fix broken links

Author: nbenn

R/data-env.R

@@ -14,7 +14,7 @@
 #' gained by applying for an account with [PhysioNet
 #' ](https://physionet.org/register/). Even though registration is required,
 #' the described datasets are all publicly available. With [AmsterdamUMCdb
-#' ](https://amsterdammedicaldatascience.nl/#amsterdamumcdb), a non-PhysioNet
+#' ](https://amsterdammedicaldatascience.nl/#amsterdamumcdb, a non-PhysioNet
 #' hosted data source is available as well. As with the PhysioNet datasets,
 #' access is public but has to be granted by the data collectors.
 #'
@@ -66,7 +66,7 @@
 #'
 #' Much care has been taken to make `ricu` extensible to new datasets. For
 #' example the publicly available ICU database [AmsterdamUMCdb
-#' ](https://amsterdammedicaldatascience.nl/amsterdamumcdb/)
+#' ](https://amsterdammedicaldatascience.nl/#amsterdamumcdb)
 #' provided by the Amsterdam University Medical Center, currently is not part
 #' of the core datasets of `ricu`, but code for integrating this dataset is
 #' available on [github](https://github.com/eth-mds/aumc).
@@ -120,7 +120,7 @@
 #'
 #' @section AmsterdamUMCdb:
 #' With similar time-resolution (for vital-sign measurements) as HiRID,
-#' [AmsterdamUMCdb](https://amsterdammedicaldatascience.nl/#amsterdamumcdb)
+#' [AmsterdamUMCdb](https://amsterdammedicaldatascience.nl/#amsterdamumcdb
 #' contains data from 23,000 admissions of adult patients from 2003-2016 to
 #' the department of Intensive Care, of Amsterdam University Medical Center.
 #' In total, nearly 10^9^ individual observations consisting of vitals signs,

man/data_env.Rd

@@ -68,7 +68,7 @@ cat(
 Included with `ricu` are functions for download and setup of the following datasets: `mimic` (MIMIC-III), `eicu`, `hirid`, `aumc` and `miiv` (MIMIC-IV), which can be invoked in several different ways.
 
 - To begin with, a directory is needed where the data can permanently be  stored. The default location is platform dependent and can be overridden using the environment variable `RICU_DATA_PATH`. The current value can be retrieved by calling `data_dir()`.
-- Access to both the PhysioNet datasets (MIMIC-III, eICU and HiRID), as well as to AUMCdb is free but credentialed. In addition to setting up an [account with PhysioNet](https://physionet.org/register/), [credentialing](https://physionet.org/settings/credentialing/) is required, which, in the case of HiRID, must also be followed by submitting an [access request](https://physionet.org/request-access/hirid/1.1.1/) to the data-owners. Details on the procedure for requesting access to AUMCdb is available from [here](https://amsterdammedicaldatascience.nl/amsterdamumcdb/) and consists of filling out a [form](https://amsterdammedicaldatascience.nl/content/uploads/sites/2/2022/12/arfeula_v1.6.pdf) and completing a training course such as [Data or Specimens Only Research (DSOR)](https://physionet.org/about/citi-course/) which, together with proof of training course completion, can be submitted by [email](mailto:access@amsterdammedicaldatascience.nl).
+- Access to both the PhysioNet datasets (MIMIC-III, eICU and HiRID), as well as to AUMCdb is free but credentialed. In addition to setting up an [account with PhysioNet](https://physionet.org/register/), [credentialing](https://physionet.org/settings/credentialing/) is required, which, in the case of HiRID, must also be followed by submitting an [access request](https://physionet.org/request-access/hirid/1.1.1/) to the data-owners. Details on the procedure for requesting access to AUMCdb is available from [here](https://amsterdammedicaldatascience.nl/#amsterdamumcdb) and consists of filling out a [form](https://amsterdammedicaldatascience.nl/arfeula_v1.6.pdf) and completing a training course such as [Data or Specimens Only Research (DSOR)](https://physionet.org/about/citi-course/) which, together with proof of training course completion, can be submitted by [email](mailto:access@amsterdammedicaldatascience.nl).
 - If raw data in `.csv` form has already been downloaded, this can be decompressed and copied to an appropriate sub-folder (`mimic`, `eicu`, `hirid` or `aumc`) to the directory identified by `data_dir()`.
 - In order to have `ricu` download the required data, login credentials can be supplied as environment variables `RICU_PHYSIONET_USER`/`RICU_PHYSIONET_PASS` and `RICU_AUMC_TOKEN` (the string the follows `token=` in the download URL received from the AUMCdb data owners) or entered into the terminal manually in interactive sessions.
 - Enabling efficient random row/column access, `ricu` converts `.csv` files into a binary format using the [fst](https://cran.r-project.org/package=fst) package.