install.packages(c("biglm", "dplyr", "ggplot2", "readr", "targets", "tidyr"))options(repos = c(RSPM = "https://packagemanager.datascience.kdhe.ks.gov/cran/latest"))library(targets)
tar_unscript()options(tidyverse.quiet = TRUE)
tar_option_set(packages = c("biglm", "dplyr", "ggplot2", "readr", "tidyr", "knitr", "scales"))
tar_source()
#> Establish _targets.R and _targets_r/globals/pkgs.R.list(
tar_target(raw_data_store, file.path("~", "Projects", "Reports", "pb_report_2025", "_targets"))
)
#> Establish _targets.R and _targets_r/targets/keydirs.R.list(
tar_target(child_tables, tar_read(child_tables, store = raw_data_store)),
tar_target(ks_sum24_df, cbls_summarize(child_tables)),
tar_target(dedup_all_df, tar_read(pb_dedup_lst, store = raw_data_store)[["distinct"]]),
tar_target(tests_count_24, count2024tests(dedup_all_df))
)
#> Establish _targets.R and _targets_r/targets/downstream-targets.R.knitr::kable(tar_read(ks_sum24_df))| FIPS | CNTYCODE | lab_collection_county | ntested | pct_tested | ge3.5.lt10_2024 | ge10_2024 | conf_elev_2024 | pct_elev | POP2024 |
|---|---|---|---|---|---|---|---|---|---|
| 20001 | AL | Allen | 127 | 14.4 | 5 | 0 | 5 | 3.9 | 884 |
| 20003 | AN | Anderson | 92 | 15.3 | 4 | 2 | 6 | 6.5 | 601 |
| 20005 | AT | Atchison | 114 | 11.1 | 4 | 1 | 5 | 4.4 | 1029 |
| 20007 | BA | Barber | 37 | 13.2 | 3 | 0 | 3 | 8.1 | 280 |
| 20009 | BT | Barton | 263 | 14.8 | 18 | 6 | 24 | 9.1 | 1783 |
| 20011 | BB | Bourbon | 157 | 13.7 | 9 | 1 | 10 | 6.4 | 1144 |
| 20013 | BR | Brown | 78 | 12.4 | 8 | 0 | 8 | 10.3 | 628 |
| 20015 | BU | Butler | 272 | 6.1 | 9 | 0 | 9 | 3.3 | 4469 |
| 20017 | CS | Chase | 18 | 12.9 | 3 | 0 | 3 | 16.7 | 140 |
| 20019 | CQ | Chautauqua | 59 | 27.3 | 5 | 1 | 6 | 10.2 | 216 |
| 20021 | CK | Cherokee | 323 | 26.0 | 20 | 2 | 22 | 6.8 | 1242 |
| 20023 | CN | Cheyenne | 37 | 18.7 | 0 | 0 | 0 | 0.0 | 198 |
| 20025 | CA | Clark | 9 | 7.3 | 1 | 0 | 1 | 11.1 | 123 |
| 20027 | CY | Clay | 72 | 13.9 | 4 | 2 | 6 | 8.3 | 517 |
| 20029 | CD | Cloud | 65 | 10.5 | 5 | 0 | 5 | 7.7 | 621 |
| 20031 | CF | Coffey | 86 | 16.2 | 4 | 0 | 4 | 4.7 | 530 |
| 20033 | CM | Comanche | 12 | 10.7 | 1 | 0 | 1 | 8.3 | 112 |
| 20035 | CL | Cowley | 728 | 30.3 | 25 | 7 | 32 | 4.4 | 2400 |
| 20037 | CR | Crawford | 447 | 17.1 | 10 | 3 | 13 | 2.9 | 2608 |
| 20039 | DC | Decatur | 25 | 14.0 | 3 | 0 | 3 | 12.0 | 178 |
| 20041 | DK | Dickinson | 122 | 9.0 | 3 | 0 | 3 | 2.5 | 1351 |
| 20043 | DP | Doniphan | 79 | 17.2 | 4 | 2 | 6 | 7.6 | 460 |
| 20045 | DG | Douglas | 571 | 9.3 | 6 | 2 | 8 | 1.4 | 6126 |
| 20047 | ED | Edwards | 36 | 18.5 | 0 | 0 | 0 | 0.0 | 195 |
