Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.

Nitrification is a major issue that utilities must address if they utilize chloramines as a secondary disinfectant. Nitrification is the oxidation of free ammonia to nitrite which is then further oxidized to nitrate. Free ammonia is found in drinking water systems as a result of overfeeding at the water treatment plant (WTP) or as a result of the decomposition of monochloramine. Premise plumbing systems (i.e., the plumbing systems within buildings and homes) are characterized by irregular usage patterns, high water age, high temperature, and high surface-to-volume ratios. These characteristics create ideal conditions for increased chloramine decay, bacterial growth, and nitrification. This review discusses factors within premise plumbing that are likely to influence nitrification, and vice versa. Factors influencing, or influenced by, nitrification include the rate at which chloramine residual decays, microbial regrowth, corrosion of pipe materials, and water conservation practices. From a regulatory standpoint, the greatest impact of nitrification within premise plumbing is likely to be a result of increased lead levels during Lead and Copper Rule (LCR) sampling. Other drinking water regulations related to nitrifying parameters are monitored in a manner to reduce premise plumbing impacts. One way to potentially control nitrification in premise plumbing systems is through the development of building management plans.

The United States Environmental Protection Agency recently released their most sweeping overhaul to the Lead and Copper Rule in three decades. One of the most significant changes is requiring a fifth-liter (L5) sample at homes with lead service lines (LSLs) rather than the original first-liter (L1) sample for a demonstration of compliance with water lead level (WLL) limits. We analyzed sequential sampling data from three large water systems and compliance data from Michigan utilitieswhich base compliance on the 90th percentile of the greater of L1 and L5 samplesto evaluate whether L5 WLLs better represent water in contact with LSLs and to explore regulatory impacts of including L5 samples in compliance monitoring. The sequential sampling data demonstrated that it is impossible to use a single sample volume within a sequential profile to universally capture the volume of water in an LSL. While L5 is not always a reliable indicator of water in contact with an LSL, Michigan compliance data showed that the L5 sample is more likely to be from an LSL and can identify utilities that benefit from an improved corrosion control treatment. Michigan compliance data indicate that it is likely that L5 sampling will result in more systems having a higher 90th percentile WLL and that a high proportion of the systems likely to exceed regulatory action levels based on L5 samples can be identified through a retrospective analysis of historic L1 data. The impact of the switch to L5 sampling on the effectiveness of corrosion control treatment over time has yet to be determined.

Historical Lead and Copper Rule (LCR) regulatory sampling data from the Philadelphia Water Department were examined to explore their potential value for guiding a water utility's progress with regard to optimal corrosion control treatment (OCCT). If a system has established a stable water treatment process with consistent corrosion control treatment (CCT) and has achieved continued decreases in lead levels during regulatory sampling, then the information collected during LCR monitoring can be used as an important data set of a broader OCCT evaluation and will help inform the benefit of additional changes in CCT. Since water utilities have LCR data dating back to 1992, these data should be used to make informed decisions. This research also showed that the addition of orthophosphate has resulted in a significant decrease in lead levels at the customer tap. Additionally, profile sampling was performed to show that first‐draw 1 L samples following a 6 h stagnation period provide a good representation of the lead concentrations measured from lead service line and home plumbing samples at the same sites and may be used to indicate overall changes in lead concentrations at the tap resulting from CCT for this system.

Key Takeaways Water systems should work toward developing data management programs that extend the knowledge gained from routine water quality monitoring. Developing routine data‐based reports or data‐driven dashboards can help utilities proactively manage their drinking water distribution systems. Adopting open‐source scripted software can help systems automate many data‐driven tasks while reducing errors, allowing operators to access needed information faster to make data‐informed decisions.