diff --git a/.gitignore b/.gitignore
index 913eeff..41bec2d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,7 @@
*.jl.cov
*.jl.*.cov
*.jl.mem
+test/csv/rds/
docs/build/
+docs/deprecated
+examples
diff --git a/Project.toml b/Project.toml
index 49fd47c..e599a68 100644
--- a/Project.toml
+++ b/Project.toml
@@ -4,14 +4,13 @@ uuid = "535c2557-d7d0-564d-8ff9-4ae146c18cfe"
version = "0.2.0"
[deps]
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
[extras]
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -21,10 +20,11 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
test = ["CSV", "Test"]
[compat]
-julia = "1.0, 1.1, 1.2"
-DataFrames = "0.19"
+julia = "1.0, 1.1, 1.2, 1.3"
Distributions = "0.16, 0.17, 0.18, 0.19, 0.20, 0.21"
StatsBase = "0.22, 0.23, 0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30, 0.31, 0.32"
-CSV = "0.5"
+DataFrames = "0.19"
QuadGK = "2.0, 2.1"
+SpecialFunctions = "0.8, 0.9"
Roots = "0.7, 0.8"
+CSV = "0.5"
diff --git a/README.md b/README.md
index 4a0740e..ee18a80 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,6 @@ The package is designed to perform calculations related to the planning and anal
using Pkg; Pkg.add("ClinicalTrialUtilities");
```
-
### Usage
**NB! Hypothesis types:**
@@ -28,9 +27,9 @@ using Pkg; Pkg.add("ClinicalTrialUtilities");
- :ei - Equivalencens: two one-sided hypothesis;
- :ns - Non-Inferiority / Superiority: one-sided hypothesis, for some cases you should use two-sided hypothesis for Non-Inferiority/Superiority, you can use alpha/2 for this;
-
### Examples
+#### SampleSize
```
#Sample size for one proportion equality
ctsamplen(param=:prop, type=:ea, group=:one, a=0.3, b=0.5)
@@ -40,18 +39,25 @@ ctsamplen(param=:mean, type=:ei, group=:two, diff=0.3, sd=1, a=0.3, b=0.5)
ctsamplen(param=:or, type=:ns, diff=-0.1, a=0.3, b=0.5, k=2)
#Odd ratio equality
ctsamplen(param=:or, type=:ea, a=0.3, b=0.5, k=2)
+```
-#Power
-ctpower(param=:mean, type=:ea, group=:one, a=1.5, b=2, sd=1,n=32, alpha=0.05)
-
-#Bioequivalence sample size
+#### Bioequivalence sample size
+```
besamplen(alpha=0.05, theta1=0.8, theta2=1.25, theta0=0.95, cv=0.15, method=:owenq)
besamplen(cv=0.20, method=:nct)
besamplen(cv=0.347, design=:parallel)
besamplen(cv=0.40)
besamplen(cv=0.347, design=:d2x2x4, method=:nct)
+```
-#Bioequivalence power for 2x2 design, default method - OwensQ
+#### Power
+```
+ctpower(param=:mean, type=:ea, group=:one, a=1.5, b=2, sd=1,n=32, alpha=0.05)
+```
+
+#### Bioequivalence power
+```
+#2x2 design, default method - OwensQ
bepower(alpha=0.05, logscale=true, theta1=0.8, theta2=1.25, theta0=0.95, cv=0.2, n=20, design=:d2x2, method=:owenq)
#Same
bepower(alpha=0.05, cv=0.2, n=20, design=:d2x2)
@@ -62,11 +68,15 @@ bepower(alpha=0.1, logscale=false, theta1=-0.1, theta2=0.1, theta0=0, cv=0.14, n
#Simple notations
bepower(cv=0.4, n=35, design=:d2x4x4)
bepower(cv=0.14, n=21)
+```
-#CV from CI
+#### Bioequivalence CV from CI
+```
cvfromci(;alpha = 0.05, theta1 = 0.9, theta2 = 1.25, n=30, design=:d2x2x4)
+```
-#Polled CV
+#### Polled CV
+```
data = DataFrame(cv = Float64[], df = Int[])
push!(data, (0.12, 12))
push!(data, (0.2, 20))
@@ -75,7 +85,6 @@ pooledcv(data; cv=:cv, df=:df, alpha=0.05, returncv=true)
```
-
### Copyrights
Clinical Trial Utilities
diff --git a/docs/CI.md b/docs/CI.md
deleted file mode 100644
index b62f40c..0000000
--- a/docs/CI.md
+++ /dev/null
@@ -1,239 +0,0 @@
-# Confidence Intervals
-
-CI submodule needs for clinical trial simulations with binomial outcomes, but can easily used for confidence interval evaluating in common practice.
-
-## Functions
-
-- [oneProp](#oneProp) - One proportion
-
-- [oneMean](#oneMean) - One mean
-
-- [twoProp](#twoProp) - Two proportions
-
-- [twoMeans](#twoMeans) - Two means
-
- - [cmh](#cmh) - Cochran–Mantel–Haenszel confidence intervals.
-
- - [Examples](#Examples)
-
-### oneProp
-
-Confidence interval calculation for one proportion.
-
-```
-CI.oneProp(x::Int, n::Int; alpha=0.05, method=:wilson)
-```
-
-**x**::Int - number of positive outcomes;
-
-**n**::Int - number of subjects;
-
-**alpha** - alpha value (all CI computed as two-sided);
-
-**method** - computation method;
-
-- wilson - Wilson's confidence interval (CI) for a single proportion (wilson score) (default);
-- wilsoncc - Wilson's CI with continuity correction (CC);
-- cp - Clopper-Pearson exact CI;
-- soc - SOC: Second-Order corrected CI;
-- blaker - Blaker exact CI for discrete distributions;
-- arcsine - Arcsine CI;
-- wald - Wald CI without CC;
-
-### twoProp
-
-Confidence interval calculation for two proportion.
-
-```
- CI.twoprop(x1::Int, n1::Int, x2::Int, n2::Int; alpha=0.05, type=[:diff|:rr|:or], method::Symbol)
- ```
-
- **x1** - number of positive outcomes in group 1;
-
- **n1** - number of subjects in group 1;
-
- **x2** - number of positive outcomes in group 2;
-
- **n2** - number of subjects in group 2;
-
- **alpha** - alpha value (all CI computed as two-sided);
-
- **type** - comparation type: difference, relative risk, odd ratio;
-
-- diff - Difference;
-- rr - Risk ratio;
-- or - Odd ratio;
-
- **method** - computation method;
-
-Difference:
-
-- nhs - Newcombes Hybrid (wilson) Score interval for the difference of proportions
-- nhscc - Newcombes Hybrid Score CC
-- ac - Agresti-Caffo interval for the difference of proportions
-- mn - Method of Mee 1984 with Miettinen and Nurminen modification
-- mee - Mee maximum likelihood method
-- wald - Wald CI
-- waldcc - Wald CC CI
-
-Risk ratio
-
-- cli - Crude log interval
-- mover - Method of variance estimates recovery
-
-Odd ratio
-
-- mn - Miettinen-Nurminen CI
-- woolf - Woolf logit CI
-- awoolf - Adjusted Woolf interval (Gart adjusted logit)
-
-### oneMean
-
-Confidence interval for one mean.
-
-```
-CI.oneMean(m::Real, s::Real, n::Int, alpha::Real; method=:norm)::ConfInt
-```
-
-**m** - mean;
-
-**s** - variance;
-
-**n** - subject number;
-
-**alpha** - Alpha;
-
-**method** - distribution:
-
-- :norm - Normal distribution (default);
-- :tdist - T Distribution.
-
-### twoMeans
-
-Confidence interval for mean difference.
-
-```
-CI.twoMeans(m1::Real, s1::Real, n1::Real, m2::Real, s2::Real, n2::Real; alpha::Real=0.05, method=:ev)::ConfInt
-```
-
-**m1** - mean group 1;
-
-**s1** - variance group 1;
-
-**n1** - subject number group 1;
-
-**m2** - mean group 2;
-
-**s2** - variance group 2;
-
-**n2** - subject number group 2;
-
-**alpha** - Alpha;
-
-**method** - equal or unequal variance;
-
-- :ev - equal variance (default);
-- :uv - unequal variance with Welch-Satterthwaite df correction.
-
-### cmh
-
-Cochran–Mantel–Haenszel confidence intervals.
-
-```
-CI.cmh(data::DataFrame; a = :a, b = :b, c = :c, d = :d, alpha = 0.05, type =:diff, method = :default, logscale = false)::ConfInt
-```
-
- **data**- dataframe with 4 columns, each line represent 2X2 table
-
-**a** **b** **c** **d** - dataframe table names (number of subjects in 2X2 table):
-
-| | outcome 1 | outcome 2 |
-|---------|-----------|-----------|
-| group 1 | a | b |
-| group 2 | c | d |
-
-**alpha** - alpha value (all CI computed as two-sided);
-
-**type** - estimation type
-- diff - risk difference (default)
-- or - odd ratio
-- rr - risk ratio
-
-**logscale** - return CI in log scale.
