jbloomlab · jbloom · Apr 10, 2024 · Apr 10, 2024 · Apr 10, 2024 · Apr 10, 2024
diff --git a/README.md b/README.md
@@ -347,7 +347,7 @@ default_process_plate_curvefit_params: &default_process_plate_curvefit_params
   frac_infectivity_ceiling: 1
   fixtop: [0.75, 1.0]
   fixbottom: 0
-  fixslope: [0.8, 5]
+  fixslope: [0.8, 10]
 ```
 
 The specific meaning of these curve-fitting parameters are as follows:
@@ -361,7 +361,7 @@ The specific meaning of these curve-fitting parameters are as follows:
 
  - `fixbottom`: how to set the bottom plateau of the neutralization curve to this value. Like `fixtop`, it can be a length-two list, a fixed value, or `false`. Typically you should set it to 0 unless you have a good reason otherwise.
 
- - `fixslope`: how to set the slope of the neutralization curve. Like `fixtop`, it can be a length-two list, a fixed value, or `false`. If you don't know the "slope" of the neutralization curve, setting to `false` is a reasonable choice. However, in many cases it is preferable to set to a range that encompasses "reasonable" slopes. Note that what is "reasonable" will depend on the units of the concentration, but when they are serum dilutions a "reasonable" range is often `[0.8, 5]`.
+ - `fixslope`: how to set the slope of the neutralization curve. Like `fixtop`, it can be a length-two list, a fixed value, or `false`. If you don't know the "slope" of the neutralization curve, setting to `false` is a reasonable choice. However, in many cases it is preferable to set to a range that encompasses "reasonable" slopes. Note that what is "reasonable" will depend on the units of the concentration, but when they are serum dilutions a "reasonable" range is often `[0.8, 10]`.
 
 #### curvefit_qc
 This key defines some parameters on quality-control performed after the curve-fitting; viral-barcode / serum-replicate combinations that fail this QC are dropped.

diff --git a/docs/aggregate_qc_drops.html b/docs/aggregate_qc_drops.html
diff --git a/docs/pilot_A23038d0_r32_75K_titers.html b/docs/pilot_A23038d0_r32_75K_titers.html
diff --git a/docs/process_H3N2_plate.html b/docs/process_H3N2_plate.html
diff --git a/docs/process_plate11.html b/docs/process_plate11.html
diff --git a/docs/process_plate2.html b/docs/process_plate2.html
diff --git a/docs/serum_M099d0_titers.html b/docs/serum_M099d0_titers.html
diff --git a/docs/serum_M099d30_titers.html b/docs/serum_M099d30_titers.html
diff --git a/docs/serum_Y044d30_titers.html b/docs/serum_Y044d30_titers.html
diff --git a/docs/serum_Y154d182_titers.html b/docs/serum_Y154d182_titers.html
diff --git a/docs/titers.html b/docs/titers.html
diff --git a/test_example/config.yml b/test_example/config.yml
@@ -58,7 +58,7 @@ default_process_plate_curvefit_params: &default_process_plate_curvefit_params
   frac_infectivity_ceiling: 1
   fixtop: [0.75, 1]
   fixbottom: 0
-  fixslope: [0.8, 5]
+  fixslope: [0.8, 10]
 
 default_process_plate_curvefit_qc:  &default_process_plate_curvefit_qc
   max_frac_infectivity_at_least: 0

diff --git a/test_example/expected_titers_for_test.csv b/test_example/expected_titers_for_test.csv
diff --git a/test_example/results/aggregated_titers/titers_pilot.csv b/test_example/results/aggregated_titers/titers_pilot.csv
@@ -1,8 +1,8 @@
 group,serum,virus,titer,titer_bound,titer_sem,n_replicates,titer_as
 pilot,A23038d0_r32_75K,A/Bangkok/P3599/2023,1863,interpolated,25.05,2,midpoint
-pilot,A23038d0_r32_75K,A/Bangkok/P3755/2023,851.5,interpolated,540.2,3,midpoint
+pilot,A23038d0_r32_75K,A/Bangkok/P3755/2023,851.5,interpolated,540.5,3,midpoint
 pilot,A23038d0_r32_75K,A/Bhutan/0006/2023,611.9,interpolated,86.66,3,midpoint
