modify README

jtimonen · Jun 15, 2021 · a0f1aeb · a0f1aeb
1 parent 08754ad
commit a0f1aeb
Show file tree

Hide file tree

Showing 2 changed files with 36 additions and 26 deletions.
diff --git a/README.md b/README.md
@@ -9,23 +9,23 @@ See overview, tutorials and documentation at https://jtimonen.github.io/lgpr-usa
 
 ## Requirements
 
-* The package should work on all major operating systems. We don't have pre-compiled binaries distributed yet, so currently *lgpr* needs to be installed from source. 
-* This is why you need to have your toolchain setup properly. See the instructions for:
+* The package should work on all major operating systems. 
+* R 3.4 or later is required, R 4.0.2 or later is recommended
+* We don't have pre-compiled binaries distributed yet, so currently *lgpr* needs to be installed from source. This is why you need to have your toolchain setup properly. See the instructions for:
   - [Linux](https://github.com/stan-dev/rstan/wiki/Configuring-C-Toolchain-for-Linux)
-  - [Windows](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Windows).
+  - [Windows](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Windows)
   - [Mac](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Mac)
-  - R 3.4 or later is required, R 4.0.2 or later is recommended
 
 ## License
 [GPL>=3](https://www.gnu.org/licenses/gpl-3.0.html)
 
 ## Installation
-* Install the dependency [rstan](https://mc-stan.org/rstan/) using [these instructions](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started)
 * Install *lgpr* by running
 ```r
 install.packages('devtools') # if you don't have devtools already
 devtools::install_github('jtimonen/lgpr', dependencies = TRUE)
 ```
+* If you have trouble installing the dependency [rstan](https://mc-stan.org/rstan/), see [these instructions](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started)
 
 * **Note:** In some cases, the exact version 2.0.0 of *rstantools* is required due
 to problems with some recently updated versions of *StanHeaders* or *rstantools* (see [this thread](https://github.com/stan-dev/rstantools/issues/76)). You can remove possible incompatible version of *rstantools* and install version 2.0.0 by
@@ -36,4 +36,4 @@ devtools::install_version("rstantools", version = "2.0.0", repos = "http://cran.
 
 ## Real data and reproducing the experiments
 For code to reproduce the experiments of our manuscript see https://github.com/jtimonen/lgpr-usage. Preprocessed longitudinal proteomics
-data is also provided there.
+data is also provided there. See also the built-in `read_proteomics_data()` function.
diff --git a/dev/README.md b/dev/README.md
@@ -11,34 +11,32 @@ itself. They are supposed to be run while in the package root directory.
 
 ## Test suite output
 
-* Version: `1.1.9000`
-* Commit: `1a84c1bac5e5263e259f4b2bb58ac7978c8a205`
-* Date: `9th June 2021`
-* TotalCPUTime: `04:54:31`
-* MaxRSS: `3240M`
+* Version: `1.1.0`
+* Date: `13th June 2021`
+* TotalCPUTime: `05:27:25`
+* MaxRSS: `3524M`
 