-
-- false (default)
-- true
-
-For example, let we have 2 sources:
-
-1:
-
-| | outcome 1 | outcome 2 |
-|---------|-----------|-----------|
-| group 1 | 8 | 98 |
-| group 2 | 5 | 115 |
-
-2:
-
-| | outcome 1 | outcome 2 |
-|---------|-----------|-----------|
-| group 1 | 22 | 76 |
-| group 2 | 16 | 69 |
-
-
-Dataframe construction:
-
-```
-data = DataFrame(a = Int[], b = Int[], c = Int[], d = Int[])
- push!(data, (8, 98, 5, 115))
- push!(data, (22, 76, 16, 69))
-```
-
-For risk difference use:
-
-```
-ci = ClinicalTrialUtilities.CI.cmh(data, alpha = 0.1)
-```
-
-## Examples
-
-```
-ClinicalTrialUtilities.CI.oneProp(81, 263, alpha=0.05, method=:wilson)
-
-ClinicalTrialUtilities.CI.twoprop(7, 34, 1, 34; alpha=0.05, type=:diff, method=:nhs)
-
-ClinicalTrialUtilities.CI.twoprop(2, 14, 1, 11; alpha=0.05, type=:or, method=:woolf)
-
-ClinicalTrialUtilities.CI.twoMeans(30, 10, 30, 40, 12, 35, alpha=0.05, method=:ev)
-
-```
-
-## References:
-
-Wilson, E.B. (1927) Probable inference, the law of succession, and statistical inference. J. Amer. Stat. Assoc22, 209–212.
-
-Clopper, C. and Pearson, E.S. (1934) The use of confidence or fiducial limits illustrated in the case of the binomial. Biometrika 26, 404–413.
-
-Blaker, H. (2000). Confidence curves and improved exact confidence intervals for discrete distributions. Canadian Journal of Statistics28 (4), 783–798.
-
-T. Tony Cai One-sided confidence intervals in discrete distributions. doi:10.1016/j.jspi.2004.01.00.
-
-Newcombe, R. G. (1998) Two-sided confidence intervals for the single proportion: comparison of seven methods. Statistics in Medicine. 17 (8): 857–872. doi:10.1002/(SICI)1097-0258(19980430)17:8<857::AID-SIM777>3.0.CO;2-E. PMID 9595616.
-
-Miettinen O. S., Nurminen M. (1985) Comparative analysis of two rates. Statistics in Medicine4,213–226
-
-Lawson, R (2005):Smallsample confidence intervals for the odds ratio. Communication in Statistics Simulation andComputation, 33, 1095-1113.
-
-Woolf, B. (1955). On estimating the relation between blood group and disease. Annals of human genetics, 19(4):251-253.
-
-Gart, JJand Nam, J (1988): Approximate interval estimation of the ratio of binomial parameters: Areview and corrections for skewness. Biometrics 44, 323-338.
-
-Donner, A. and Zou, G. (2012). Closed-form confidence intervals for functions of the normal mean and standard deviation. Statistical Methods in Medical Research, 21(4):347-359.
-
-Newcombe RG (1998): Interval Estimation for the Difference Between Independent Proportions: Comparison of Eleven Methods. Statistics in Medicine 17, 873-890.
-
-Agresti A, Caffo B., “Simple and effective confidence intervals for proportions and differences of proportions result from adding two successes and two failures”, American Statistician 54: 280–288 (2000)
-
-Mee RW (1984) Confidence bounds for the difference between two probabilities,Biometrics40:1175-1176
-
-Rothman, K. J., Greenland, S., & Lash, T. L. (2008). Modern epidemiology (3rd ed.). Philadelphia: Lippincott Williams & Wilkins.
diff --git a/docs/PK.md b/docs/PK.md
deleted file mode 100644
index 7eb2092..0000000
--- a/docs/PK.md
+++ /dev/null
@@ -1,77 +0,0 @@
-# Pharmacokinetics
-
-Pharmacokinetics module.
-
-## Functions
-
-- [nca](#nca) - Non-noncompartment analysis.
-
-### nca
-
-Non-noncompartment analysis.
-
-```
-PK.nca(data::DataFrame; conc=:Concentration, time=:Time, sort = NaN, calcm = :lint, bl::Float64 = NaN, th::Float64 = NaN)
-```
-
-**conc**::Symbol - concentration column of dataframe data;
-
-**time**::Symbol - time column of dataframe data;
-
-**sort**::Symbol[] - sorting columns in dataframe (NaN by default in only one profile);
-
-**calcm**::Symbol - calculation method:
-
-- :lint - linear trapezoidal;
-- :logt - linear trapezoidal before tmax and linear up log down after;
-- :lulg - linear up log down: if c2 >= c1 - linear, else log;
-
-**bl**::Float64 - Baseline for pharmacodynamics;
-
-**th**::Float64 - Threshold for pharmacodynamics;
-
-### Simple example
-
-```
-data = DataFrame(Concentration = Float64[], Time = Float64[], Subject = String[], Formulation = String[])
- push!(data, (0.0, 0, "1", "T"))
- push!(data, (0.2, 1, "1", "T"))
- push!(data, (0.3, 2, "1", "T"))
- push!(data, (0.4, 3, "1", "T"))
- push!(data, (0.3, 4, "1", "T"))
- push!(data, (0.2, 5, "1", "T"))
- push!(data, (0.1, 6, "1", "T"))
-
-pk = ClinicalTrialUtilities.PK.nca(data)
-
-pk = ClinicalTrialUtilities.PK.nca(data, conc = :Concentration, time = :Time, bl = 2.5, th = 1.5)
-```
-
-### Example with sorting
-
-```
-data = DataFrame(Concentration = Float64[], Time = Float64[], Subject = String[], Formulation = String[])
- push!(data, (0.0, 0, "1", "T"))
- push!(data, (0.2, 1, "1", "T"))
- push!(data, (0.3, 2, "1", "T"))
- push!(data, (0.4, 3, "1", "T"))
- push!(data, (0.3, 4, "1", "T"))
- push!(data, (0.2, 5, "1", "T"))
- push!(data, (0.1, 6, "1", "T"))
- push!(data, (0.0, 0, "2", "T"))
- push!(data, (0.3, 1, "2", "T"))
- push!(data, (0.4, 2, "2", "T"))
- push!(data, (0.5, 3, "2", "T"))
- push!(data, (0.3, 4, "2", "T"))
- push!(data, (0.1, 5, "2", "T"))
- push!(data, (0.05, 6, "2", "T"))
- push!(data, (0.1, 0, "1", "R"))
- push!(data, (0.2, 1, "1", "R"))
- push!(data, (0.9, 2, "1", "R"))
- push!(data, (0.8, 3, "1", "R"))
- push!(data, (0.3, 4, "1", "R"))
- push!(data, (0.2, 5, "1", "R"))
- push!(data, (0.1, 6, "1", "R"))
-pk = ClinicalTrialUtilities.PK.nca(data; sort=[:Formulation, :Subject], calcm = :logt)
-
-```
diff --git a/docs/SIM.md b/docs/SIM.md
deleted file mode 100644
index f78ecc5..0000000
--- a/docs/SIM.md
+++ /dev/null
@@ -1,47 +0,0 @@
-# Simulations
-
-Simulation submodule.
