From 53d3a2cdff042ffb2cc45a9b7fd66c5c40df45c1 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Fri, 20 Sep 2024 17:15:58 +0100 Subject: [PATCH] move lnorm dispersion from parameters into summary_statistics in JSON DB --- inst/extdata/parameters.json | 286 ++++++++++++++++------------------- 1 file changed, 130 insertions(+), 156 deletions(-) diff --git a/inst/extdata/parameters.json b/inst/extdata/parameters.json index ae89a7b20..99f0b1d30 100644 --- a/inst/extdata/parameters.json +++ b/inst/extdata/parameters.json @@ -5,18 +5,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.26, - "dispersion_ci_limits": [1.13, 1.38], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [4.8, 6.5], "quantile_names": ["25", "75"], "median": 5.6, "median_ci_limits": [4.8, 6.3], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.26, + "dispersion_ci_limits": [1.13, 1.38], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -73,18 +72,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.15, - "dispersion_ci_limits": [1.07, 1.34], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [2.9, 3.5], "quantile_names": ["25", "75"], "median": 3.2, "median_ci_limits": [2.8, 3.7], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.15, + "dispersion_ci_limits": [1.07, 1.34], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -141,18 +139,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.81, - "dispersion_ci_limits": [1.67, 1.95], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [1.5, 2.7, 5.9, 10.6], "quantile_names": ["5", "25", "75", "95"], "median": 4, "median_ci_limits": [3.6, 4.4], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.81, + "dispersion_ci_limits": [1.67, 1.95], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -209,18 +206,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.51, - "dispersion_ci_limits": [1.43, 1.6], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [0.7, 1.1, 1.9, 2.8], "quantile_names": ["5", "25", "75", "95"], "median": 1.4, "median_ci_limits": [1.3, 1.5], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.51, + "dispersion_ci_limits": [1.43, 1.6], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -277,18 +273,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.23, - "dispersion_ci_limits": [1.17, 1.29], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [1.4, 1.7, 2.2, 2.7], "quantile_names": ["5", "25", "75", "95"], "median": 1.9, "median_ci_limits": [1.8, 2], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.23, + "dispersion_ci_limits": [1.17, 1.29], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -345,18 +340,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.51, - "dispersion_ci_limits": [1.37, 1.64], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [0.3, 0.4, 0.7, 1.1], "quantile_names": ["5", "25", "75", "95"], "median": 0.6, "median_ci_limits": [0.5, 0.6], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.51, + "dispersion_ci_limits": [1.37, 1.64], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -413,18 +407,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.23, - "dispersion_ci_limits": [1.18, 1.28], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [8.9, 10.9, 14.4, 17.7], "quantile_names": ["5", "25", "75", "95"], "median": 12.5, "median_ci_limits": [11.8, 13.3], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.23, + "dispersion_ci_limits": [1.18, 1.28], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -481,18 +474,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.35, - "dispersion_ci_limits": [1.16, 1.55], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [2.1, 3.2], "quantile_names": ["25", "75"], "median": 2.6, "median_ci_limits": [2.1, 3.1], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.35, + "dispersion_ci_limits": [1.16, 1.55], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -549,18 +541,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.24, - "dispersion_ci_limits": [1.13, 1.35], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [3.1, 3.8, 5.1, 6.3], "quantile_names": ["5", "25", "75", "95"], "median": 4.4, "median_ci_limits": [3.9, 4.9], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.24, + "dispersion_ci_limits": [1.13, 1.35], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -617,18 +608,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.68, - "dispersion_ci_limits": [1.36, 2.01], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [0.8, 1.3, 2.7, 4.5], "quantile_names": ["5", "25", "75", "95"], "median": 1.9, "median_ci_limits": [1.4, 2.4], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.68, + "dispersion_ci_limits": [1.36, 2.01], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -685,18 +675,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.53, - "dispersion_ci_limits": [1.44, 1.61], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [0.73, 2.94], "quantile_names": ["5", "95"], "median": 1.46, "median_ci_limits": [1.35, 1.57], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.53, + "dispersion_ci_limits": [1.44, 1.61], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -745,18 +734,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.51, - "dispersion_ci_limits": [1.43, 1.6], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [0.73, 2.83], "quantile_names": ["5", "95"], "median": 1.43, "median_ci_limits": [1.33, 1.54], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.51, + "dispersion_ci_limits": [1.43, 1.6], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -805,18 +793,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.25, - "dispersion_ci_limits": [1.14, 1.36], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [3.05, 