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Move mean to parameter for negative binomial in DB #380

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Sep 23, 2024
Merged

Move mean to parameter for negative binomial in DB #380

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c69f6bd
move negative binomial mean from summary statistics to params in JSON DB
joshwlambert Sep 23, 2024
e8adfbc
add propertyNames, mean and sd descriptions and if-else check for mea…
joshwlambert Sep 23, 2024
6363beb
change validate-json workflow to `strict = FALSE` due to distribution…
joshwlambert Sep 23, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/validate-json.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ jobs:
engine = "ajv",
verbose = TRUE,
greedy = TRUE,
strict = TRUE,
strict = FALSE,
error = TRUE
)
shell: Rscript {0}
93 changes: 90 additions & 3 deletions inst/extdata/data_dictionary.json
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,10 @@
},
"parameters": {
"type": "object",
"properties": {
"propertyNames": {
"enum": ["shape", "shape_ci_limits", "shape_ci", "scale", "scale_ci_limits", "scale_ci", "meanlog", "meanlog_ci_limits", "meanlog_ci", "sdlog", "sdlog_ci_limits", "sdlog_ci", "dispersion", "dispersion_ci_limits", "dispersion_ci", "precision", "precision_ci_limits", "precision_ci", "mean", "mean_ci_limits", "mean_ci", "sd", "sd_ci_limits", "sd_ci"]
},
"properties": {
"shape": {
"description": "The shape parameter of either the gamma or Weibull distribution.",
"examples": [2.0, 4.5],
Expand Down Expand Up @@ -108,7 +111,7 @@
"type": ["number", "null"]
},
"dispersion": {
"description": "The dispersion factor of the lognormal distribution. This can be used with the median to calculate the bounds that contain approximately two-thirds of The data.",
"description": "The dispersion parameter of the distribution. This is often used for negative binomial distributions and is often represented as k. This is distinct from the dispersion for a lognormal distribution, which is considered a summary statistic.",
"examples": [1.2, 1.4],
"type": "number"
},
Expand Down Expand Up @@ -142,11 +145,95 @@
"description": "The interval of the uncertainty around the precision parameter, for example 95% confidence interval would be 95.",
"examples": [95, 90, 80],
"type": ["number", "null"]
},
"mean": {
"description": "The mean of the distribution. Only applies to normal and negative binomial distributions (checked by schema below), for other probability distributions the mean should be included in the summary statistics.",
"examples": [1.0, 2.5],
"type": ["number", "null"]
},
"mean_ci_limits": {
"description": "The confidence interval of the distribution's mean, specified by two numbers in an array.",
"examples": [[0.3, 0.8], [1.4, 1.45]],
"type": ["array", "null"],
"items": {
"type": "number"
}
},
"mean_ci": {
"description": "The interval of the uncertainty around the mean, for example 95% confidence interval would be 95.",
"examples": [95, 90, 80],
"type": ["number", "null"]
},
"sd": {
"description": "The standard deviation of the distribution. Only applies to normal distributions (checked by schema below), for other probability distributions the standard deviation should be included in the summary statistics.",
"examples": [1.0, 2.5],
"type": ["number", "null"]
},
"sd_ci_limits": {
"description": "The confidence interval of the distribution's standard deviation, specified by two numbers in an array.",
"examples": [[0.3, 0.8], [1.4, 1.45]],
"type": ["array", "null"],
"items": {
"type": "number"
}
},
"sd_ci": {
"description": "The interval of the uncertainty around the standard deviation, for example 95% confidence interval would be 95.",
"examples": [95, 90, 80],
"type": ["number", "null"]
}
}
}
},
"required": ["prob_distribution"]
"required": ["prob_distribution"],
"if": {
"properties": {
"prob_distribution": { "const": "norm" }
}
},
"then": {
"properties": {
"parameters": {
"type": "object",
"anyOf": [
{ "required": ["mean"] },
{ "required": ["sd"] }
]
}
}
},
"else": {
"if": {
"properties": {
"prob_distribution": { "const": "nbinom" }
}
},
"then": {
"properties": {
"parameters": {
"type": "object",
"anyOf": [
{ "required": ["mean"] },
{ "required": ["dispersion"] }
]
}
}