-
-## Functions
-
-Bioequivalence power simulation
-
-bepower(;alpha, logscale, theta1, theta2, theta0, cv, n, simnum, seed)
-
-Proportion power simulation
-
-ctPropPower(p1, n1, p2, n2, ref; alpha, type, citype, method, simnum, seed)
-
-Proportion simulation sample size
-
-ctPropSampleN(p1, p2, ref; alpha, beta, type, citype, method, simnum, seed)
-
-### bepower
-
-```
-bepower(;alpha=0.05, logscale=true, theta1=0.8, theta2=1.25, theta0=0.95, cv=0.0, n=0, simnum=5, seed=0)
-```
-
-### ctPropPower
-
-```
-ctPropPower(p1, n1, p2, n2, diff; alpha=0.05, type=:or, method=:mn, seed=0, simnum=5)
-```
-
-### ctPropSampleN
-
-```
-ctPropSampleN(p1, p2, ref; alpha=0.05, beta=0.2, type=:notdef, citype =:notdef, method=:notdef, simnum=5, seed=0)
-```
-
-### ctMeansPower
-
-```
-ctMeansPower(m1, s1, n1, m2, s2, n2, ref; alpha=0.05, method=:notdef, simnum=5, seed=0)
-```
-
-### ctMeansPowerFS
-
-```
-ctMeansPowerFS(m1, s1, n1, m2, s2, n2, ref;alpha=0.05, method=:notdef, simnum::Real=5, seed=0)
-```
diff --git a/docs/atomicFunc.md b/docs/atomicFunc.md
deleted file mode 100644
index b0792f9..0000000
--- a/docs/atomicFunc.md
+++ /dev/null
@@ -1,134 +0,0 @@
-
-
-μ₀ - Test Mean
-μ₁ - Reference Mean
-p₀ - Test Proportion
-p₁ - Reference Proportion
-σ - SD
-δ - Margin Difference
-α - Alpha (Type I Error)
-β - Beta (Type II Error)
-
-# Sample Size
-
-## Means
-
-### One Sample Means
-
-```
-one_mean_equality(μ₀::Real, μ₁::Real, σ::Real, α::Float64, β::Float64)::Float64
-
-one_mean_equivalence(μ₀::Real, μ₁::Real, σ::Real, δ::Real, α::Float64, β::Float64)::Float64
-
-one_mean_superiority(μ₀::Real, μ₁::Real, σ::Real, δ::Real, α::Float64, β::Float64)::Float64
-```
-
-### Two Sample Means
-
-```
-two_mean_equality(μ₀::Real, μ₁::Real, σ::Real, α::Float64, β::Float64, k::Real)::Float64
-
-two_mean_equivalence(μ₀::Real, μ₁::Real, σ::Real, δ::Real, α::Float64, β::Float64, k::Real)::Float64
-
-two_mean_superiority(μ₀::Real, μ₁::Real, σ::Real, δ::Real, α::Float64, β::Float64, k::Real)::Float64
-```
-
-## Compare Proportion
-
-### One Sample Proportion
-
-```
-one_proportion_equality(p₀::Float64, p₁::Float64, α::Float64, β::Float64)::Float64
-
-one_proportion_equivalence(p₀::Float64, p₁::Float64, δ::Real, α::Float64, β::Float64)::Float64
-
-one_proportion_superiority(p₀::Float64, p₁::Float64, δ::Real, α::Float64, β::Float64)::Float64
-```
-
-### Two Sample Proportion
-
-```
-two_proportion_equality(p₀::Float64, p₁::Float64, α::Float64, β::Float64, k::Real)::Float64
-
-two_proportion_equivalence(p₀::Float64, p₁::Float64, δ::Real, α::Float64, β::Float64, k::Real)::Float64
-
-two_proportion_superiority(p₀::Float64, p₁::Float64, δ::Real, α::Float64, β::Float64, k::Real)::Float64
-```
-
-## Odd ratio
-
-```
-or_equality(p₀::Float64, p₁::Float64, α::Float64, β::Float64, k::Real)::Float64
-
-or_equivalence(p₀::Float64, p₁::Float64, δ::Real, α::Float64, β::Float64, k::Real)::Float64
-
-or_superiority(p₀::Float64, p₁::Float64, δ::Real, α::Float64, β::Float64, k::Real)::Float64
-```
-
-## McNemar's Equality test
-
-```
-mcnm(p10::Float64, p01::Float64, α::Float64, β::Float64)::Float64
-```
-
-# Power
-
-## Means
-
-### One Sample Means
-
-```
-one_mean_equality_pow(μ₀::Real, μ₁::Real, σ::Real, n::Int, α::Float64)::Float64
-
-one_mean_equivalence_pow(μ₀::Real, μ₁::Real, σ::Real, δ::Real, n::Int, α::Float64)::Float64
-
-one_mean_superiority_pow(μ₀::Real, μ₁::Real, σ::Real, δ::Real, n::Int, α::Float64)::Float64
-```
-
-### Two Sample Means
-
-```
-two_mean_equality_pow(μ₀::Real, μ₁::Real, σ::Real, n::Int, α::Float64, k::Real)::Float64
-
-two_mean_equivalence_pow(μ₀::Real, μ₁::Real, σ::Real, δ::Real, n::Int, α::Float64, k::Real)::Float64
-
-two_mean_superiority_pow(μ₀::Real, μ₁::Real, σ::Real, δ::Real, n::Int, α::Float64, k::Real)::Float64
-```
-
-## Compare Proportion
-
-### One Sample proportion
-
-```
-one_proportion_equality_pow(p₀::Float64, p₁::Float64, n::Int, α::Float64)::Float64
-
-one_proportion_equivalence_pow(p₀::Float64, p₁::Float64, δ::Real, n::Int, α::Float64)::Float64
-
-one_proportion_superiority_pow(p₀::Float64, p₁::Float64, δ::Real, n, α::Float64)::Float64
-```
-
-### Two Sample Proportion
-
-```
-two_proportion_equality_pow(p₀::Float64, p₁::Float64, n::Int, α::Float64, k::Real)::Float64
-
-two_proportion_equivalence_pow(p₀::Float64, p₁::Float64, δ::Real, n::Int, α::Float64, k::Real)::Float64
-
-two_proportion_superiority_pow(p₀::Float64, p₁::Float64, δ::Real, n::Int, α::Float64, k::Real)::Float64
-```
-
-## Odd Ratio
-
-```
-or_equality_pow(p₀::Float64, p₁::Float64, n::Int, α::Float64, k::Real)::Float64
-
-or_equivalence_pow(p₀::Float64, p₁::Float64, δ::Real, n::Int, α::Float64, k::Real)::Float64
-
-or_superiority_pow(p₀::Float64, p₁::Float64, δ::Real, n::Int, α::Float64, k::Real)::Float64
-```
-
-## McNemar's Equality test
-
-```
-mcnm_pow(p10::Float64, p01::Float64, n::Int, α::Float64)::Float64
-```
diff --git a/docs/exceptions.md b/docs/exceptions.md
deleted file mode 100644
index 73c1588..0000000
--- a/docs/exceptions.md
+++ /dev/null
@@ -1,20 +0,0 @@
-## CTUExeption codes
-
-
-100*: owensQo
-
-101*: owensQ
-
-102*: powerTOST
-
-1031: designProp
-
-104*: besamplen
-
-1051: cv2ci
-
-111*: SIM.bepower
-
-12**: sampleSize
-
-13**: CI
diff --git a/docs/src/ci.md b/docs/src/ci.md
index 85cc37c..a3a2920 100644
--- a/docs/src/ci.md
+++ b/docs/src/ci.md
@@ -1,40 +1,40 @@
-## Confidence Intervals
+# Confidence Intervals
-### Proportions
+## Proportions
-#### propci
+### propci
```@docs
ClinicalTrialUtilities.propci
```
-#### diffpropci
+### diffpropci
```@docs
ClinicalTrialUtilities.diffpropci
```
-#### rrpropci
+### rrpropci
```@docs
ClinicalTrialUtilities.rrpropci
```
-#### orpropci
+### orpropci
```@docs
ClinicalTrialUtilities.orpropci
```
-### Means
+## Means
-#### meanci
+### meanci
```@docs
ClinicalTrialUtilities.meanci
```
-#### .diffmeanci
+### .diffmeanci
```@docs
ClinicalTrialUtilities.diffmeanci
```
-### Cochran–Mantel–Haenszel confidence intervals
+## Cochran–Mantel–Haenszel confidence intervals
Table cell map:
@@ -43,17 +43,17 @@ Table cell map:
| group 1 | a | b |
| group 2 | c | d |
-#### diffcmhci
+### diffcmhci
```@docs
ClinicalTrialUtilities.diffcmhci
```
-#### orcmhci
+### orcmhci
```@docs
ClinicalTrialUtilities.orcmhci
```
-#### rrcmhci
+### rrcmhci
```@docs
ClinicalTrialUtilities.rrcmhci
```
diff --git a/docs/src/ds.md b/docs/src/ds.md
index ace16df..5867909 100644
--- a/docs/src/ds.md
+++ b/docs/src/ds.md
@@ -1,4 +1,4 @@
-## Descriptive statistics
+# Descriptive statistics
Calculation descriptive statistics by groups.
diff --git a/docs/src/examples.md b/docs/src/examples.md
index ef09f85..6342b72 100644
--- a/docs/src/examples.md
+++ b/docs/src/examples.md
@@ -1,8 +1,8 @@
-## Examples
+# Examples
-### Sample size
+## Sample size
-#### Equivalence for two means
+### Equivalence for two means
```julia
using ClinicalTrialUtilities
@@ -10,7 +10,7 @@ using ClinicalTrialUtilities
ctsamplen(param=:mean, type=:ei, group=:two, diff=0.3, sd=1, a=0.3, b=0.5)
```
-#### One proportion equality
+### One proportion equality
```julia
using ClinicalTrialUtilities
@@ -18,7 +18,7 @@ using ClinicalTrialUtilities
ctsamplen(param=:prop, type=:ea, group=:one, a=0.3, b=0.5)
```
-#### Odd ratio non-inferiority
+### Odd ratio non-inferiority
```julia
using ClinicalTrialUtilities
@@ -26,7 +26,7 @@ using ClinicalTrialUtilities
ctsamplen(param=:or, type=:ns, diff=-0.1, a=0.3, b=0.5, k=2)
```
-#### Odd ratio equality
+### Odd ratio equality
```julia
using ClinicalTrialUtilities
@@ -34,7 +34,7 @@ using ClinicalTrialUtilities
ctsamplen(param=:or, type=:ea, a=0.3, b=0.5, k=2)
```
-#### Bioequivalence
+### Bioequivalence
```julia
using ClinicalTrialUtilities
@@ -50,9 +50,9 @@ besamplen(cv=0.40)
besamplen(cv=0.347, design=:d2x2x4, method=:nct)
```
-### Power
+## Power
-#### Equality for one mean
+### Equality for one mean
```julia
using ClinicalTrialUtilities
@@ -60,7 +60,7 @@ using ClinicalTrialUtilities
ctpower(param=:mean, type=:ea, group=:one, a=1.5, b=2, sd=1,n=32, alpha=0.05)
```
-#### Bioequivalence
+### Bioequivalence
```julia
using ClinicalTrialUtilities
@@ -82,7 +82,7 @@ bepower(cv=0.4, n=35, design=:d2x4x4)
bepower(cv=0.14, n=21)
```
-### Confidence intervals
+## Confidence intervals
```julia
using ClinicalTrialUtilities
@@ -99,9 +99,9 @@ diffmeanci(30, 10, 30, 40, 12, 35, alpha=0.05, method=:ev)
```
-### Utilities
+## Utilities
-#### CV from CI
+### CV from CI
```julia
using ClinicalTrialUtilities
@@ -109,7 +109,7 @@ using ClinicalTrialUtilities
cvfromci(;alpha = 0.05, theta1 = 0.9, theta2 = 1.25, n=30, design=:d2x2x4)
```
-#### Polled CV
+### Polled CV
```julia
using DataFrames, ClinicalTrialUtilities
@@ -121,7 +121,7 @@ push!(data, (0.25, 30))
pooledcv(data; cv=:cv, df=:df, alpha=0.05, returncv=true)
```
-### Simulations
+## Simulations
```julia
using ClinicalTrialUtilities
diff --git a/docs/src/export.md b/docs/src/export.md
index ea66dcb..186fadb 100644
--- a/docs/src/export.md
+++ b/docs/src/export.md
@@ -1,4 +1,4 @@
-## Export
+# Export
### htmlexport
```@docs
diff --git a/docs/src/nca.md b/docs/src/nca.md
index 2ec55f2..eb30851 100644
--- a/docs/src/nca.md
+++ b/docs/src/nca.md
@@ -1,4 +1,4 @@
-## Non-compartment analysis
+# Non-compartment analysis
NCA analysis based on following steps:
@@ -16,37 +16,37 @@ ClinicalTrialUtilities.nca!
