpoint = 0, verbose = FALSE, kernel = "triangular")
+  bw <- tryCatch({
    IKbandwidth(df$relative_week, df$log1p_count, cutpoint = 0, verbose = FALSE, kernel = "triangular")
  }, error = function(e) {
    NA
  })
 }
 mean_optimal_bandwidth <- df %>%
  group_by(project_id) %>%
  summarise(optimal_bandwidth = get_optimal_bandwidth(cur_data())) %>%
  drop_na(optimal_bandwidth) |>
  summarise(mean_optimal_bandwidth = mean(optimal_bandwidth))
-#Mean Optimal Bandwidth: 5.44841
+#Mean Optimal Bandwidth: 5.471781
--- a/plots/cr-0203-contributing-blup.png
+++ b/plots/cr-0203-contributing-blup.png
--- a/plots/cr-0203-ranef-readability.png
+++ b/plots/cr-0203-ranef-readability.png
--- a/plots/cr-0203-wc-density.png
+++ b/plots/cr-0203-wc-density.png
--- a/plots/cr-020325-gam-introduction.png
+++ b/plots/cr-020325-gam-introduction.png
--- a/validation/020525_CONTRIBUTING_manifest.csv
+++ b/validation/020525_CONTRIBUTING_manifest.csv
@ -0,0 +1,715 @@
 commit_hash,upstream_vcs_link,repo_id,project_handle,lagged_hash,project_index,new_filepath
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 2b36be98c48515fab027193b18620849343db752,https://github.com/webcamoid/webcamoid.git,webcamoid_webcamoid.git,webcamoid/webcamoid.git,421010bfbaff89e557be30a1b8ceb701ac0f44fc,13,13_webcamoid_webcamoid.git_CONTRIBUTING.md
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 b3a33927a0c1e97dd7d73570c81b730041304699,https://github.com/lualdap/lualdap.git,lualdap_lualdap.git,lualdap/lualdap.git,b3a33927a0c1e97dd7d73570c81b730041304699,16,16_lualdap_lualdap.git_CONTRIBUTING.md
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