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Merge pull request #31 from PharmCat/dev
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Dev
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@PharmCat
PharmCat committed Nov 30, 2019
2 parents 7434444 + f73553c commit c2d4757
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3 changes: 3 additions & 0 deletions .gitignore
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@@ -1,4 +1,7 @@
*.jl.cov
*.jl.*.cov
*.jl.mem
test/csv/rds/
docs/build/
docs/deprecated
examples
12 changes: 6 additions & 6 deletions Project.toml
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Expand Up @@ -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"
Expand All @@ -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"
29 changes: 19 additions & 10 deletions README.md
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Expand Up @@ -19,7 +19,6 @@ The package is designed to perform calculations related to the planning and anal
using Pkg; Pkg.add("ClinicalTrialUtilities");
```


### <a name="Usage">Usage</a>

**NB! Hypothesis types:**
Expand All @@ -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;


### <a name="Examples">Examples</a>

#### SampleSize
```
#Sample size for one proportion equality
ctsamplen(param=:prop, type=:ea, group=:one, a=0.3, b=0.5)
Expand All @@ -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)
Expand All @@ -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))
Expand All @@ -75,7 +85,6 @@ pooledcv(data; cv=:cv, df=:df, alpha=0.05, returncv=true)
```


### <a name="Copyrights">Copyrights</a>

Clinical Trial Utilities
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239 changes: 0 additions & 239 deletions docs/CI.md
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2 comments on commit c2d4757

@PharmCat
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@JuliaRegistrator register

Release notes:

v0.2.0

Breaking changes(!):

  • Renamed exported functions: ctsamplen, ctpower, besamplen, bepower, ets (now in lower case).
  • nca() -> nca!() - renamed;
  • Changes in ctsamplen() in one group estimation. In version 0.1.x test mean/proportion denoted as parameter/keyword "a" was a "Reference".
    This situation was inconsistent with two group analysis where "a" - T, "b" - R. Now everywhere "a" means "Test group", "b" means "Reference group".
    Hypothesis testing for difference is A-B everywhere.
  • Keyword "logdiff" removed in ctsamplen(), because this was inconsistent with bepower/besamplen, new parameter logscale using instead.
  • Keyword "out" removed everywhere. Output via Base.show(io::IO, obj::TaskResult);
  • twoProp(), oneProp(), oneMean. twoMeans() removed;
  • No submodule politics.

Major changes:

  • using DataFrames 19.0+
  • Task types for many functions (sample size, power functions, random ets.);
  • Sample size and power functions now return TaskResult{T <: CTask};
  • descriptive() rewrited;
  • DataSet type;
  • make DataFrame from DataSet;
  • Descriptive type;
  • CMH CI split;
  • randomtable() return DF
  • Include CI in ClinicalTrialUtilities & StatsBase methods for AbstractParameter types.

Other changes:

  • Changes in error messages. Now throw(ArgumentError(msg));
  • LimitRule for PK;
  • RMIN/RMAX/TH/BL for PD;
  • Steady-state PK and other PK parameters;
  • Descriptive stats add SES and SEK;
  • Descriptive performance;
  • Test procedures restructured;
  • 4x4 design;
  • Documentation;
  • Minor changes, bugfix, code cleaning, cosmetics.

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Registration pull request created: JuliaRegistries/General/6081

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if Julia TagBot is installed, or can be done manually through the github interface, or via:

git tag -a v0.2.0 -m "<description of version>" c2d4757739cdc2195f589d6506c43024c4d6ff94
git push origin v0.2.0

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