### Scenario
-1. Loading DataFrame
+1 Loading DataFrame
```julia
using CSV, DataFrames, ClinicalTrialUtilities
pkdata2 = CSV.File("pkdata.csv") |> DataFrame
```
-2. Subject list
+2 Subject list
```julia
pkds = pkimport(pkdata2, [:Subject, :Formulation]; time = :Time, conc = :Concentration)
```
-3. NCA analysis with default settings
+3 NCA analysis with default settings
```julia
pk = nca!(pkds)
```
-4. Exporting
+4 Exporting
```julia
ncadf = DataFrame(pk; unst = true)
```
-5. Descriptive statistics
+5 Descriptive statistics
```julia
ds = ClinicalTrialUtilities.descriptive(ncadf, stats = [:n, :mean, :sd], sort = [:Formulation])
```
-6. Exporting
+6 Exporting
```julia
dsdf = ClinicalTrialUtilities.DataFrame(ds; unst = true)
diff --git a/docs/src/power.md b/docs/src/power.md
index 1ea13c2..56dec89 100644
--- a/docs/src/power.md
+++ b/docs/src/power.md
@@ -1,4 +1,4 @@
-## Power
+# Power
### ctpower
```@docs
diff --git a/docs/src/random.md b/docs/src/random.md
index 2da72b6..42156e5 100644
--- a/docs/src/random.md
+++ b/docs/src/random.md
@@ -1,4 +1,4 @@
-## Randomization
+# Randomization
### randomseq
```@docs
diff --git a/docs/src/ref.md b/docs/src/ref.md
index 1b93b40..d3ab28c 100644
--- a/docs/src/ref.md
+++ b/docs/src/ref.md
@@ -1,4 +1,4 @@
-## References
+# References
### Sample size / power
diff --git a/docs/src/samplesize.md b/docs/src/samplesize.md
index 7d24a4a..d1d8f8e 100644
--- a/docs/src/samplesize.md
+++ b/docs/src/samplesize.md
@@ -1,4 +1,4 @@
-## SampleSize
+# SampleSize
Sample size estimation.
diff --git a/docs/src/sim.md b/docs/src/sim.md
index 8d47ce9..f6a8fc2 100644
--- a/docs/src/sim.md
+++ b/docs/src/sim.md
@@ -1,4 +1,4 @@
-## Simulations
+# Simulations
### ctsim
```@docs
diff --git a/docs/src/utils.md b/docs/src/utils.md
index 50f4c06..76dbcca 100644
--- a/docs/src/utils.md
+++ b/docs/src/utils.md
@@ -1,4 +1,4 @@
-## Utilities
+# Utilities
### cvfromci
```@docs
diff --git a/docs/src/validation.md b/docs/src/validation.md
index 48d9054..1451dac 100644
--- a/docs/src/validation.md
+++ b/docs/src/validation.md
@@ -1,3 +1,3 @@
-## Validation
+# Validation
See test procedures.
diff --git a/src/ClinicalTrialUtilities.jl b/src/ClinicalTrialUtilities.jl
index d4a5797..e59cccb 100644
--- a/src/ClinicalTrialUtilities.jl
+++ b/src/ClinicalTrialUtilities.jl
@@ -13,7 +13,7 @@
# If you want to check and get R code you can find some here: http://powerandsamplesize.com/Calculators/
__precompile__(true)
module ClinicalTrialUtilities
-using Distributions, StatsBase, Statistics, Random, Roots, QuadGK, DataFrames
+using Distributions, StatsBase, Random, Roots, QuadGK, DataFrames
import SpecialFunctions
import Base.show
import Base.showerror
diff --git a/src/testdata/MOESM1.csv b/src/testdata/MOESM1.csv
deleted file mode 100644
index 20f789d..0000000
--- a/src/testdata/MOESM1.csv
+++ /dev/null
@@ -1,37 +0,0 @@
-Subj Seq Per Trt Var
-3 TR 1 T 225.95
-1 RT 1 R 181.09
-2 RT 1 R 114.48
-4 RT 1 R 176.91
-5 TR 1 T 147.01
-6 TR 1 T 97.53
-7 RT 1 R 146.60
-8 TR 1 T 45.58
-9 RT 1 R 109.20
-10 RT 1 R 125.61
-11 TR 1 T 92.26
-12 RT 1 R 237.95
-13 TR 1 T 145.46
-14 TR 1 T 179.96
-15 TR 1 T 173.86
-16 RT 1 R 144.00
-17 RT 1 R 185.10
-18 TR 1 T 117.99
-1 RT 2 T 210.14
-2 RT 2 T 98.72
-3 TR 2 R 241.09
-4 RT 2 T 186.65
-5 TR 2 R 139.56
-6 TR 2 R 124.77
-7 RT 2 T 137.62
-8 TR 2 R 57.71
-9 RT 2 T 139.36
-10 RT 2 T 120.43
-11 TR 2 R 116.10
-12 RT 2 T 228.63
-13 TR 2 R 165.09
-14 TR 2 R 181.09
-15 TR 2 R 206.66
-16 RT 2 T 143.25
-17 RT 2 T 192.22
-18 TR 2 R 125.50
diff --git a/src/testdata/MOESM2.csv b/src/testdata/MOESM2.csv
deleted file mode 100644
index 64cbf07..0000000
--- a/src/testdata/MOESM2.csv
+++ /dev/null
@@ -1,37 +0,0 @@
-ObsNumber Subj Seq Per Trt Var
-1 1 TR 1 T 2.52
-2 2 TR 1 T 8.87
-3 3 TR 1 T 0.79
-4 4 TR 1 T 1.68
-5 5 TR 1 T 6.95
-6 6 TR 1 T 1.05
-7 7 TR 1 T 0.99
-8 8 TR 1 T 5.6
-9 9 TR 1 T 3.16
-10 1 TR 2 R 5.47
-11 2 TR 2 R 4.84
-12 3 TR 2 R 2.25
-13 4 TR 2 R 1.82
-14 5 TR 2 R 7.87
-15 6 TR 2 R 3.25
-16 7 TR 2 R 12.39
-17 8 TR 2 R 4.77
-18 9 TR 2 R 1.88
-19 10 RT 1 R 4.98
-20 11 RT 1 R 7.14
-21 12 RT 1 R 1.81
-22 13 RT 1 R 7.34
-23 14 RT 1 R 4.25
-24 15 RT 1 R 6.66
-25 16 RT 1 R 4.76
-26 17 RT 1 R 7.16
-27 18 RT 1 R 5.52
-28 10 RT 2 T 3.19
-29 11 RT 2 T 9.83
-30 12 RT 2 T 2.91
-31 13 RT 2 T 4.58
-32 14 RT 2 T 7.05
-33 15 RT 2 T 3.41
-34 16 RT 2 T 2.49
-35 17 RT 2 T 6.18
-36 18 RT 2 T 2.85
diff --git a/src/testdata/MOESM3.csv b/src/testdata/MOESM3.csv
deleted file mode 100644
index ec845a1..0000000
--- a/src/testdata/MOESM3.csv
+++ /dev/null
@@ -1,27 +0,0 @@
-ObsNumber Subj Seq Per Trt Var
-1 1 TR 1 T 2.52
-10 1 TR 2 R 5.47
-4 4 TR 1 T 1.68
-13 4 TR 2 R 1.82
-5 5 TR 1 T 6.95
-14 5 TR 2 R 7.87
-7 7 TR 1 T 0.99
-16 7 TR 2 R 12.39
-19 10 RT 1 R 4.98
-28 10 RT 2 T 3.19
-20 11 RT 1 R 7.14
-29 11 RT 2 T 9.83
-21 12 RT 1 R 1.81
-30 12 RT 2 T 2.91
-22 13 RT 1 R 7.34
-31 13 RT 2 T 4.58
-23 14 RT 1 R 4.25
-32 14 RT 2 T 7.05
-24 15 RT 1 R 6.66
-33 15 RT 2 T 3.41
-25 16 RT 1 R 4.76
-34 16 RT 2 T 2.49
-26 17 RT 1 R 7.16
-35 17 RT 2 T 6.18
-27 18 RT 1 R 5.52
-36 18 RT 2 T 2.85
diff --git a/src/testdata/MOESM4.csv b/src/testdata/MOESM4.csv
deleted file mode 100644
index 805080e..0000000
--- a/src/testdata/MOESM4.csv
+++ /dev/null
@@ -1,37 +0,0 @@
-ObsNumber Subj Seq Per Trt Var
-1 1 TR 1 T 2.52
-10 1 TR 2 R 5.47
-2 2 TR 1 T 8.87
-11 2 TR 2 R 4.84
-3 3 TR 1 T 0.79
-12 3 TR 2 R 2.25
-4 4 TR 1 T 1680000
-13 4 TR 2 R 1820000
-5 5 TR 1 T 6.95