-pilot,A23038d0_r32_75K,A/Bhutan/FLU-BTG-00988/2022,552,interpolated,183.5,3,midpoint
+pilot,A23038d0_r32_75K,A/Bhutan/FLU-BTG-00988/2022,552,interpolated,183.8,3,midpoint
 pilot,A23038d0_r32_75K,A/Brisbane/429/2023,1534,interpolated,331.1,2,midpoint
 pilot,A23038d0_r32_75K,A/Busan/1301/2023,773.6,interpolated,57.66,2,midpoint
 pilot,A23038d0_r32_75K,A/California/81/2023,1454,interpolated,901.2,2,midpoint
@@ -12,11 +12,11 @@ pilot,A23038d0_r32_75K,A/Catalonia/NSVH102124476/2023,655.3,interpolated,119.3,3
 pilot,A23038d0_r32_75K,A/Chipata/15-NIC-001/2023,1137,interpolated,639.8,3,midpoint
 pilot,A23038d0_r32_75K,A/EHIME/50/2023,1167,interpolated,285.7,3,midpoint
 pilot,A23038d0_r32_75K,A/Georgia/40/2023,1123,interpolated,345,3,midpoint
-pilot,A23038d0_r32_75K,A/Hong_Kong/2671/2019,8785,interpolated,1455,3,midpoint
+pilot,A23038d0_r32_75K,A/Hong_Kong/2671/2019,8621,interpolated,1408,3,midpoint
 pilot,A23038d0_r32_75K,A/Hong_Kong/45/2019,1040,interpolated,12.96,3,midpoint
 pilot,A23038d0_r32_75K,A/Hong_Kong/4801/2014,5075,interpolated,2410,2,midpoint
-pilot,A23038d0_r32_75K,A/Hong_Kong/4801/2014_(15/192),1.28e+04,lower,20.92,3,midpoint
-pilot,A23038d0_r32_75K,A/Jeju/1047/2023,1049,interpolated,505.2,2,midpoint
+pilot,A23038d0_r32_75K,A/Hong_Kong/4801/2014_(15/192),1.28e+04,lower,437.4,3,midpoint
+pilot,A23038d0_r32_75K,A/Jeju/1047/2023,1039,interpolated,515,2,midpoint
 pilot,A23038d0_r32_75K,A/Kansas/14/2017,4041,interpolated,2384,2,midpoint
 pilot,A23038d0_r32_75K,A/Krabi/THIS050/2023,3116,interpolated,2069,2,midpoint
 pilot,A23038d0_r32_75K,A/Malaysia/IMR-SARI1989/2023,1422,interpolated,3.266,2,midpoint
@@ -28,20 +28,20 @@ pilot,A23038d0_r32_75K,A/SOUTH_AFRICA/R07876/202023,797.5,interpolated,83.49,3,m
 pilot,A23038d0_r32_75K,A/Saint-Petersburg/RII-MH144113/2023,1685,interpolated,222.5,3,midpoint
 pilot,A23038d0_r32_75K,A/Saskatchewan/SKFLU317847/2023,2104,interpolated,432.1,2,midpoint
 pilot,A23038d0_r32_75K,A/Schleswig-Holstein/4/2023,1451,interpolated,332.6,3,midpoint
-pilot,A23038d0_r32_75K,A/Singapore/INFIMH-16-0019/2016,3345,interpolated,699.5,3,midpoint
+pilot,A23038d0_r32_75K,A/Singapore/INFIMH-16-0019/2016,3274,interpolated,754.6,3,midpoint
 pilot,A23038d0_r32_75K,A/Singapore/INFIMH-16-0019/2016_X-307A,1.28e+04,lower,0,3,midpoint
 pilot,A23038d0_r32_75K,A/SouthAfrica/PET28931/2023,1104,interpolated,211.5,3,midpoint
 pilot,A23038d0_r32_75K,A/SouthSudan/631/2023,721.3,interpolated,118.5,3,midpoint
 pilot,A23038d0_r32_75K,A/South_Africa/K056872/2023,1115,interpolated,366.8,2,midpoint
-pilot,A23038d0_r32_75K,A/South_Africa/R05384/2023,448.6,interpolated,180.2,3,midpoint
+pilot,A23038d0_r32_75K,A/South_Africa/R05384/2023,427.8,interpolated,183.2,3,midpoint
 pilot,A23038d0_r32_75K,A/South_Africa/R05510/2023,3338,interpolated,1670,2,midpoint
 pilot,A23038d0_r32_75K,A/South_Africa/R06240/2023,1397,interpolated,224.3,2,midpoint
 pilot,A23038d0_r32_75K,A/South_Africa/R06359/2023,558.4,interpolated,178.9,2,midpoint
 pilot,A23038d0_r32_75K,A/South_Africa/R06477/2023,1876,interpolated,778.1,2,midpoint
 pilot,A23038d0_r32_75K,A/South_Africa/R06506/2023,1036,interpolated,175.3,3,midpoint
 pilot,A23038d0_r32_75K,A/South_Africa/R07188/2023,1987,interpolated,46.67,2,midpoint
 pilot,A23038d0_r32_75K,A/Switzerland/9715293/2013,4503,interpolated,132.2,2,midpoint
-pilot,A23038d0_r32_75K,A/Switzerland/9715293/2013_NIB-88,6760,interpolated,2281,2,midpoint
+pilot,A23038d0_r32_75K,A/Switzerland/9715293/2013_NIB-88,6733,interpolated,2317,2,midpoint
 pilot,A23038d0_r32_75K,A/Sydney/332/2023,1350,interpolated,164.2,3,midpoint
 pilot,A23038d0_r32_75K,A/Sydney/710/2023,805.1,interpolated,314.3,3,midpoint
 pilot,A23038d0_r32_75K,A/Sydney/715/2023,1176,interpolated,12.84,2,midpoint