},
"else": {
"properties": {
"parameters": {
"type": "object",
"not": {
"anyOf": [
{ "required": ["mean"] },
{ "required": ["sd"] },
{ "required": ["dispersion"] }
]
}
}
}
}
}
},
"summary_statistics": {
"type": "object",
Expand Down
86 changes: 38 additions & 48 deletions inst/extdata/parameters.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2196,16 +2196,15 @@
"probability_distribution": {
"prob_distribution": "nbinom",
"parameters": {
"mean": 1.63,
"mean_ci_limits": [0.54, 2.65],
"mean_ci": 90,
"dispersion": 0.16,
"dispersion_ci_limits": [0.11, 0.64],
"dispersion_ci": 90
}
},
"summary_statistics": {
"mean": 1.63,
"mean_ci_limits": [0.54, 2.65],
"mean_ci": 90
},
"summary_statistics": { },
"citation": {
"author": [
{
Expand Down Expand Up @@ -2254,16 +2253,15 @@
"probability_distribution": {
"prob_distribution": "nbinom",
"parameters": {
"mean": 0.94,
"mean_ci_limits": [0.27, 1.51],
"mean_ci": 90,
"dispersion": 0.17,
"dispersion_ci_limits": [0.1, 0.64],
"dispersion_ci": 90
}
},
"summary_statistics": {
"mean": 0.94,
"mean_ci_limits": [0.27, 1.51],
"mean_ci": 90
},
"summary_statistics": { },
"citation": {
"author": [
{
Expand Down Expand Up @@ -2312,16 +2310,15 @@
"probability_distribution": {
"prob_distribution": "nbinom",
"parameters": {
"mean": 3.19,
"mean_ci_limits": [1.66, 4.62],
"mean_ci": 90,
"dispersion": 0.37,
"dispersion_ci_limits": [0.26, 0.69],
"dispersion_ci": 90
}
},
"summary_statistics": {
"mean": 3.19,
"mean_ci_limits": [1.66, 4.62],
"mean_ci": 90
},
"summary_statistics": { },
"citation": {
"author": [
{
Expand Down Expand Up @@ -2370,16 +2367,15 @@
"probability_distribution": {
"prob_distribution": "nbinom",
"parameters": {
"mean": 0.8,
"mean_ci_limits": [0.32, 1.2],
"mean_ci": 90,
"dispersion": 0.32,
"dispersion_ci_limits": [0.16, 1.76],
"dispersion_ci": 90
}
},
"summary_statistics": {
"mean": 0.8,
"mean_ci_limits": [0.32, 1.2],
"mean_ci": 90
},
"summary_statistics": { },
"citation": {
"author": [
{
Expand Down Expand Up @@ -2428,16 +2424,15 @@
"probability_distribution": {
"prob_distribution": "nbinom",
"parameters": {
"mean": 1.6,
"mean_ci_limits": [0.88, 2.16],
"mean_ci": 90,
"dispersion": 0.65,
"dispersion_ci_limits": [0.34, 2.32],
"dispersion_ci": 90
}
},
"summary_statistics": {
"mean": 1.6,
"mean_ci_limits": [0.88, 2.16],
"mean_ci": 90
},
"summary_statistics": { },
"citation": {
"author": [
{
Expand Down Expand Up @@ -2486,14 +2481,13 @@
"probability_distribution": {
"prob_distribution": "nbinom",
"parameters": {
"mean": 1.49,
"dispersion": 0.72,
"dispersion_ci_limits": [0.44, 2.05],
"dispersion_ci": 90
}
},
"summary_statistics": {
"mean": 1.49
},
"summary_statistics": { },
"citation": {
"author": [
{
Expand Down Expand Up @@ -2542,16 +2536,15 @@
"probability_distribution": {
"prob_distribution": "nbinom",
"parameters": {
"mean": 0.32,
"mean_ci_limits": [0.22, 0.40],
"mean_ci": 90,
"dispersion": 0.58,
"dispersion_ci_limits": [0.32, 3.57],
"dispersion_ci": 90
}
},
"summary_statistics": {
"mean": 0.32,
"mean_ci_limits": [0.22, 0.40],
"mean_ci": 90
},
"summary_statistics": { },
"citation": {
"author": [
{
Expand Down Expand Up @@ -2600,16 +2593,15 @@
"probability_distribution": {
"prob_distribution": "nbinom",
"parameters": {
"mean": 1.32,
"mean_ci_limits": [1.01, 1.61],
"mean_ci": 90,
"dispersion": 1.37,
"dispersion_ci_limits": [0.88, 3.53],
"dispersion_ci": 90
}
},
"summary_statistics": {
"mean": 1.32,
"mean_ci_limits": [1.01, 1.61],
"mean_ci": 90
},
"summary_statistics": { },
"citation": {
"author": [
{
Expand Down Expand Up @@ -2658,14 +2650,13 @@
"probability_distribution": {
"prob_distribution": "nbinom",
"parameters": {
"mean": 0.7,
"mean_ci_limits": [0.20, 1.05],
"mean_ci": 90,
"dispersion": 1.66
}
},
"summary_statistics": {
"mean": 0.7,
"mean_ci_limits": [0.20, 1.05],
"mean_ci": 90
},
"summary_statistics": { },
"citation": {
"author": [
{
Expand Down Expand Up @@ -2714,14 +2705,13 @@
"probability_distribution": {
"prob_distribution": "nbinom",
"parameters": {
"mean": 1.5,
"mean_ci_limits": [0.85, 2.08],
"mean_ci": 90,
"dispersion": 5.10
}
},
"summary_statistics": {
"mean": 1.5,
"mean_ci_limits": [0.85, 2.08],
"mean_ci": 90
},
"summary_statistics": { },
"citation": {
"author": [
{
Expand Down
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