-14 5 TR 2 R 7.87
-6 6 TR 1 T 1.05
-15 6 TR 2 R 3.25
-7 7 TR 1 T 0.99
-16 7 TR 2 R 12.39
-8 8 TR 1 T 5.6
-17 8 TR 2 R 4.77
-9 9 TR 1 T 3.16
-18 9 TR 2 R 1.88
-19 10 RT 1 R 4.98
-28 10 RT 2 T 3.19
-20 11 RT 1 R 7.14
-29 11 RT 2 T 9.83
-21 12 RT 1 R 1.81
-30 12 RT 2 T 2.91
-22 13 RT 1 R 7.34
-31 13 RT 2 T 4.58
-23 14 RT 1 R 4250000
-32 14 RT 2 T 7050000
-24 15 RT 1 R 6.66
-33 15 RT 2 T 3.41
-25 16 RT 1 R 4.76
-34 16 RT 2 T 2.49
-26 17 RT 1 R 7.16
-35 17 RT 2 T 6.18
-27 18 RT 1 R 5520000
-36 18 RT 2 T 2850000
diff --git a/src/testdata/MOESM5.csv b/src/testdata/MOESM5.csv
deleted file mode 100644
index a8244c6..0000000
--- a/src/testdata/MOESM5.csv
+++ /dev/null
@@ -1,37 +0,0 @@
-ObsNumber Subj Seq Per Trt Var
-1 1 TR 1 T 2.52
-2 2 TR 1 T 8.87
-3 3 TR 1 T 79.0
-4 4 TR 1 T 1.68
-5 5 TR 1 T 6.95
-6 6 TR 1 T 1.05
-7 7 TR 1 T 0.99
-8 8 TR 1 T 5.6
-9 9 TR 1 T 3.16
-10 1 TR 2 R 5.47
-11 2 TR 2 R 4.84
-12 3 TR 2 R 2.25
-13 4 TR 2 R 1.82
-14 5 TR 2 R 7.87
-15 6 TR 2 R 3.25
-16 7 TR 2 R 12.39
-17 8 TR 2 R 4.77
-18 9 TR 2 R 1.88
-19 10 RT 1 R 4.98
-20 11 RT 1 R 7.14
-21 12 RT 1 R 1.81
-22 13 RT 1 R 7.34
-23 14 RT 1 R 4.25
-24 15 RT 1 R 6.66
-25 16 RT 1 R 4.76
-26 17 RT 1 R 7.16
-27 18 RT 1 R 5.52
-28 10 RT 2 T 3.19
-29 11 RT 2 T 9.83
-30 12 RT 2 T 2.91
-31 13 RT 2 T 4.58
-32 14 RT 2 T 7.05
-33 15 RT 2 T 3.41
-34 16 RT 2 T 2.49
-35 17 RT 2 T 6.18
-36 18 RT 2 T 2.85
diff --git a/src/testdata/MOESM6.csv b/src/testdata/MOESM6.csv
deleted file mode 100644
index 9a18077..0000000
--- a/src/testdata/MOESM6.csv
+++ /dev/null
@@ -1,201 +0,0 @@
-ObsNumber Subj Seq Per Trt Var
-1 1 TR 1 T 4.34635
-2 1 TR 2 R 4.45488
-3 2 TR 1 T 3.22579
-4 2 TR 2 R 1.78912
-5 3 TR 1 T 1.46572
-6 3 TR 2 R 2.55294
-7 4 TR 1 T 4.05118
-8 4 TR 2 R 4.58297
-9 5 TR 1 T 3.65939
-10 5 TR 2 R 2.12957
-11 6 TR 1 T 1.40002
-12 6 TR 2 R 2.14148
-13 7 TR 1 T 3.67227
-14 7 TR 2 R 4.58497
-15 8 TR 1 T 4.04046
-16 8 TR 2 R 2.53935
-17 9 TR 1 T 1.46176
-18 9 TR 2 R 1.79842
-19 10 TR 1 T 3.2398
-20 10 TR 2 R 4.46071
-21 11 TR 1 T 4.33865
-22 11 TR 2 R 2.98584
-23 12 TR 1 T 1.64605
-24 12 TR 2 R 1.55107
-25 13 TR 1 T 2.78824
-26 13 TR 2 R 4.22009
-27 14 TR 1 T 4.5302
-28 14 TR 2 R 3.43345
-29 15 TR 1 T 1.93819
-30 15 TR 2 R 1.41915
-31 16 TR 1 T 2.35354
-32 16 TR 2 R 3.88228
-33 17 TR 1 T 4.59986
-34 17 TR 2 R 3.84653
-35 18 TR 1 T 2.31491
-36 18 TR 2 R 1.41315
-37 19 TR 1 T 1.97034
-38 19 TR 2 R 3.47419
-39 20 TR 1 T 4.54207
-40 20 TR 2 R 4.19218
-41 21 TR 1 T 2.7462
-42 21 TR 2 R 1.53357
-43 22 TR 1 T 1.66916
-44 22 TR 2 R 3.02832
-45 23 TR 1 T 4.36145
-46 23 TR 2 R 4.44286
-47 24 TR 1 T 3.19772
-48 24 TR 2 R 1.77079
-49 25 TR 1 T 1.474
-50 25 TR 2 R 2.5802
-51 26 TR 1 T 4.07237
-52 26 TR 2 R 4.5786
-53 27 TR 1 T 3.63348
-54 27 TR 2 R 2.10594
-55 28 TR 1 T 1.40039
-56 28 TR 2 R 2.16552
-57 29 TR 1 T 3.69786
-58 29 TR 2 R 4.5886
-59 30 TR 1 T 4.01878
-60 30 TR 2 R 2.5123
-61 31 TR 1 T 1.45421
-62 31 TR 2 R 1.81731
-63 32 TR 1 T 3.26777
-64 32 TR 2 R 4.47204
-65 33 TR 1 T 4.32293
-66 33 TR 2 R 2.95752
-67 34 TR 1 T 1.63117
-68 34 TR 2 R 1.56332
-69 35 TR 1 T 2.81634
-70 35 TR 2 R 4.23823
-71 36 TR 1 T 4.52169
-72 36 TR 2 R 3.40612
-73 37 TR 1 T 1.91716
-74 37 TR 2 R 1.42377
-75 38 TR 1 T 2.37955
-76 38 TR 2 R 3.90577
-77 39 TR 1 T 4.59923
-78 39 TR 2 R 3.82237
-79 40 TR 1 T 2.28942
-80 40 TR 2 R 1.40978
-81 41 TR 1 T 1.99218
-82 41 TR 2 R 3.50117
-83 42 TR 1 T 4.54938
-84 42 TR 2 R 4.1731
-85 43 TR 1 T 2.71828
-86 43 TR 2 R 1.52247
-87 44 TR 1 T 1.68509
-88 44 TR 2 R 3.05664
-89 45 TR 1 T 4.37611
-90 45 TR 2 R 4.43039
-91 46 TR 1 T 3.16958
-92 46 TR 2 R 1.75285
-93 47 TR 1 T 1.48275
-94 47 TR 2 R 2.6076
-95 48 TR 1 T 4.09322
-96 48 TR 2 R 4.57374
-97 49 TR 1 T 3.60737
-98 49 TR 2 R 2.08259
-99 50 TR 1 T 1.40127
-100 50 TR 2 R 2.18981
-101 51 RT 1 R 3.72324
-102 51 RT 2 T 4.59172
-103 52 RT 1 R 3.99678
-104 52 RT 2 T 2.4854
-105 53 RT 1 R 1.44714
-106 53 RT 2 T 1.83657
-107 54 RT 1 R 3.29565
-108 54 RT 2 T 4.48291
-109 55 RT 1 R 4.30679
-110 55 RT 2 T 2.92921
-111 56 RT 1 R 1.61672
-112 56 RT 2 T 1.57601
-113 57 RT 1 R 2.84451
-114 57 RT 2 T 4.25597
-115 58 RT 1 R 4.5127
-116 58 RT 2 T 3.37866
-117 59 RT 1 R 1.89648
-118 59 RT 2 T 1.42888
-119 60 RT 1 R 2.40575
-120 60 RT 2 T 3.92898
-121 61 RT 1 R 4.5981
-122 61 RT 2 T 3.79794
-123 62 RT 1 R 2.26415
-124 62 RT 2 T 1.4069
-125 63 RT 1 R 2.01434
-126 63 RT 2 T 3.52799
-127 64 RT 1 R 4.55621
-128 64 RT 2 T 4.15366
-129 65 RT 1 R 2.69044
-130 65 RT 2 T 1.51183
-131 66 RT 1 R 1.70143
-132 66 RT 2 T 3.08493
-133 67 RT 1 R 4.39035
-134 67 RT 2 T 4.41748
-135 68 RT 1 R 3.14139
-136 68 RT 2 T 1.73531
-137 69 RT 1 R 1.49198
-138 69 RT 2 T 2.63512
-139 70 RT 1 R 4.11373
-140 70 RT 2 T 4.56838
-141 71 RT 1 R 3.58107
-142 71 RT 2 T 2.05953
-143 72 RT 1 R 1.40265
-144 72 RT 2 T 2.21437
-145 73 RT 1 R 3.74839
-146 73 RT 2 T 4.59435
-147 74 RT 1 R 3.97447
-148 74 RT 2 T 2.45867
-149 75 RT 1 R 1.44056
-150 75 RT 2 T 1.8562
-151 76 RT 1 R 3.32344
-152 76 RT 2 T 4.49331
-153 77 RT 1 R 4.29024
-154 77 RT 2 T 2.90093
-155 78 RT 1 R 1.6027
-156 78 RT 2 T 1.58914
-157 79 RT 1 R 2.87272
-158 79 RT 2 T 4.27332
-159 80 RT 1 R 4.50323
-160 80 RT 2 T 3.35108
-161 81 RT 1 R 1.87615
-162 81 RT 2 T 1.43448
-163 82 RT 1 R 2.43214
-164 82 RT 2 T 3.95189
-165 83 RT 1 R 4.59648
-166 83 RT 2 T 3.77327
-167 84 RT 1 R 2.23912
-168 84 RT 2 T 1.40452
-169 85 RT 1 R 2.0368
-170 85 RT 2 T 3.55464
-171 86 RT 1 R 4.56255
-172 86 RT 2 T 4.13385
-173 87 RT 1 R 2.6627
-174 87 RT 2 T 1.50166