6.39], "quantile_names": ["5", "95"], "median": 4.41, "median_ci_limits": [3.9, 4.92], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.25, + "dispersion_ci_limits": [1.14, 1.36], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -865,18 +852,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.24, - "dispersion_ci_limits": [1.12, 1.35], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [3.11, 6.26], "quantile_names": ["5", "95"], "median": 4.41, "median_ci_limits": [3.89, 4.94], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.24, + "dispersion_ci_limits": [1.12, 1.35], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -2941,18 +2927,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.5, - "dispersion_ci_limits": [1.2, 1.9], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [3.2, 4.6, 7.6, 11.2], "quantile_names": ["5" ,"25", "75", "95"], "median": 5.9, "median_ci_limits": [4.4, 7.6], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.5, + "dispersion_ci_limits": [1.2, 1.9], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -3026,18 +3011,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.04, - "dispersion_ci_limits": [1.04, 1.08], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [2.9, 3], "quantile_names": ["25", "75"], "median": 3, "median_ci_limits": [0.5, 3.1], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.04, + "dispersion_ci_limits": [1.04, 1.08], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -3091,18 +3075,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.41, - "dispersion_ci_limits": [1.34, 1.5], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [4.5, 7.1], "quantile_names": ["25", "75"], "median": 5.6, "median_ci_limits": [5.3, 6], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.41, + "dispersion_ci_limits": [1.34, 1.5], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -3155,18 +3138,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.37, - "dispersion_ci_limits": [1.27, 1.52], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [4.3, 6.6], "quantile_names": ["25", "75"], "median": 5.3, "median_ci_limits": [5, 5.7], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.37, + "dispersion_ci_limits": [1.27, 1.52], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -3220,18 +3202,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.04, - "dispersion_ci_limits": [1.04, 1.05], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [8.1, 8.6], "quantile_names": ["25", "75"], "median": 8.4, "median_ci_limits": [5.1, 9.4], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.04, + "dispersion_ci_limits": [1.04, 1.05], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -3285,18 +3266,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.5, - "dispersion_ci_limits": [1.22, 1.82], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [3.1, 5.3], "quantile_names": ["25", "75"], "median": 4, "median_ci_limits": [3.4, 4.9], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.5, + "dispersion_ci_limits": [1.22, 1.82], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -3350,18 +3330,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.82, - "dispersion_ci_limits": [1.27, 2.67], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [1, 1.7, 3.8, 7], "quantile_names": ["5", "25", "75", "95"], "median": 2.6, "median_ci_limits": [1.6, 3.5], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.82, + "dispersion_ci_limits": [1.27, 2.67], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -3414,18 +3393,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.04, - "dispersion_ci_limits": [1.04, 1.29], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [2.8, 3], "quantile_names": ["25", "75"], "median": 2.9, "median_ci_limits": [0.5, 3.1], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.04, + "dispersion_ci_limits": [1.04, 1.29], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -3479,18 +3457,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.35, - "dispersion_ci_limits": [1.12, 1.47], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [8.7, 13.3], "quantile_names": ["25", "75"], "median": 10.8, "median_ci_limits": [8.4, 14.2], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.35, + "dispersion_ci_limits": [1.12, 1.47], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -3543,18 +3520,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.66, - "dispersion_ci_limits": [1.48, 1.82], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [1.9, 3.2, 6.3, 10.3], "quantile_names": ["5", "25", "75", "95"], "median": 4.4, "median_ci_limits": [4, 5], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.66, + "dispersion_ci_limits": [1.48, 1.82], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -3607,18 +3583,17 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.67, - "dispersion_ci_limits": [1.47, 1.84], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "quantile_values": [1.9, 3.1, 6.2, 10.3], "quantile_names": ["5", "25", "75", "95"], "median": 4.4, "median_ci_limits": [3.9, 5], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.67, + "dispersion_ci_limits": [1.47, 1.84], + "dispersion_ci": 95 }, "citation": { "author": [ @@ -10106,11 +10081,7 @@ "epi_distribution": "incubation period", "probability_distribution": { "prob_distribution": "lnorm", - "parameters": { - "dispersion": 1.52, - "dispersion_ci_limits": [1.32, 1.72], - "dispersion_ci": 95 - } + "parameters": { } }, "summary_statistics": { "mean": 5.5, @@ -10118,7 +10089,10 @@ "quantile_names": ["2.5", "97.5"], "median": 5.1, "median_ci_limits": [4.5, 5.8], - "median_ci": 95 + "median_ci": 95, + "dispersion": 1.52, + "dispersion_ci_limits": [1.32, 1.72], + "dispersion_ci": 95 }, "citation": { "author": [