 Proteomics data experiment's (4-5) relevance results confirmed to agree with paper.
 
 ```
-
                    name obs_model f_sampled n_obs n_comps t_ch_mean t_ch_sd
-1         01_sleepstudy  gaussian     FALSE   180       2    170.74    3.01
-2          02_orthodont  gaussian     FALSE   108       3     74.94    4.77
-3 03_two-age-components  gaussian     FALSE    70       2     14.07    0.85
-4        04_protein-liu  gaussian     FALSE   189       5    524.67   20.78
-5  05_protein-liu-heter  gaussian     FALSE   189       5   1360.18   59.49
+1         01_sleepstudy  gaussian     FALSE   180       2    193.56    3.13
+2          02_orthodont  gaussian     FALSE   108       3     78.50    5.00
+3 03_two-age-components  gaussian     FALSE    70       2     16.10    0.23
+4        04_protein-liu  gaussian     FALSE   189       5    572.94   22.37
+5  05_protein-liu-heter  gaussian     FALSE   189       5   1528.20   66.63
 
      t_fit t_pred t_post  t_total size_fit size_small size_disk n_div max_Rhat
-1  1397.94  44.95   9.58  1456.06  44.9 Mb       1 Mb   40.1 Mb     0    1.002
-2   615.33  23.24  10.00   650.88  34.1 Mb     1.1 Mb   27.9 Mb     0    1.002
-3   119.50  11.55   3.83   136.21  18.1 Mb       1 Mb   17.3 Mb     0    1.004
-4  4270.24 102.16  15.64  4393.96  82.1 Mb     1.4 Mb   63.6 Mb     0    1.005
-5 10966.25  97.41  17.81 11086.60  82.8 Mb     2.1 Mb   64.5 Mb     0    1.005
+1  1578.72  51.27  11.23  1645.33  44.9 Mb       1 Mb   40.1 Mb     0    1.002
+2   643.12  24.99  10.82   681.67  34.1 Mb     1.1 Mb   27.9 Mb     0    1.002
+3   136.60  12.39   4.16   154.59  18.1 Mb       1 Mb   17.3 Mb     0    1.002
+4  4642.29  98.22  16.55  4763.23  82.1 Mb     1.4 Mb   63.6 Mb     0    1.005
+5 12283.78 100.55  18.40 12408.22  82.8 Mb     2.1 Mb   64.5 Mb     0    1.005
 
   min_TESS min_BESS
 1     2517     2036
 2     2087     1753
-3     2066     1662
+3     1775     1618
 4     1344     1470
 5     1015      690
 
@@ -48,16 +46,19 @@ Proteomics data experiment's (4-5) relevance results confirmed to agree with pap
            gp(Days) gp(Days)*zs(Subject)    noise
 Relevance 0.3096018            0.5637252 0.126673
 Expected  0.3096018            0.5637252 0.126673
+
 -----------------------------------------------------------------------
 02_orthodont.R: 
             gp(age) gp(age)*zs(Subject) gp(age)*zs(Sex)     noise
 Relevance 0.2818898           0.4012653       0.1506231 0.1662218
 Expected  0.2818898           0.4012653       0.1506231 0.1662218
+
 -----------------------------------------------------------------------
 03_two-age-components.R: 
-            gp(age) gp(age_fast)     noise
-Relevance 0.1034861    0.7895722 0.1069417
-Expected  0.0764848    0.8130515 0.1104637
+             gp(age) gp(age_fast)     noise
+Relevance 0.05237128    0.8587906 0.0888381
+Expected  0.07648480    0.8130515 0.1104637
+
 -----------------------------------------------------------------------
 04_protein-liu.R: 
           gp(age)*zs(id)   gp(age) gp_vm(diseaseAge) zs(sex)*gp(age)
@@ -66,6 +67,7 @@ Expected       0.2286768 0.1573663        0.02842119      0.03088412
             zs(group)     noise
 Relevance 0.007530387 0.5471212
 Expected  0.007530387 0.5471212
+
 -----------------------------------------------------------------------
 05_protein-liu-heter.R: 
           gp(age)*zs(id)   gp(age) het(id)*gp_vm(diseaseAge) zs(sex)*gp(age)
@@ -77,6 +79,14 @@ Expected  0.003777137 0.4955653
 -----------------------------------------------------------------------
 
 
+                     file                                          rds
+1         01_sleepstudy.R         test_suite_out/rds/01_sleepstudy.rds
+2          02_orthodont.R          test_suite_out/rds/02_orthodont.rds
+3 03_two-age-components.R test_suite_out/rds/03_two-age-components.rds
+4        04_protein-liu.R        test_suite_out/rds/04_protein-liu.rds
+5  05_protein-liu-heter.R  test_suite_out/rds/05_protein-liu-heter.rds
+
+
 R version 3.6.1 (2019-07-05)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: CentOS Linux 7 (Core)