| 20049 | EK | Elk | 7 | 5.3 | 1 | 0 | 1 | 14.3 | 133 |
| 20051 | EL | Ellis | 259 | 15.0 | 12 | 2 | 14 | 5.4 | 1722 |
| 20053 | EW | Ellsworth | 54 | 15.9 | 4 | 0 | 4 | 7.4 | 339 |
| 20055 | FI | Finney | 611 | 17.8 | 10 | 2 | 12 | 2.0 | 3431 |
| 20057 | FO | Ford | 640 | 19.1 | 11 | 6 | 17 | 2.7 | 3352 |
| 20059 | FR | Franklin | 178 | 9.7 | 6 | 0 | 6 | 3.4 | 1828 |
| 20061 | GE | Geary | 613 | 13.3 | 5 | 1 | 6 | 1.0 | 4626 |
| 20063 | GO | Gove | 18 | 8.2 | 2 | 0 | 2 | 11.1 | 219 |
| 20065 | GH | Graham | 40 | 26.5 | 2 | 1 | 3 | 7.5 | 151 |
| 20067 | GT | Grant | 83 | 13.2 | 0 | 0 | 0 | 0.0 | 627 |
| 20069 | GY | Gray | 43 | 8.5 | 1 | 1 | 2 | 4.7 | 506 |
| 20071 | GL | Greeley | 37 | 44.6 | 1 | 0 | 1 | 2.7 | 83 |
| 20073 | GW | Greenwood | 34 | 9.4 | 7 | 1 | 8 | 23.5 | 360 |
| 20075 | HM | Hamilton | 39 | 16.4 | 0 | 0 | 0 | 0.0 | 238 |
| 20077 | HP | Harper | 47 | 11.5 | 2 | 0 | 2 | 4.3 | 407 |
| 20079 | HV | Harvey | 291 | 12.9 | 8 | 1 | 9 | 3.1 | 2261 |
| 20081 | HS | Haskell | 35 | 10.4 | 0 | 0 | 0 | 0.0 | 335 |
| 20083 | HG | Hodgeman | 3 | 2.4 | 0 | 0 | 0 | 0.0 | 124 |
| 20085 | JA | Jackson | 83 | 7.4 | 1 | 0 | 1 | 1.2 | 1120 |
| 20087 | JF | Jefferson | 109 | 9.4 | 3 | 2 | 5 | 4.6 | 1161 |
| 20089 | JW | Jewell | 27 | 15.8 | 2 | 0 | 2 | 7.4 | 171 |
| 20091 | JO | Johnson | 4819 | 11.2 | 39 | 5 | 44 | 0.9 | 43068 |
| 20093 | KE | Kearny | 60 | 17.0 | 0 | 0 | 0 | 0.0 | 352 |
| 20095 | KM | Kingman | 57 | 11.9 | 4 | 0 | 4 | 7.0 | 477 |
| 20097 | KW | Kiowa | 15 | 7.1 | 1 | 0 | 1 | 6.7 | 210 |
| 20099 | LB | Labette | 186 | 13.1 | 10 | 2 | 12 | 6.5 | 1424 |
| 20101 | LE | Lane | 9 | 8.6 | 0 | 0 | 0 | 0.0 | 105 |
| 20103 | LV | Leavenworth | 760 | 12.7 | 15 | 4 | 19 | 2.5 | 6007 |
| 20105 | LC | Lincoln | 43 | 21.6 | 3 | 0 | 3 | 7.0 | 199 |
| 20107 | LN | Linn | 78 | 12.4 | 3 | 0 | 3 | 3.8 | 631 |
| 20109 | LG | Logan | 52 | 21.8 | 3 | 2 | 5 | 9.6 | 238 |
| 20111 | LY | Lyon | 364 | 17.1 | 22 | 4 | 26 | 7.1 | 2127 |
| 20113 | MP | McPherson | 254 | 13.0 | 8 | 0 | 8 | 3.1 | 1954 |
| 20115 | MN | Marion | 98 | 13.8 | 7 | 1 | 8 | 8.2 | 709 |
| 20117 | MS | Marshall | 91 | 13.3 | 11 | 1 | 12 | 13.2 | 685 |
| 20119 | ME | Meade | 27 | 9.0 | 0 | 0 | 0 | 0.0 | 301 |
| 20121 | MI | Miami | 306 | 13.1 | 3 | 1 | 4 | 1.3 | 2327 |
| 20123 | MC | Mitchell | 20 | 4.5 | 1 | 1 | 2 | 10.0 | 448 |
| 20125 | MG | Montgomery | 381 | 19.1 | 33 | 7 | 40 | 10.5 | 1997 |
| 20127 | MR | Morris | 30 | 10.3 | 0 | 0 | 0 | 0.0 | 291 |
| 20129 | MT | Morton | 9 | 5.4 | 0 | 0 | 0 | 0.0 | 167 |
| 20131 | NM | Nemaha | 69 | 8.8 | 8 | 1 | 9 | 13.0 | 782 |