-175 88 RT 1 R 1.71818
-176 88 RT 2 T 3.1132
-177 89 RT 1 R 4.40414
-178 89 RT 2 T 4.40412
-179 90 RT 1 R 3.11316
-180 90 RT 2 T 1.71816
-181 91 RT 1 R 1.50168
-182 91 RT 2 T 2.66275
-183 92 RT 1 R 4.13389
-184 92 RT 2 T 4.56254
-185 93 RT 1 R 3.55459
-186 93 RT 2 T 2.03676
-187 94 RT 1 R 1.40453
-188 94 RT 2 T 2.23916
-189 95 RT 1 R 3.77331
-190 95 RT 2 T 4.59648
-191 96 RT 1 R 3.95185
-192 96 RT 2 T 2.4321
-193 97 RT 1 R 1.43447
-194 97 RT 2 T 1.87618
-195 98 RT 1 R 3.35113
-196 98 RT 2 T 4.50325
-197 99 RT 1 R 4.27329
-198 99 RT 2 T 2.87267
-199 100 RT 1 R 1.58912
-200 100 RT 2 T 1.60272
diff --git a/src/testdata/MOESM7.csv b/src/testdata/MOESM7.csv
deleted file mode 100644
index bd84c35..0000000
--- a/src/testdata/MOESM7.csv
+++ /dev/null
@@ -1,2001 +0,0 @@
-ObsNumber Subj Trt Per Seq Var
-1 1 T 1 TR 168.406971
-2 1 R 2 TR 210.919302
-3 2 T 1 TR 131.030557
-4 2 R 2 TR 67.431371
-5 3 T 1 TR 151.736588
-6 3 R 2 TR 85.12962
-7 4 T 1 TR 375.575338
-8 4 R 2 TR 147.501644
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-1985 993 R 1 RT 185.817376
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-1989 995 R 1 RT 90.175789
-1990 995 T 2 RT 47.07753
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diff --git a/src/testdata/MOESM8.csv b/src/testdata/MOESM8.csv
deleted file mode 100644
index d1ba179..0000000
--- a/src/testdata/MOESM8.csv
+++ /dev/null
@@ -1,1435 +0,0 @@
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diff --git a/src/utilities.jl b/src/utilities.jl
index 6c9fca4..d6a5c82 100644
--- a/src/utilities.jl
+++ b/src/utilities.jl
@@ -72,7 +72,6 @@ Calculate CV and MS
- false(default)
- true
"""
-
function cvfromci(;alpha = 0.05, theta1 = 0.8, theta2 = 1.25, n, design=:d2x2, mso=false, cvms=false)::Union{Float64, Tuple{Float64, Float64}}
d = Design(design)
df = d.df(n)
diff --git a/test/benchmark.txt b/test/benchmark.txt
deleted file mode 100644
index b17e284..0000000
--- a/test/benchmark.txt
+++ /dev/null
@@ -1,35 +0,0 @@
-# Clinical Trial Utilities
-
-#R
-benchmark(a<-sampleN.TOST(theta0=1, theta1=0.8, theta2=1.25, CV=0.3, alpha=0.05, targetpower=0.9, logscale=TRUE, design="2x2", method="owenq", robust=TRUE, print=FALSE), columns = c("test", "replications", "elapsed", "relative", "user.self", "sys.self", "user.child", "sys.child"),replications = 10000)
- test
-1 a <- sampleN.TOST(theta0 = 1, theta1 = 0.8, theta2 = 1.25, CV = 0.3, alpha = 0.05, targetpower = 0.9, logscale = TRUE, design = "2x2", method = "owenq", robust = TRUE, print = FALSE)
- replications elapsed relative user.self sys.self user.child sys.child
-1 10000 18.86 1 18.7 0.02 NA NA
->
-
-#Julia
-
-julia> b = @benchmark ClinicalTrialUtilities.besamplen(;theta0=1.0, theta1=0.8, theta2=1.25, cv=0.3, alpha=0.05, beta=0.1, logscale=true, method="owenq");
-
-julia> bBenchmarkTools.Trial:
- memory estimate: 5.48 KiB
- allocs estimate: 222
- --------------
- minimum time: 54.655 μs (0.00% GC)
- median time: 56.066 μs (0.00% GC)
- mean time: 65.078 μs (1.61% GC)
- maximum time: 5.405 ms (97.76% GC)
- --------------
- samples: 10000
- evals/sample: 1
-
-
-
- > library(rbenchmark)
- > benchmark(blakerci(38,100,conf.level=0.95,tolerance=1e-05))
- test replications elapsed
- 1 blakerci(38, 100, conf.level = 0.95, tolerance = 1e-05) 100 1.52
- relative user.self sys.self user.child sys.child
- 1 1 1.5 0 NA NA
- >
diff --git a/test/csv/descriptivedat.csv b/test/csv/descriptivedat.csv
new file mode 100644
index 0000000..db19065
--- /dev/null
+++ b/test/csv/descriptivedat.csv
@@ -0,0 +1,201 @@
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+774.9687587;1.23391E-05;R;C;11
+37.43099105;0.038559722;R;C;11
+43.94072862;0.139709139;R;C;11
+1627.434393;0.091972078;R;C;11
+0.010763455;4.158E-06;R;C;11
+0.000107635;20960.31059;R;C;11
+1.07635E-05;661299.2367;R;C;11
+543.5544766;3696.703808;R;C;11
+26.25368122;942842.4761;R;C;11
+30.81953882;527054800.3;R;C;11
+1141.464401;1.16975E+15;R;C;11
+114.1464401;0.860373704;R;C;11
+11.41464401;58.16529035;R;C;11
+11414.64401;270.9667751;R;C;11
+1141.464401;4.38749E-05;R;C;11
+114.1464401;0.066647729;R;C;11
+11.41464401;7.61862466;R;C;11
+652.2653719;2.80365E-05;R;C;11
+652.2653719;4.73117E-06;R;C;11
+652.2653719;1481060.634;R;C;11
+31.50441746;126164.4244;R;C;11
+36.98344659;596.1269052;R;C;11
+1369.757281;1.784839368;R;C;11
+136.9757281;1847659.801;R;C;11
+13.69757281;1.48576E+14;R;C;11
+13697.57281;9.309114138;R;C;11
+1369.757281;6.786344207;R;C;11
+136.9757281;910.6742091;R;C;11
+13.69757281;0.000578029;R;C;11
+782.7184463;3.23122E-08;R;C;11
+489.199029;0.00275252;R;C;11
+782.7184463;0.00074318;R;C;11
+37.80530096;7.4318E-06;R;C;11
+44.38013591;1.30057E-06;R;C;11
+1643.708737;1.18909E-06;R;C;11
+0.01087109;6.50283E-05;R;C;11
+0.000108711;0.00023561;R;C;11
+1.08711E-05;0.000155104;R;C;11
+548.9900214;1.4518E-07;R;C;11
+26.51621803;623.4232819;R;C;11
+1.19474E-06;531.0642772;R;C;11
+0.32165392;29.68682295;R;C;11
+0.032165392;75716.09496;R;C;11
+1.838022398;42325.76737;R;C;11
+1.148763998;9.39381E+11;R;C;11
+1.838022398;0.006909334;R;C;11
+0.088776482;4.671033348;R;C;11
+0.10421587;0.380805453;R;C;11
+3.859847035;9.8656E-08;R;C;11
+2.55281E-05;9.36639E-05;R;C;11
+2.55281E-07;0.221674922;R;C;11
+2.55281E-08;6.9491E-07;R;C;11
+1.289168487;3.16618E-09;R;C;11
+0.062266838;149862319.9;R;C;11
+2.80556E-09;1276604947;R;C;11
+0.000755325;60319583.77;R;C;11
+7.55325E-05;0.003576246;R;C;11
+0.004316145;76648.40357;R;C;11
+5792.598158;1.36794E+20;R;C;11
+279.782491;31.83553791;R;C;11
+328.4403156;232.0810714;R;C;11
+12164.45613;545.0105675;R;C;11
+1216.445613;0.000553492;R;C;11
+121.6445613;1.93379E-08;R;C;11
+121644.5613;0.034105561;R;C;11
+12164.45613;0.007844279;R;C;11
+1216.445613;2.11796E-06;R;C;11
+121.6445613;0.056041098;R;C;11
+6951.11779;5.12375755;R;C;11
+6951.11779;2802.05491;R;C;11
+6951.11779;0.000201037;R;C;11
+335.7389892;0.002740061;R;C;11
+394.1283787;56.92180489;R;C;11
+14597.34736;907907.5424;R;C;11
+1459.734736;7734027.213;R;C;11
+145.9734736;7565.896187;R;C;11
+145973.4736;14.37829834;R;C;11
+14597.34736;166.4090699;R;C;11
diff --git a/test/csv/freqdat.csv b/test/csv/freqdat.csv
new file mode 100644
index 0000000..357fab4
--- /dev/null
+++ b/test/csv/freqdat.csv
@@ -0,0 +1,44 @@
+row;col
+q;p
+q;p
+q;p
+q;p
+q;p
+q;p
+q;p
+q;p
+q;p
+q;l
+q;l
+q;l
+q;l
+q;l
+q;l
+q;l
+q;l
+w;p
+w;p
+w;p
+w;p
+w;p
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
+w;l
diff --git a/test/csv/negdat.csv b/test/csv/negdat.csv
new file mode 100644
index 0000000..626cef3
--- /dev/null
+++ b/test/csv/negdat.csv
@@ -0,0 +1,6 @@
+P1
+2.3
+1.2
+1.5
+-4
+0
diff --git a/test/csv/pddata.csv b/test/csv/pddata.csv
new file mode 100644
index 0000000..e549dac
--- /dev/null
+++ b/test/csv/pddata.csv
@@ -0,0 +1,14 @@
+time;effect
+0;0
+1;1
+2;4
+2.5;7
+3;5
+3.3;4
+3.6;3
+4;2
+5;8
+6;1
+7;2
+8;1
+9;1
diff --git a/test/csv/pkdata.csv b/test/csv/pkdata.csv
new file mode 100644
index 0000000..e163d80
--- /dev/null
+++ b/test/csv/pkdata.csv
@@ -0,0 +1,22 @@
+Concentration,Time,Subject,Formulation
+0,0,1,T
+0.2,1,1,T
+0.3,2,1,T
+0.4,3,1,T
+0.3,4,1,T
+0.2,5,1,T
+0.1,6,1,T
+0,0,2,T
+0.3,1,2,T
+0.4,2,2,T
+0.5,3,2,T
+0.3,4,2,T
+0.1,5,2,T
+0.05,6,2,T
+0.1,0,1,R
+0.2,1,1,R
+0.9,2,1,R
+0.8,3,1,R
+0.3,4,1,R
+0.2,5,1,R
+0.1,6,1,R
diff --git a/test/dstest.jl b/test/dstest.jl
index c0af0ab..027dc43 100644
--- a/test/dstest.jl
+++ b/test/dstest.jl
@@ -1,7 +1,6 @@
println(" ---------------------------------- ")
@testset " descriptives " begin
-
- df = CSV.read(IOBuffer(descriptivedat)) |> DataFrame
+ df = descriptivedat
ds = ClinicalTrialUtilities.descriptive(df, stats = :all, sort = [:C1, :C2], vars=[:P1, :P2])
@test ds[1,:n] ≈ 20 atol=1E-5
@test ds[1,:min] ≈ 11.30162773 atol=1E-5
@@ -46,7 +45,7 @@ println(" ---------------------------------- ")
@test ds[3,:sem] ≈ 48.65 atol=1E-5
@test ds[3,:median] ≈ 51.35 atol=1E-3
- df = CSV.read(IOBuffer(negdat)) |> DataFrame
+ df = negdat
ds = ClinicalTrialUtilities.descriptive(df, stats = :all, vars=[:P1])
@test ds[1,:harmmean] === NaN
@test ds[1,:geomean] === NaN
diff --git a/test/test.jl b/test/test.jl
index 1d37d4e..b279fae 100644
--- a/test/test.jl
+++ b/test/test.jl
@@ -2,17 +2,10 @@
# Copyright © 2019 Vladimir Arnautov aka PharmCat (mail@pharmcat.net)
using Distributions, Random, DataFrames, CSV, Test
-include("testdata.jl")
-
path = dirname(@__FILE__)
io = IOBuffer();
-# Multiple subjects PK DataFrame
-pkdata2 = CSV.File(path*"/csv/pkdata2.csv") |> DataFrame
-#Glucose2
-#Pinheiro, J. C. and Bates, D. M. (2000), Mixed-Effects Models in S and S-PLUS, Springer, New York. (Appendix A.10)
-#Hand, D. and Crowder, M. (1996), Practical Longitudinal Data Analysis, Chapman and Hall, London.
-glucose2 = CSV.File(path*"/csv/glucose2.csv") |> DataFrame
+include("testdata.jl")
@testset " Info: " begin
ClinicalTrialUtilities.info()
@@ -452,7 +445,7 @@ include("dstest.jl")
println(" ---------------------------------- ")
@testset " Frequency " begin
- df = CSV.read(IOBuffer(freqdat)) |> DataFrame
+ df = freqdat
ctab = ClinicalTrialUtilities.contab(df, row = :row, col = :col)
@test ctab == [9 8; 5 21]
diff --git a/test/testdata.jl b/test/testdata.jl
index f49b70c..22cf00a 100644
--- a/test/testdata.jl
+++ b/test/testdata.jl
@@ -1,294 +1,16 @@
#Simple PK DataFrame
-pkdata = CSV.read(IOBuffer("""Concentration,Time,Subject,Formulation
-0,0,1,T
-0.2,1,1,T
-0.3,2,1,T
-0.4,3,1,T
-0.3,4,1,T
-0.2,5,1,T
-0.1,6,1,T
-0,0,2,T
-0.3,1,2,T
-0.4,2,2,T
-0.5,3,2,T
-0.3,4,2,T
-0.1,5,2,T
-0.05,6,2,T
-0.1,0,1,R
-0.2,1,1,R
-0.9,2,1,R
-0.8,3,1,R
-0.3,4,1,R
-0.2,5,1,R
-0.1,6,1,R""")) |> DataFrame
-
+pkdata = CSV.File(path*"/csv/pkdata.csv") |> DataFrame
#Simple PD DataFrame
-pddata = CSV.read(IOBuffer("""time;effect
-0;0
-1;1
-2;4
-2.5;7
-3;5
-3.3;4
-3.6;3
-4;2
-5;8
-6;1
-7;2
-8;1
-9;1""")) |> DataFrame
-
-
-freqdat = """row;col
-q;p
-q;p
-q;p
-q;p
-q;p
-q;p
-q;p
-q;p
-q;p
-q;l
-q;l
-q;l
-q;l
-q;l
-q;l
-q;l
-q;l
-w;p
-w;p
-w;p
-w;p
-w;p
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l
-w;l"""
-
-negdat = """P1
-2.3
-1.2
-1.5
--4
-0"""
-
-descriptivedat = """P1;P2;C1;C2;C3
-2.3;2.3;T;A;1
-2.7;2.7;T;A;2
-100;100;T;A;2
-10;10;T;A;3
-1;1;T;A;3
-1000;1000;T;A;3
-100;100;T;A;3
-10;10;T;A;3
-1;1;T;A;3
-50;50;T;A;3
-50;50;T;A;3
-50;50;T;A;3
-50;6.5205;T;A;3
-50;283.5;T;A;3
-50;1050;T;A;3
-50;10.5;T;A;3
-50;1050;T;A;3
-2.415;105000;T;A;3
-2.835;1050;T;A;3
-105;10.5;T;A;3
-10.5;60;T;A;3
-1.05;3000;T;A;3
-1050;3000;T;A;3
-105;144.9;T;A;3
-10.5;22.182741;T;A;3
-1.05;35721;T;A;3
-60;13230;T;A;3
-60;13.23;T;A;3
-60;1323000;T;A;3
-2.898;13230000;T;A;3
-3.402;13230;T;A;4
-126;13.23;T;A;4
-12.6;4320;T;A;4
-1.26;135000;T;A;4
-1260;0.0506;T;A;4
-126;1.229813665;T;A;4
-12.6;38.80070547;T;A;4
-1.26;0.104761905;T;A;4
-72;0.104761905;T;A;4
-45;1047.619048;T;A;4
-72;0.104761905;T;A;4
-3.4776;0.104761905;T;A;4
-4.0824;0.104761905;T;A;4
-151.2;52.38095238;T;A;4
-0.001;0.916666667;T;A;4