| 20133 | NO | Neosho | 144 | 13.2 | 9 | 0 | 9 | 6.2 | 1095 |
| 20135 | NS | Ness | 24 | 12.2 | 2 | 1 | 3 | 12.5 | 196 |
| 20137 | NT | Norton | 51 | 15.7 | 2 | 0 | 2 | 3.9 | 325 |
| 20139 | OS | Osage | 78 | 8.2 | 4 | 1 | 5 | 6.4 | 954 |
| 20141 | OB | Osborne | 22 | 9.6 | 2 | 0 | 2 | 9.1 | 229 |
| 20143 | OT | Ottawa | 53 | 14.0 | 5 | 2 | 7 | 13.2 | 378 |
| 20145 | PN | Pawnee | 84 | 27.4 | 8 | 4 | 12 | 14.3 | 307 |
| 20147 | PL | Phillips | 25 | 8.1 | 1 | 0 | 1 | 4.0 | 309 |
| 20149 | PT | Pottawatomie | 185 | 8.1 | 1 | 0 | 1 | 0.5 | 2271 |
| 20151 | PR | Pratt | 56 | 8.3 | 4 | 1 | 5 | 8.9 | 678 |
| 20153 | RA | Rawlins | 35 | 17.9 | 0 | 0 | 0 | 0.0 | 196 |
| 20155 | RN | Reno | 590 | 15.2 | 29 | 2 | 31 | 5.3 | 3888 |
| 20157 | RP | Republic | 25 | 8.4 | 1 | 0 | 1 | 4.0 | 298 |
| 20159 | RC | Rice | 88 | 12.8 | 6 | 1 | 7 | 8.0 | 687 |
| 20161 | RL | Riley | 583 | 14.8 | 9 | 1 | 10 | 1.7 | 3935 |
| 20163 | RO | Rooks | 31 | 9.9 | 1 | 0 | 1 | 3.2 | 314 |
| 20165 | RH | Rush | 28 | 17.9 | 2 | 0 | 2 | 7.1 | 156 |
| 20167 | RS | Russell | 60 | 15.3 | 5 | 4 | 9 | 15.0 | 391 |
| 20169 | SA | Saline | 502 | 13.6 | 36 | 7 | 43 | 8.6 | 3683 |
| 20171 | SC | Scott | 75 | 17.9 | 0 | 1 | 1 | 1.3 | 420 |
| 20173 | SG | Sedgwick | 4791 | 12.0 | 96 | 19 | 115 | 2.4 | 39988 |
| 20175 | SW | Seward | 201 | 9.0 | 6 | 0 | 6 | 3.0 | 2227 |
| 20177 | SN | Shawnee | 1455 | 12.3 | 48 | 5 | 53 | 3.6 | 11862 |
| 20179 | SD | Sheridan | 34 | 21.5 | 2 | 0 | 2 | 5.9 | 158 |
| 20181 | SH | Sherman | 70 | 17.9 | 0 | 0 | 0 | 0.0 | 391 |
| 20183 | SM | Smith | 9 | 4.4 | 2 | 0 | 2 | 22.2 | 203 |
| 20185 | SF | Stafford | 39 | 14.8 | 3 | 1 | 4 | 10.3 | 263 |
| 20187 | ST | Stanton | 34 | 17.7 | 2 | 0 | 2 | 5.9 | 192 |
| 20189 | SV | Stevens | 29 | 7.2 | 1 | 0 | 1 | 3.4 | 401 |
| 20191 | SU | Sumner | 157 | 10.0 | 9 | 1 | 10 | 6.4 | 1573 |
| 20193 | TH | Thomas | 120 | 19.9 | 1 | 1 | 2 | 1.7 | 604 |
| 20195 | TR | Trego | 21 | 13.0 | 0 | 0 | 0 | 0.0 | 161 |
| 20197 | WB | Wabaunsee | 32 | 6.5 | 2 | 0 | 2 | 6.2 | 495 |
| 20199 | WA | Wallace | 30 | 20.4 | 1 | 0 | 1 | 3.3 | 147 |
| 20201 | WS | Washington | 26 | 5.9 | 3 | 1 | 4 | 15.4 | 442 |
| 20203 | WH | Wichita | 54 | 28.6 | 1 | 0 | 1 | 1.9 | 189 |
| 20205 | WL | Wilson | 64 | 11.2 | 1 | 0 | 1 | 1.6 | 572 |
| 20207 | WO | Woodson | 11 | 6.5 | 2 | 0 | 2 | 18.2 | 169 |
| 20209 | WY | Wyandotte | 2705 | 18.7 | 82 | 13 | 95 | 3.5 | 14439 |
| 20 | N/A | Kansas | 27429 | 13.0 | 792 | 141 | 933 | 3.4 | 210714 |
tar_make()
#> ✔ skipped pipeline [112ms, 5 skipped]Total Number of tests for 2024 = 45,090
tar_visnetwork()