-0.00001;0.916666667;T;A;4
-0.000001;0.1195425;T;A;4
-50.5;107.6086957;T;A;4
-2.43915;339.5061728;T;A;4
-2.86335;0.091666667;T;A;4
-106.05;91.66666667;T;B;5
-10.605;91666.66667;T;B;6
-1.0605;0.916666667;T;B;6
-1060.5;0.091666667;T;B;6
-106.05;5.238095238;T;B;6
-10.605;2619.047619;T;B;6
-1.0605;45.83333333;T;B;6
-60.6;3.542;T;B;6
-60.6;0.338902988;T;B;6
-60.6;11298.91304;T;B;6
-2.92698;3564.814815;T;B;6
-3.43602;0.09625;T;B;6
-127.26;1455300000;T;B;6
-12.726;1.4553E+12;T;B;6
-1.2726;14553000000;T;B;6
-1272.6;0.288178218;T;B;6
-127.26;1948.219667;T;B;6
-12.726;51862.32909;T;B;6
-1.2726;0.000524847;T;B;6
-72.72;0.127562002;T;B;6
-45.45;40.24589912;T;B;6
-72.72;0.000108664;T;B;6
-3.512376;0.001086639;T;B;6
-4.123224;108.6639276;T;B;6
-152.712;0.108663928;T;B;6
-0.00101;0.001901619;T;B;6
-0.0000101;0.001901619;T;B;6
-0.00000101;0.950809367;T;B;6
-51.005;0.344496147;T;B;6
-2.4635415;0.293459681;T;B;6
-0.000000111;0.001033292;T;B;6
-0.029883891;9.301395978;T;B;6
-0.002988389;293.4596811;T;B;6
-0.170765094;7.92341E-05;T;B;6
-0.106728184;0.792341139;T;B;6
-0.170765094;7923.411389;T;B;6
-0.008247954;0.792341139;T;B;6
-0.009682381;0.001386597;T;B;6
-0.358606697;0.126774582;T;B;6
-2.37174E-06;39.61705694;T;B;6
-2.37174E-08;14.35400614;T;B;6
-2.37174E-09;0.944940173;T;B;6
-0.119772739;0.002441153;T;B;6
-0.005785023;12305746.88;T;B;6
-2.60656E-10;388247158;T;B;6
-7.0175E-05;104826.7327;T;B;6
-7.0175E-06;31385746.5;T;B;6
-0.000401;6.49808E+11;T;B;6
-538.1727491;1.44219E+17;T;B;6
-25.99374378;10.60758907;T;B;6
-30.51439488;717122.6819;R;B;6
-1130.162773;334076.2494;R;B;6
-113.0162773;0.005409363;R;B;6
-11.30162773;0.821703073;R;B;6
-11301.62773;5367.450997;R;B;6
-1130.162773;0.012345137;R;B;6
-113.0162773;0.003333187;R;B;6
-11.30162773;50397788.48;R;B;6
-645.8072989;5039778.848;R;B;6
-645.8072989;881961.2984;R;B;6
-645.8072989;0.01746458;R;B;7
-31.19249254;180.7927553;R;B;8
-36.61727385;1453813996;R;B;9
-1356.195328;4600.009694;R;B;10
-135.6195328;161.9695613;R;B;11
-13.56195328;25515.05377;R;B;11
-13561.95328;0.599817902;R;B;11
-1356.195328;3.35302E-06;R;B;11
-135.6195328;0.028562757;R;B;11
-13.56195328;7.711944451;R;B;11
-774.9687587;0.007711944;R;C;11
-484.3554742;0.000134959;R;C;11
-774.9687587;1.23391E-05;R;C;11
-37.43099105;0.038559722;R;C;11
-43.94072862;0.139709139;R;C;11
-1627.434393;0.091972078;R;C;11
-0.010763455;4.158E-06;R;C;11
-0.000107635;20960.31059;R;C;11
-1.07635E-05;661299.2367;R;C;11
-543.5544766;3696.703808;R;C;11
-26.25368122;942842.4761;R;C;11
-30.81953882;527054800.3;R;C;11
-1141.464401;1.16975E+15;R;C;11
-114.1464401;0.860373704;R;C;11
-11.41464401;58.16529035;R;C;11
-11414.64401;270.9667751;R;C;11
-1141.464401;4.38749E-05;R;C;11
-114.1464401;0.066647729;R;C;11
-11.41464401;7.61862466;R;C;11
-652.2653719;2.80365E-05;R;C;11
-652.2653719;4.73117E-06;R;C;11
-652.2653719;1481060.634;R;C;11
-31.50441746;126164.4244;R;C;11
-36.98344659;596.1269052;R;C;11
-1369.757281;1.784839368;R;C;11
-136.9757281;1847659.801;R;C;11
-13.69757281;1.48576E+14;R;C;11
-13697.57281;9.309114138;R;C;11
-1369.757281;6.786344207;R;C;11
-136.9757281;910.6742091;R;C;11
-13.69757281;0.000578029;R;C;11
-782.7184463;3.23122E-08;R;C;11
-489.199029;0.00275252;R;C;11
-782.7184463;0.00074318;R;C;11
-37.80530096;7.4318E-06;R;C;11
-44.38013591;1.30057E-06;R;C;11
-1643.708737;1.18909E-06;R;C;11
-0.01087109;6.50283E-05;R;C;11
-0.000108711;0.00023561;R;C;11
-1.08711E-05;0.000155104;R;C;11
-548.9900214;1.4518E-07;R;C;11
-26.51621803;623.4232819;R;C;11
-1.19474E-06;531.0642772;R;C;11
-0.32165392;29.68682295;R;C;11
-0.032165392;75716.09496;R;C;11
-1.838022398;42325.76737;R;C;11
-1.148763998;9.39381E+11;R;C;11
-1.838022398;0.006909334;R;C;11
-0.088776482;4.671033348;R;C;11
-0.10421587;0.380805453;R;C;11
-3.859847035;9.8656E-08;R;C;11
-2.55281E-05;9.36639E-05;R;C;11
-2.55281E-07;0.221674922;R;C;11
-2.55281E-08;6.9491E-07;R;C;11
-1.289168487;3.16618E-09;R;C;11
-0.062266838;149862319.9;R;C;11
-2.80556E-09;1276604947;R;C;11
-0.000755325;60319583.77;R;C;11
-7.55325E-05;0.003576246;R;C;11
-0.004316145;76648.40357;R;C;11
-5792.598158;1.36794E+20;R;C;11
-279.782491;31.83553791;R;C;11
-328.4403156;232.0810714;R;C;11
-12164.45613;545.0105675;R;C;11
-1216.445613;0.000553492;R;C;11
-121.6445613;1.93379E-08;R;C;11
-121644.5613;0.034105561;R;C;11
-12164.45613;0.007844279;R;C;11
-1216.445613;2.11796E-06;R;C;11
-121.6445613;0.056041098;R;C;11
-6951.11779;5.12375755;R;C;11
-6951.11779;2802.05491;R;C;11
-6951.11779;0.000201037;R;C;11
-335.7389892;0.002740061;R;C;11
-394.1283787;56.92180489;R;C;11
-14597.34736;907907.5424;R;C;11
-1459.734736;7734027.213;R;C;11
-145.9734736;7565.896187;R;C;11
-145973.4736;14.37829834;R;C;11
-14597.34736;166.4090699;R;C;11"""
+pddata = CSV.File(path*"/csv/pddata.csv") |> DataFrame
+# Multiple subjects PK DataFrame
+pkdata2 = CSV.File(path*"/csv/pkdata2.csv") |> DataFrame
+#Glucose2
+#Pinheiro, J. C. and Bates, D. M. (2000), Mixed-Effects Models in S and S-PLUS, Springer, New York. (Appendix A.10)
+#Hand, D. and Crowder, M. (1996), Practical Longitudinal Data Analysis, Chapman and Hall, London.
+glucose2 = CSV.File(path*"/csv/glucose2.csv") |> DataFrame
+#Simple frequency dataset
+freqdat = CSV.File(path*"/csv/freqdat.csv") |> DataFrame
+#Small dataset with negative and zero value
+negdat = CSV.File(path*"/csv/negdat.csv") |> DataFrame
+#Dataset foe descriptive statistics check
+descriptivedat = CSV.File(path*"/csv/descriptivedat.csv") |> DataFrame